Publications

Selected Publications

High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels

Presenting measurements of neuronal preparations with a novel CMOS-based microelectrode array at high-spatiotemporal-resolution on subcellular, cellular, and network level.

J. Müller, M. Ballini, P. Livi, Y. Chen, M. Radivojevic, A. Shadmani, V. Viswam, I. L. Jones, M. Fiscella, R. Diggelmann, A. Stettler, U. Frey, D. J. Bakkum, and A. Hierlemann, “High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels,” Lab Chip, vol. 15, no. 13, pp. 2767–2780, May 2015.

Revealing Neuronal Function through Microelectrode Array Recordings

Reviewing the current understanding of microelectrode signals and the techniques for analyzing them, with focus on the ongoing advancements in microelectrode technology (in vivo and in vitro) and recent advanced microelectrode array measurement methods that facilitate the understanding of single neurons and network function.

M. E. J. Obien, K. Deligkaris, T. Bullmann, D. J. Bakkum, and U. Frey, “Revealing Neuronal Function through Microelectrode Array Recordings,” Front. Neurosci., 8:423, Jan 2015.

A 1024-Channel CMOS Microelectrode Array With 26,400 Electrodes for Recording and Stimulation of Electrogenic Cells In Vitro

A high-resolution CMOS-based microelectrode array featuring 1,024 low-noise readout channels, 26,400 electrodes at a density of 3,265 electrodes per mm², including on-chip 10bit ADCs and consuming only 75 mW.

M. Ballini, J. Muller, P. Livi, Y. Chen, U. Frey, A. Stettler, A. Shadmani, V. Viswam, I. L. Jones, D. Jackel, M. Radivojevic, M. K. Lewandowska, W. Gong, M. Fiscella, D. J. Bakkum, F. Heer, and A. Hierlemann, “A 1024-Channel CMOS Microelectrode Array With 26,400 Electrodes for Recording and Stimulation of Electrogenic Cells In Vitro,” IEEE Journal of Solid-State Circuits, vol. 49, no. 11, pp. 2705-2719, 2014.

Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites

Demonstrating a method to electrically visualize action potential propagation on axons and revealing
large variations in velocity.

D. J. Bakkum, U. Frey, M. Radivojevic, T. L. Russell, J. Muller, M. Fiscella, H. Takahashi, and A. Hierlemann, “Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites,” Nature Communications, 4:2181, Jul 2013.

Microelectronic System for High-Resolution Mapping of Extracellular Electric Fields Applied to Brain Slices

Recording and modeling extracellular action potentials of Purkinje cells at subcellular resolution.

U. Frey, U. Egert, F. Heer, S. Hafizovic, and A. Hierlemann, “Microelectronic System for High-Resolution Mapping of Extracellular Electric Fields Applied to Brain Slices,” Biosensors and Bioelectronics, vol. 24, no. 7, pp. 2191-2198, 2009.

Modulation of Cardiomyocyte Electrical Properties Using Regulated Bone Morphogenetic Protein-2 Expression

Controlling BMP-2 expression to modulate the electrophysiological properties of cardiomyocytes using an HD-MEA for detailed monitoring.

C. D. Sanchez-Bustamante, U. Frey, J. M. Kelm, A. Hierlemann, and M. Fussenegger,
“Modulation of Cardiomyocyte Electrical Properties Using Regulated Bone Morphogenetic Protein-2 Expression,” Tissue Engineering Part A, vol. 14, no. 12, pp. 1969-1988, 2008.

All Publications

141 entries « ‹ 2 of 3 › »

2020
	Bandarabadi, Mojtaba; Vassalli, Anne; Tafti, Mehdi Sleep as a default state of cortical and subcortical networks Journal Article Current Opinion in Physiology, 15 , pp. 60-67, 2020. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks, Review, Sleep @article{Bandarabadi2020, title = {Sleep as a default state of cortical and subcortical networks}, author = {Mojtaba Bandarabadi and Anne Vassalli and Mehdi Tafti}, url = {https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub}, doi = {10.1016/j.cophys.2019.12.004}, year = {2020}, date = {2020-06-20}, journal = {Current Opinion in Physiology}, volume = {15}, pages = {60-67}, abstract = {Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field.}, keywords = {Neuronal Networks, Review, Sleep}, pubstate = {published}, tppubtype = {article} } Close Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field. Close https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub doi:10.1016/j.cophys.2019.12.004 Close
	Masumori, Atsushi; Sinapayen, Lana; Maruyama, Norihiro; Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Takahashi, Hirokazu; Ikegami, Takashi Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks Journal Article Artificial Life, 26 (1), pp. 130-151, 2020, ISSN: 1064-5462. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks @article{Masumori2020, title = {Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks}, author = {Atsushi Masumori and Lana Sinapayen and Norihiro Maruyama and Takeshi Mita and Douglas J. Bakkum and Urs Frey and Hirokazu Takahashi and Takashi Ikegami}, url = {https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314}, doi = {10.1162/artl_a_00314}, issn = {1064-5462}, year = {2020}, date = {2020-04-28}, journal = {Artificial Life}, volume = {26}, number = {1}, pages = {130-151}, abstract = {Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance.}, keywords = {Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance. Close https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314 doi:10.1162/artl_a_00314 Close
	Idrees, Saad; Baumann, Matthias P; Franke, Felix; Münch, Thomas A; Hafed, Ziad M Perceptual saccadic suppression starts in the retina Journal Article Nature Communications, 11 (1977), 2020. Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne, Retina @article{Idrees2020, title = {Perceptual saccadic suppression starts in the retina}, author = {Saad Idrees and Matthias P. Baumann and Felix Franke and Thomas A. Münch and Ziad M. Hafed}, url = {https://www.nature.com/articles/s41467-020-15890-w}, doi = {10.1038/s41467-020-15890-w}, year = {2020}, date = {2020-04-24}, journal = {Nature Communications}, volume = {11}, number = {1977}, keywords = {ETH-CMOS-MEA, MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close https://www.nature.com/articles/s41467-020-15890-w doi:10.1038/s41467-020-15890-w Close
	Obaid, Abdulmalik; Hanna, Mina-Elrahb; Wu, Yu-Wei; Kollo, Mihaly; Racz, Romeo; Angle, Matthew R; Muller, Jan; Brackbill, Nora; Wray, William; Franke, Felix; Chichilnski, E J; Hierlemann, Andreas; Ding, Jun B; Schaefer, Andreas T; Melosh, Nicholas A Massively parallel microwire arrays integrated withCMOS chips for neural recording Journal Article Science Advances, 2020. Abstract \| Links \| BibTeX \| Tags: Electrodes, ETH-CMOS-MEA @article{Obaid2020, title = {Massively parallel microwire arrays integrated withCMOS chips for neural recording}, author = {Abdulmalik Obaid and Mina-Elrahb Hanna and Yu-Wei Wu and Mihaly Kollo and Romeo Racz and Matthew R Angle and Jan Muller and Nora Brackbill and William Wray and Felix Franke and E J Chichilnski and Andreas Hierlemann and Jun B. Ding and Andreas T. Schaefer and Nicholas A. Melosh}, url = {https://advances.sciencemag.org/content/6/12/eaay2789}, doi = {10.1126/sciadv.aay2789}, year = {2020}, date = {2020-03-20}, journal = {Science Advances}, abstract = {Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface.}, keywords = {Electrodes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface. Close https://advances.sciencemag.org/content/6/12/eaay2789 doi:10.1126/sciadv.aay2789 Close
	Kajiwara, Motoki; Nomura, Ritsuki; Goetze, Felix; Akutsu, Tatsuya; Shimono, Masanori Inhibitory neurons are a Central Controlling regulator in the effective cortical microconnectome Journal Article bioRxiv , 2020. Abstract \| Links \| BibTeX \| Tags: Inhibitory Neurons @article{Kajiwara2020, title = {Inhibitory neurons are a Central Controlling regulator in the effective cortical microconnectome}, author = {Motoki Kajiwara and Ritsuki Nomura and Felix Goetze and Tatsuya Akutsu and Masanori Shimono}, url = {https://www.biorxiv.org/content/10.1101/2020.02.18.954016v1}, doi = {10.1101/2020.02.18.954016}, year = {2020}, date = {2020-02-18}, journal = {bioRxiv }, abstract = {The brain is a network system in which excitatory and inhibitory neurons keep the activity balanced in the highly non-uniform connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neurons. So, in general, how the inhibitory neurons can keep the balance with the surrounding excitatory neurons is an important question. We observed effective networks, reflecting causal interactions, of ~1000 neurons in cortical acute slices. Surprisingly, we found that inhibitory neurons are not only located at more central positions than excitatory neurons but also have stronger controlling ability of other neurons than excitatory neurons. Besides, we found that the precedence in centrality and controlling ability of inhibitory neurons are well observed in deep cortical layers by comparing with distribution of neurons coloured by NeuN immunostaining data. Preceding the observation, we also found that inhibitory neurons show higher firing rate than excitatory neurons, and that their firing rate also closely obey a log-normal distribution as previously known about excitatory neurons. Additionally, their connectivity strengths also obeyed a log-normal distribution. In summary, within the network interaction of huge numbers of neurons, inhibitory neurons seem to produce a central controlling system that sustains the homeostatic behavior of the brain. A similar evaluation in different life stages and in disease states etc. will not only provide deeper understandings in the homeostasis of the brain, but also will provide a selective and effective way to stimulate individual neurons to modulate neuropsychiatry or neurodegeneration disease states.}, keywords = {Inhibitory Neurons}, pubstate = {published}, tppubtype = {article} } Close The brain is a network system in which excitatory and inhibitory neurons keep the activity balanced in the highly non-uniform connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neurons. So, in general, how the inhibitory neurons can keep the balance with the surrounding excitatory neurons is an important question. We observed effective networks, reflecting causal interactions, of ~1000 neurons in cortical acute slices. Surprisingly, we found that inhibitory neurons are not only located at more central positions than excitatory neurons but also have stronger controlling ability of other neurons than excitatory neurons. Besides, we found that the precedence in centrality and controlling ability of inhibitory neurons are well observed in deep cortical layers by comparing with distribution of neurons coloured by NeuN immunostaining data. Preceding the observation, we also found that inhibitory neurons show higher firing rate than excitatory neurons, and that their firing rate also closely obey a log-normal distribution as previously known about excitatory neurons. Additionally, their connectivity strengths also obeyed a log-normal distribution. In summary, within the network interaction of huge numbers of neurons, inhibitory neurons seem to produce a central controlling system that sustains the homeostatic behavior of the brain. A similar evaluation in different life stages and in disease states etc. will not only provide deeper understandings in the homeostasis of the brain, but also will provide a selective and effective way to stimulate individual neurons to modulate neuropsychiatry or neurodegeneration disease states. Close https://www.biorxiv.org/content/10.1101/2020.02.18.954016v1 doi:10.1101/2020.02.18.954016 Close
2019
	Shimba, Kenta; Asahina, Takahiro; Sakai, Koji; JImbo, Yasuhiko; Kotani, Kiyoshi Evaluation of Conduction Properties of Sensory Axons with High-Density Microelectrode Array Conference 2019. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Shimba2019, title = {Evaluation of Conduction Properties of Sensory Axons with High-Density Microelectrode Array}, author = {Kenta Shimba and Takahiro Asahina and Koji Sakai and Yasuhiko JImbo and Kiyoshi Kotani}, url = {https://ieeexplore.ieee.org/abstract/document/8990233}, doi = {10.1109/BMEiCON47515.2019.8990233}, year = {2019}, date = {2019-11-20}, abstract = {In vitro modeling of neurodegenerative disorder is a promising method for developing new treatment. However, little is known about myelination and subsequent increase of conduction velocity in vitro. Here, we aim to develop a new method for evaluating salutatory conduction from myelinated sensory axons. First, sensory neurons and Schwann cells were cultured on high-density microelectrode array chips. Myelin sheath formation was confirmed with immunocytochemistry. Axonal signal was detected, and instantaneous conduction velocity was evaluated. As a result, we observed that relatively fast conduction sites between slow conduction sites. Our method is suitable for evaluating conduction properties of sensory axons.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close In vitro modeling of neurodegenerative disorder is a promising method for developing new treatment. However, little is known about myelination and subsequent increase of conduction velocity in vitro. Here, we aim to develop a new method for evaluating salutatory conduction from myelinated sensory axons. First, sensory neurons and Schwann cells were cultured on high-density microelectrode array chips. Myelin sheath formation was confirmed with immunocytochemistry. Axonal signal was detected, and instantaneous conduction velocity was evaluated. As a result, we observed that relatively fast conduction sites between slow conduction sites. Our method is suitable for evaluating conduction properties of sensory axons. Close https://ieeexplore.ieee.org/abstract/document/8990233 doi:10.1109/BMEiCON47515.2019.8990233 Close
	Kubota, Tomoyuki; Nakajima, Kohei; Takahashi, Hirokazu Echo State Property of Neuronal Cell Cultures Book Chapter 11731 , Springer, 2019, ISBN: 978-3-030-30493-5. Abstract \| Links \| BibTeX \| Tags: Action Potential, MaxOne, Neuronal cell culture @inbook{Kubota2019b, title = {Echo State Property of Neuronal Cell Cultures}, author = {Tomoyuki Kubota and Kohei Nakajima and Hirokazu Takahashi }, url = {https://link.springer.com/chapter/10.1007%2F978-3-030-30493-5_13}, doi = {10.1007/978-3-030-30493-5_13}, isbn = {978-3-030-30493-5}, year = {2019}, date = {2019-09-09}, volume = {11731}, publisher = {Springer}, abstract = {Physical reservoir computing (PRC) utilizes the nonlinear dynamics of physical systems, which is called a reservoir, as a computational resource. The prerequisite for physical dynamics to be a successful reservoir is to have the echo state property (ESP), asymptotic properties of transient trajectory to driving signals, with some memory held in the system. In this study, the prerequisites in dissociate cultures of cortical neuronal cells are estimated. With a state-of-the-art measuring system of high-dense CMOS array, our experiments demonstrated that each neuron exhibited reproducible spike trains in response to identical driving stimulus. Additionally, the memory function was estimated, which found that input information in the dynamics of neuronal activities in the culture up to at least 20 ms was retrieved. These results supported the notion that the cultures had ESP and could thereby serve as PRC.}, keywords = {Action Potential, MaxOne, Neuronal cell culture}, pubstate = {published}, tppubtype = {inbook} } Close Physical reservoir computing (PRC) utilizes the nonlinear dynamics of physical systems, which is called a reservoir, as a computational resource. The prerequisite for physical dynamics to be a successful reservoir is to have the echo state property (ESP), asymptotic properties of transient trajectory to driving signals, with some memory held in the system. In this study, the prerequisites in dissociate cultures of cortical neuronal cells are estimated. With a state-of-the-art measuring system of high-dense CMOS array, our experiments demonstrated that each neuron exhibited reproducible spike trains in response to identical driving stimulus. Additionally, the memory function was estimated, which found that input information in the dynamics of neuronal activities in the culture up to at least 20 ms was retrieved. These results supported the notion that the cultures had ESP and could thereby serve as PRC. Close https://link.springer.com/chapter/10.1007%2F978-3-030-30493-5_13 doi:10.1007/978-3-030-30493-5_13 Close
	Bullmann Torsten; Radivojevic, Milos; Huber Stefan Deligkaris Kosmas; Hierlemann Andreas; Frey Urs T: Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays Journal Article Frontiers in Cellular Neuroscience , 13 , 2019, ISSN: 1662-5102. Abstract \| Links \| BibTeX \| Tags: Axonal Arbors, HD-MEA @article{Bullmann2019, title = {Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays}, author = {Bullmann, Torsten; Radivojevic, Milos; Huber, Stefan T: Deligkaris, Kosmas; Hierlemann, Andreas; Frey, Urs}, url = {https://www.frontiersin.org/articles/10.3389/fncel.2019.00404/full}, doi = {10.3389/fncel.2019.00404}, issn = {1662-5102}, year = {2019}, date = {2019-09-06}, journal = {Frontiers in Cellular Neuroscience }, volume = {13}, abstract = {Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours.}, keywords = {Axonal Arbors, HD-MEA}, pubstate = {published}, tppubtype = {article} } Close Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours. Close https://www.frontiersin.org/articles/10.3389/fncel.2019.00404/full doi:10.3389/fncel.2019.00404 Close
	Obien, Marie Engelene J; Frey, Urs Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks Book Chapter Springer, 2019. Abstract \| Links \| BibTeX \| Tags: In-Vitro, Neuronal Networks @inbook{Obien2019b, title = {Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks}, author = {Marie Engelene J Obien and Urs Frey}, url = {https://link.springer.com/book/10.1007%2F978-3-030-11135-9#about}, doi = {10.1007/978-3-030-11135-9}, year = {2019}, date = {2019-05-20}, publisher = {Springer}, abstract = {This book provides a comprehensive overview of the incredible advances achieved in the study of in vitro neuronal networks for use in basic and applied research. These cultures of dissociated neurons offer a perfect trade-off between complex experimental models and theoretical modeling approaches giving new opportunities for experimental design but also providing new challenges in data management and interpretation. Topics include culturing methodologies, neuroengineering techniques, stem cell derived neuronal networks, techniques for measuring network activity, and recent improvements in large-scale data analysis. The book ends with a series of case studies examining potential applications of these technologies.}, keywords = {In-Vitro, Neuronal Networks}, pubstate = {published}, tppubtype = {inbook} } Close This book provides a comprehensive overview of the incredible advances achieved in the study of in vitro neuronal networks for use in basic and applied research. These cultures of dissociated neurons offer a perfect trade-off between complex experimental models and theoretical modeling approaches giving new opportunities for experimental design but also providing new challenges in data management and interpretation. Topics include culturing methodologies, neuroengineering techniques, stem cell derived neuronal networks, techniques for measuring network activity, and recent improvements in large-scale data analysis. The book ends with a series of case studies examining potential applications of these technologies. Close https://link.springer.com/book/10.1007%2F978-3-030-11135-9#about doi:10.1007/978-3-030-11135-9 Close
	Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Hierlemann, Andreas; Kanzaki, Ryohei; Takahashi, Hirokazu Classification of Inhibitory and Excitatory Neurons of Dissociated Cultures Based on Action Potential Waveforms on High-density CMOS Microelectrode Arrays Journal Article IEEJ Transactions on Electronics, Information and Systems, 139 (5), pp. 615-624, 2019, ISSN: 1348-8155. Abstract \| Links \| BibTeX \| Tags: Action Potential, HD-MEA @article{Mita2019, title = {Classification of Inhibitory and Excitatory Neurons of Dissociated Cultures Based on Action Potential Waveforms on High-density CMOS Microelectrode Arrays}, author = {Takeshi Mita and Douglas J. Bakkum and Urs Frey and Andreas Hierlemann and Ryohei Kanzaki and Hirokazu Takahashi }, url = {https://www.jstage.jst.go.jp/article/ieejeiss/139/5/139_615/_article/-char/en}, doi = {10.1541/ieejeiss.139.615}, issn = {1348-8155}, year = {2019}, date = {2019-05-01}, journal = {IEEJ Transactions on Electronics, Information and Systems}, volume = {139}, number = {5}, pages = {615-624}, abstract = {Electrophysiological data from in vivo and slice preparations show that inhibitory neurons had shorter duration action potentials (AP) than excitatory neurons. However, this criterion has not yet been established in dissociated cultured neurons. In the present study, we used a high-density CMOS microelectrode array to extracellularly investigate neural signals in primary dissociated cultures of rat neocortex, and we characterized AP waveforms to discriminate excitatory and inhibitory neurons. The CMOS array offers the possibility to acquire comprehensive spatio-temporal neural activity patterns with 11,011 electrodes in about 2×1.75 mm2 area at 20-kHz sampling rate. The waveforms of APs were investigated around cell bodies of neurons, which were classified into either excitatory neurons or inhibitory neurons on the basis of MAP2 and GABA immunostaining images. Consistent with previous in vivo and slice studies, we demonstrated that AP waveforms of inhibitory neurons had shorter durations and recovery time than those of excitatory neurons. The discrimination accuracy was around 0.9 in the receiver-operating characteristics (ROC) analyses. Additionally, taking advantage of non-invasive CMOS recording, we investigated AP waveforms throughout development of cultures. We confirmed that APs were classified into two classes, i.e., putative excitatory and inhibitory neurons, regardless of developmental stages, and found that the duration and recovery time of AP shortened in matured cultures. Thus, AP waveforms have rich information about cell types and developmental stages, which are of worth to elucidate underlying mechanisms of neuronal dynamics in spatio-temporal patterns.}, keywords = {Action Potential, HD-MEA}, pubstate = {published}, tppubtype = {article} } Close Electrophysiological data from in vivo and slice preparations show that inhibitory neurons had shorter duration action potentials (AP) than excitatory neurons. However, this criterion has not yet been established in dissociated cultured neurons. In the present study, we used a high-density CMOS microelectrode array to extracellularly investigate neural signals in primary dissociated cultures of rat neocortex, and we characterized AP waveforms to discriminate excitatory and inhibitory neurons. The CMOS array offers the possibility to acquire comprehensive spatio-temporal neural activity patterns with 11,011 electrodes in about 2×1.75 mm2 area at 20-kHz sampling rate. The waveforms of APs were investigated around cell bodies of neurons, which were classified into either excitatory neurons or inhibitory neurons on the basis of MAP2 and GABA immunostaining images. Consistent with previous in vivo and slice studies, we demonstrated that AP waveforms of inhibitory neurons had shorter durations and recovery time than those of excitatory neurons. The discrimination accuracy was around 0.9 in the receiver-operating characteristics (ROC) analyses. Additionally, taking advantage of non-invasive CMOS recording, we investigated AP waveforms throughout development of cultures. We confirmed that APs were classified into two classes, i.e., putative excitatory and inhibitory neurons, regardless of developmental stages, and found that the duration and recovery time of AP shortened in matured cultures. Thus, AP waveforms have rich information about cell types and developmental stages, which are of worth to elucidate underlying mechanisms of neuronal dynamics in spatio-temporal patterns. Close https://www.jstage.jst.go.jp/article/ieejeiss/139/5/139_615/_article/-char/en doi:10.1541/ieejeiss.139.615 Close
	Emmenegger, Vishalini; Obien, Marie Engelene J; Franke, Felix; Hierlemann, Andreas Technologies to Study Action Potential Propagation With a Focus on HD-MEAs Journal Article Frontiers in Cellular Neuroscience, 13 , pp. 1-11, 2019, ISSN: 1662-5102 . Abstract \| Links \| BibTeX \| Tags: Action Potential, HD-MEA @article{Emmenegger2019, title = {Technologies to Study Action Potential Propagation With a Focus on HD-MEAs}, author = {Vishalini Emmenegger and Marie Engelene J. Obien and Felix Franke and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fncel.2019.00159/full}, doi = {10.3389/fncel.2019.00159 }, issn = {1662-5102 }, year = {2019}, date = {2019-04-26}, journal = {Frontiers in Cellular Neuroscience}, volume = {13}, pages = {1-11}, abstract = {Axons convey information in neuronal circuits via reliable conduction of action potentials from the axon initial segment to the presynaptic terminals. Recent experimental findings increasingly evidence that the axonal function is not limited to the simple transmission of action potentials. Advances in subcellular-resolution recording techniques have shown that axons display activity-dependent modulation in spike shape and conduction velocity, which influence synaptic strength and latency. We briefly review, here, how recent methodological developments facilitate the understanding of the axon physiology. We included the three most common methods, i.e. genetically encoded voltage imaging, subcellular patch-clamp and high-density microelectrode arrays (HD-MEAs). We then describe the potential of using HD-MEAs in studying axonal physiology in more detail. Due to their robustness, amenability to high-throughput and high spatiotemporal resolution, HD-MEAs can provide a direct functional electrical readout of single cells and cellular ensembles at subcellular resolution. HD-MEAs can, therefore, be employed in investigating axonal pathologies, the effects of large-scale genomic interventions (e.g., with RNAi or CRISPR) or in compound screenings. A combination of extracellular microelectrode arrays, intracellular microelectrodes and optical imaging may potentially reveal yet unexplored repertoires of axonal functions.}, keywords = {Action Potential, HD-MEA}, pubstate = {published}, tppubtype = {article} } Close Axons convey information in neuronal circuits via reliable conduction of action potentials from the axon initial segment to the presynaptic terminals. Recent experimental findings increasingly evidence that the axonal function is not limited to the simple transmission of action potentials. Advances in subcellular-resolution recording techniques have shown that axons display activity-dependent modulation in spike shape and conduction velocity, which influence synaptic strength and latency. We briefly review, here, how recent methodological developments facilitate the understanding of the axon physiology. We included the three most common methods, i.e. genetically encoded voltage imaging, subcellular patch-clamp and high-density microelectrode arrays (HD-MEAs). We then describe the potential of using HD-MEAs in studying axonal physiology in more detail. Due to their robustness, amenability to high-throughput and high spatiotemporal resolution, HD-MEAs can provide a direct functional electrical readout of single cells and cellular ensembles at subcellular resolution. HD-MEAs can, therefore, be employed in investigating axonal pathologies, the effects of large-scale genomic interventions (e.g., with RNAi or CRISPR) or in compound screenings. A combination of extracellular microelectrode arrays, intracellular microelectrodes and optical imaging may potentially reveal yet unexplored repertoires of axonal functions. Close https://www.frontiersin.org/articles/10.3389/fncel.2019.00159/full doi:10.3389/fncel.2019.00159 Close
	Viswam, Vijay; Obien, Marie Engelene J; Franke, Felix; Frey, Urs; Hierlemann, Andreas Optimal Electrode Size for Multi-Scale Extracellular-Potential Recording From Neuronal Assemblies Journal Article Frontiers in Neuroscience, 13 , 2019, ISSN: 1662-453X. Abstract \| Links \| BibTeX \| Tags: Neuronal Assemblies @article{Viswam2019, title = {Optimal Electrode Size for Multi-Scale Extracellular-Potential Recording From Neuronal Assemblies}, author = {Vijay Viswam and Marie Engelene J. Obien and Felix Franke and Urs Frey and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2019.00385/full}, doi = {10.3389/fnins.2019.00385}, issn = {1662-453X}, year = {2019}, date = {2019-04-26}, journal = {Frontiers in Neuroscience}, volume = {13}, abstract = {Advances in microfabrication technology have enabled the production of devices containing arrays of thousands of closely spaced recording electrodes, which afford subcellular resolution of electrical signals in neurons and neuronal networks. Rationalizing the electrode size and configuration in such arrays demands consideration of application-specific requirements and inherent features of the electrodes. Tradeoffs among size, spatial density, sensitivity, noise, attenuation, and other factors are inevitable. Although recording extracellular signals from neurons with planar metal electrodes is fairly well established, the effects of the electrode characteristics on the quality and utility of recorded signals, especially for small, densely packed electrodes, have yet to be fully characterized. Here, we present a combined experimental and computational approach to elucidating how electrode size, and size-dependent parameters, such as impedance, baseline noise, and transmission characteristics, influence recorded neuronal signals. Using arrays containing platinum electrodes of different sizes, we experimentally evaluated the electrode performance in the recording of local-field-potentials (LFPs) and extracellular-action-potentials (EAPs) from the following cell preparations: acute brain slices, dissociated cell cultures, and organotypic slice cultures. Moreover, we simulated the potential spatial decay of point-current sources to investigate signal averaging using known signal sources. We demonstrated that the noise and signal attenuation depend more on the electrode impedance than on electrode size, per se, especially for electrodes < 10 µm in width or diameter to achieve high-spatial-resolution readout. By minimizing electrode impedance in small electrodes (< 10 µm), via surface modification, we could maximize the signal-to-noise ratio to electrically visualize the propagation of axonal EAPs and to isolate single-unit spikes. Due to the large amplitude of LFP signals, recording quality was high and nearly independent of electrode size. These findings should be of value in configuring in vitro and in vivo microelectrode arrays for extracellular recordings with high spatial resolution in various applications.}, keywords = {Neuronal Assemblies}, pubstate = {published}, tppubtype = {article} } Close Advances in microfabrication technology have enabled the production of devices containing arrays of thousands of closely spaced recording electrodes, which afford subcellular resolution of electrical signals in neurons and neuronal networks. Rationalizing the electrode size and configuration in such arrays demands consideration of application-specific requirements and inherent features of the electrodes. Tradeoffs among size, spatial density, sensitivity, noise, attenuation, and other factors are inevitable. Although recording extracellular signals from neurons with planar metal electrodes is fairly well established, the effects of the electrode characteristics on the quality and utility of recorded signals, especially for small, densely packed electrodes, have yet to be fully characterized. Here, we present a combined experimental and computational approach to elucidating how electrode size, and size-dependent parameters, such as impedance, baseline noise, and transmission characteristics, influence recorded neuronal signals. Using arrays containing platinum electrodes of different sizes, we experimentally evaluated the electrode performance in the recording of local-field-potentials (LFPs) and extracellular-action-potentials (EAPs) from the following cell preparations: acute brain slices, dissociated cell cultures, and organotypic slice cultures. Moreover, we simulated the potential spatial decay of point-current sources to investigate signal averaging using known signal sources. We demonstrated that the noise and signal attenuation depend more on the electrode impedance than on electrode size, per se, especially for electrodes < 10 µm in width or diameter to achieve high-spatial-resolution readout. By minimizing electrode impedance in small electrodes (< 10 µm), via surface modification, we could maximize the signal-to-noise ratio to electrically visualize the propagation of axonal EAPs and to isolate single-unit spikes. Due to the large amplitude of LFP signals, recording quality was high and nearly independent of electrode size. These findings should be of value in configuring in vitro and in vivo microelectrode arrays for extracellular recordings with high spatial resolution in various applications. Close https://www.frontiersin.org/articles/10.3389/fnins.2019.00385/full doi:10.3389/fnins.2019.00385 Close
	Russell, Thomas L; Zhang, Jichang; Okoniewksi, Michal; Franke, Felix; Bichet, Sandrine; Hierlemann, Andreas Medullary Respiratory Circuit Is Reorganized by a Seasonally-Induced Program in Preparation for Hibernation Journal Article Frontiers in Neuroscience , 13 , 2019, ISSN: 1662-453X. Abstract \| Links \| BibTeX \| Tags: Respiratory Circuit @article{Russell2019, title = {Medullary Respiratory Circuit Is Reorganized by a Seasonally-Induced Program in Preparation for Hibernation }, author = {Thomas L. Russell and Jichang Zhang and Michal Okoniewksi and Felix Franke and Sandrine Bichet and Andreas Hierlemann}, url = {https://www.frontiersin.org/article/10.3389/fnins.2019.00376}, doi = {10.3389/fnins.2019.00376 }, issn = {1662-453X}, year = {2019}, date = {2019-04-26}, journal = {Frontiers in Neuroscience }, volume = {13}, abstract = {Deep hibernators go through several cycles of profound drops in body temperature during the winter season, with core temperatures sometimes reaching near freezing. Yet unlike non-hibernating mammals, they can sustain breathing rhythms. The physiological processes that make this possible are still not understood. In this study, we focused on the medullary Ventral Respiratory Column of a facultative hibernator, the Syrian hamster. Using shortened day-lengths, we induced a "winter-adapted" physiological state, which is a prerequisite for hibernation. When recording electrophysiological signals from acute slices in the winter-adapted pre-Bötzinger complex, spike trains showed higher spike rates, amplitudes, complexity, as well as higher temperature sensitivity, suggesting an increase in connectivity and/or synaptic strength during the winter season. We further examined action potential waveforms and found that the depolarization integral, as measured by the area under the curve, is selectively enhanced in winter-adapted animals. This suggests that a shift in the ion handling kinetics is also being induced by the winter-adaptation program. RNA sequencing of respiratory pre-motor neurons, followed by gene set enrichment analysis, revealed differential regulation and splicing in structural, synaptic, and ion handling genes. Splice junction analysis suggested that differential exon usage is occurring in a select subset of ion handling subunits (ATP1A3, KCNC3, SCN1B), and synaptic structure genes (SNCB, SNCG, RAB3A). Our findings show that the hamster respiratory center undergoes a seasonally-cued alteration in electrophysiological properties, likely protecting against respiratory failure at low temperatures.}, keywords = {Respiratory Circuit}, pubstate = {published}, tppubtype = {article} } Close Deep hibernators go through several cycles of profound drops in body temperature during the winter season, with core temperatures sometimes reaching near freezing. Yet unlike non-hibernating mammals, they can sustain breathing rhythms. The physiological processes that make this possible are still not understood. In this study, we focused on the medullary Ventral Respiratory Column of a facultative hibernator, the Syrian hamster. Using shortened day-lengths, we induced a "winter-adapted" physiological state, which is a prerequisite for hibernation. When recording electrophysiological signals from acute slices in the winter-adapted pre-Bötzinger complex, spike trains showed higher spike rates, amplitudes, complexity, as well as higher temperature sensitivity, suggesting an increase in connectivity and/or synaptic strength during the winter season. We further examined action potential waveforms and found that the depolarization integral, as measured by the area under the curve, is selectively enhanced in winter-adapted animals. This suggests that a shift in the ion handling kinetics is also being induced by the winter-adaptation program. RNA sequencing of respiratory pre-motor neurons, followed by gene set enrichment analysis, revealed differential regulation and splicing in structural, synaptic, and ion handling genes. Splice junction analysis suggested that differential exon usage is occurring in a select subset of ion handling subunits (ATP1A3, KCNC3, SCN1B), and synaptic structure genes (SNCB, SNCG, RAB3A). Our findings show that the hamster respiratory center undergoes a seasonally-cued alteration in electrophysiological properties, likely protecting against respiratory failure at low temperatures. Close https://www.frontiersin.org/article/10.3389/fnins.2019.00376 doi:10.3389/fnins.2019.00376 Close
	Ronchi, Silvia; Fiscella, Michele; Marchetti, Camilla; Viswam, Vijay; Muller, Jan; Frey, Urs; Hierlemann, Andreas Single-Cell Electrical Stimulation Using CMOS-Based High-Density Microelectrode Arrays Journal Article Frontiers in Neuroscience, 13 , 2019, ISSN: 1662-453X . Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @article{Ronchi2019, title = {Single-Cell Electrical Stimulation Using CMOS-Based High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Michele Fiscella and Camilla Marchetti and Vijay Viswam and Jan Muller and Urs Frey and Andreas Hierlemann}, url = {https://www.frontiersin.org/article/10.3389/fnins.2019.00208 }, doi = {10.3389/fnins.2019.00208 }, issn = {1662-453X }, year = {2019}, date = {2019-03-13}, journal = {Frontiers in Neuroscience}, volume = {13}, abstract = {Non-invasive electrical stimulation can be used to study and control neural activity in the brain or to alleviate somatosensory dysfunctions. One intriguing prospect is to precisely stimulate individual targeted neurons. Here, we investigated single-neuron current and voltage stimulation in vitro using high-density microelectrode arrays featuring 26’400 bidirectional electrodes at a pitch of 17.5 µm and an electrode area of 5 × 9 µm². We determined optimal waveforms, amplitudes and durations for both stimulation modes. Owing to the high spatial resolution of our arrays and the close proximity of the electrodes to the respective neurons, we were able to stimulate the axon initial segments (AIS) with charges of less than 2 picoCoulombs. This resulted in minimal artifact production and reliable readout of stimulation efficiency directly at the soma of the stimulated cell. Stimulation signals as low as 70 mV or 100 nA,with pulse durations as short as 18 µs, yielded measurable action potential initiation and propagation. We found that the required stimulation signal amplitudes decreased with cell growth and development and that stimulation efficiency did not improve at higher electric fields generated by simultaneous multi-electrode stimulation.}, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Non-invasive electrical stimulation can be used to study and control neural activity in the brain or to alleviate somatosensory dysfunctions. One intriguing prospect is to precisely stimulate individual targeted neurons. Here, we investigated single-neuron current and voltage stimulation in vitro using high-density microelectrode arrays featuring 26’400 bidirectional electrodes at a pitch of 17.5 µm and an electrode area of 5 × 9 µm². We determined optimal waveforms, amplitudes and durations for both stimulation modes. Owing to the high spatial resolution of our arrays and the close proximity of the electrodes to the respective neurons, we were able to stimulate the axon initial segments (AIS) with charges of less than 2 picoCoulombs. This resulted in minimal artifact production and reliable readout of stimulation efficiency directly at the soma of the stimulated cell. Stimulation signals as low as 70 mV or 100 nA,with pulse durations as short as 18 µs, yielded measurable action potential initiation and propagation. We found that the required stimulation signal amplitudes decreased with cell growth and development and that stimulation efficiency did not improve at higher electric fields generated by simultaneous multi-electrode stimulation. Close https://www.frontiersin.org/article/10.3389/fnins.2019.00208 doi:10.3389/fnins.2019.00208 Close
	Obien, Marie Engelene J; Hierlemann, Andreas; Frey, Urs Accurate signal-source localization in brain slices by means of high-density microelectrode arrays Journal Article Scientific Reports, 9 (788), 2019. Abstract \| Links \| BibTeX \| Tags: Brain Slice @article{Obien2019, title = {Accurate signal-source localization in brain slices by means of high-density microelectrode arrays}, author = {Marie Engelene J. Obien and Andreas Hierlemann and Urs Frey}, url = {https://www.nature.com/articles/s41598-018-36895-y}, doi = {10.1038/s41598-018-36895-y}, year = {2019}, date = {2019-01-28}, journal = {Scientific Reports}, volume = {9}, number = {788}, abstract = {Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 μm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 μm systematic mean error, compared to 22.0 μm obtained with MoI. These results suggest that the medium volume or “saline height”, the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 μm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation.}, keywords = {Brain Slice}, pubstate = {published}, tppubtype = {article} } Close Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 μm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 μm systematic mean error, compared to 22.0 μm obtained with MoI. These results suggest that the medium volume or “saline height”, the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 μm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation. Close https://www.nature.com/articles/s41598-018-36895-y doi:10.1038/s41598-018-36895-y Close
	Dudina, Alexandra; Seichepine, Florent; Chen, Yihui; and Stettler, Alexander; Hierlemann, Andreas; and Frey, Urs Monolithic CMOS sensor platform featuring an array of 9’216 carbon-nanotube-sensor elements and low-noise, wide-bandwidth and wide-dynamic-range readout circuitry Journal Article Sensors and Actuators B: Chemical, 279 , pp. 255-266, 2019. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Dudina2019, title = {Monolithic CMOS sensor platform featuring an array of 9’216 carbon-nanotube-sensor elements and low-noise, wide-bandwidth and wide-dynamic-range readout circuitry}, author = {Alexandra Dudina and Florent Seichepine and Yihui Chen and and Alexander Stettler and Andreas Hierlemann and and Urs Frey}, url = {https://www.sciencedirect.com/science/article/pii/S0925400518317672?via%3Dihub}, doi = {10.1016/j.snb.2018.10.004}, year = {2019}, date = {2019-01-15}, journal = {Sensors and Actuators B: Chemical}, volume = {279}, pages = {255-266}, abstract = {We present the design and characterization of a monolithic complementary metal–oxide–semiconductor (CMOS) biosensor platform comprising of a switch-matrix-based array of 9′216 carbon nanotube field-effect transistors (CNTFETs) and associated readout circuitry. The switch-matrix allows for flexible selection and simultaneous routing of 96 sensor elements to the corresponding readout channels. A low-noise, wide-bandwidth, wide-dynamic-range transimpedance continuous-time amplifier architecture has been implemented to facilitate resistance measurements in the range between 50 kΩ and 1 GΩ at a bandwidth of up to 1 MHz. The achieved accuracy of the resistance measurements over the whole range is 4%. The system has been successfully fabricated and tested and shows a noise performance equal to 2.14 pArms at a bandwidth of 1 kHz and 0.84 nArms at a bandwidth of 1 MHz. A batch integration of the CNTFETs has been achieved by using a dielectrophoresis (DEP)–based manipulation technique. The current-voltage curves of CNTFETs have been acquired, and the sensing capabilities of the system have been demonstrated by recording resistance changes of CNTFETs upon exposure to solutions with different pH values and different concentrations of NaCl. The smallest resolvable concentrations for the respective analytes were estimated to amount to 0.025 pH-units and 4 mM NaCl.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close We present the design and characterization of a monolithic complementary metal–oxide–semiconductor (CMOS) biosensor platform comprising of a switch-matrix-based array of 9′216 carbon nanotube field-effect transistors (CNTFETs) and associated readout circuitry. The switch-matrix allows for flexible selection and simultaneous routing of 96 sensor elements to the corresponding readout channels. A low-noise, wide-bandwidth, wide-dynamic-range transimpedance continuous-time amplifier architecture has been implemented to facilitate resistance measurements in the range between 50 kΩ and 1 GΩ at a bandwidth of up to 1 MHz. The achieved accuracy of the resistance measurements over the whole range is 4%. The system has been successfully fabricated and tested and shows a noise performance equal to 2.14 pArms at a bandwidth of 1 kHz and 0.84 nArms at a bandwidth of 1 MHz. A batch integration of the CNTFETs has been achieved by using a dielectrophoresis (DEP)–based manipulation technique. The current-voltage curves of CNTFETs have been acquired, and the sensing capabilities of the system have been demonstrated by recording resistance changes of CNTFETs upon exposure to solutions with different pH values and different concentrations of NaCl. The smallest resolvable concentrations for the respective analytes were estimated to amount to 0.025 pH-units and 4 mM NaCl. Close https://www.sciencedirect.com/science/article/pii/S0925400518317672?via%3Dihub doi:10.1016/j.snb.2018.10.004 Close
	Shadmani, Amir; Viswam, Vijay; Chen, Yihui; Bounik, Raziyeh; Dragas, Jelena; Radivojevic, Milos; Geissler, Sydney; Sitnikov, Sergey; Muller, Jan; Hierlemann, Andreas Stimulation and Artifact-suppression Techniques for in-vitro High-density Microelectrode Array Systems. Journal Article IEEE Transactions on Biomedical Engineering, 2019. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Shadmani2019b, title = {Stimulation and Artifact-suppression Techniques for in-vitro High-density Microelectrode Array Systems.}, author = {Amir Shadmani and Vijay Viswam and Yihui Chen and Raziyeh Bounik and Jelena Dragas and Milos Radivojevic and Sydney Geissler and Sergey Sitnikov and Jan Muller and Andreas Hierlemann }, url = {https://ieeexplore.ieee.org/document/8599003}, doi = {10.1109/TBME.2018.2890530}, year = {2019}, date = {2019-01-01}, journal = {IEEE Transactions on Biomedical Engineering}, abstract = {We present novel voltage stimulation buffers with controlled output current, along with recording circuits featuring adjustable high-pass cut-off filtering to perform efficient stimulation while actively suppressing stimulation artifacts in high-density microelectrode arrays. Owing to the dense packing and close proximity of the electrodes in such systems, a stimulation through one electrode can cause large electrical artifacts on neighboring electrodes that easily saturate the corresponding recording amplifiers. To suppress such artifacts, the high-pass corner frequencies of all available 2048 recording channels can be raised from several Hz to several kHz by applying a "soft-reset" or pole-shifting technique. With the implemented artifact suppression technique, the saturation time of the recording circuits, connected to electrodes in immediate vicinity to the stimulation site, could be reduced to less than 150μs. For the stimulation buffer, we developed a circuit, which can operate in two modes: either control of only the stimulation voltage, or control of current and voltage during stimulation. The voltage-only controlled mode employs a local common-mode feedback operational transconductance amplifier with a near rail-to-rail input/output range, suitable for driving high capacitive loads. The current/voltage controlled mode is based on a positive current conveyor generating adjustable output currents, while its upper and lower output voltages are limited by two feedback loops. The current/voltage controlled circuit can generate stimulation pulses up to 30 μA with less than ±0.1% linearity error in the low-current mode, and up to 300 μA with less than ±0.2% linearity error in the high-current mode.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close We present novel voltage stimulation buffers with controlled output current, along with recording circuits featuring adjustable high-pass cut-off filtering to perform efficient stimulation while actively suppressing stimulation artifacts in high-density microelectrode arrays. Owing to the dense packing and close proximity of the electrodes in such systems, a stimulation through one electrode can cause large electrical artifacts on neighboring electrodes that easily saturate the corresponding recording amplifiers. To suppress such artifacts, the high-pass corner frequencies of all available 2048 recording channels can be raised from several Hz to several kHz by applying a "soft-reset" or pole-shifting technique. With the implemented artifact suppression technique, the saturation time of the recording circuits, connected to electrodes in immediate vicinity to the stimulation site, could be reduced to less than 150μs. For the stimulation buffer, we developed a circuit, which can operate in two modes: either control of only the stimulation voltage, or control of current and voltage during stimulation. The voltage-only controlled mode employs a local common-mode feedback operational transconductance amplifier with a near rail-to-rail input/output range, suitable for driving high capacitive loads. The current/voltage controlled mode is based on a positive current conveyor generating adjustable output currents, while its upper and lower output voltages are limited by two feedback loops. The current/voltage controlled circuit can generate stimulation pulses up to 30 μA with less than ±0.1% linearity error in the low-current mode, and up to 300 μA with less than ±0.2% linearity error in the high-current mode. Close https://ieeexplore.ieee.org/document/8599003 doi:10.1109/TBME.2018.2890530 Close
2018
	Bakkum, Douglas J; Obien, Marie Engelene J; Radivojevic, Milos; Jäckel, David; Frey, Urs; Takahashi, Hirokazu; Hierlemann, Andreas The Axon Initial Segment is the Dominant Contributor to the Neuron's Extracellular Electrical Potential Landscape Journal Article Advanced Biosystems, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Bakkum2018b, title = {The Axon Initial Segment is the Dominant Contributor to the Neuron's Extracellular Electrical Potential Landscape}, author = {Douglas J. Bakkum and Marie Engelene J. Obien and Milos Radivojevic and David Jäckel and Urs Frey and Hirokazu Takahashi and Andreas Hierlemann}, url = {https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201800308}, doi = {10.1002/adbi.201800308}, year = {2018}, date = {2018-11-29}, journal = {Advanced Biosystems}, abstract = {Extracellular voltage fields, produced by a neuron's action potentials, provide a widely used means for studying neuronal and neuronal‐network function. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP) landscape, while the axon's contribution is usually considered less important. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices through hundreds of densely packed electrodes, it is found, instead, that the axon initial segment dominates the measured EAP landscape, and, surprisingly, the soma only contributes to a minor extent. As expected, the recorded dominant signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage landscape is important for interpreting results from all electrical readout schemes. Finally, initiation of the electrical activity at the distal end of the axon initial segment (AIS) and subsequent spreading into the axon proper and backward through the proximal AIS toward the soma are confirmed. The corresponding extracellular waveforms across different neuronal compartments could be tracked.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Extracellular voltage fields, produced by a neuron's action potentials, provide a widely used means for studying neuronal and neuronal‐network function. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP) landscape, while the axon's contribution is usually considered less important. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices through hundreds of densely packed electrodes, it is found, instead, that the axon initial segment dominates the measured EAP landscape, and, surprisingly, the soma only contributes to a minor extent. As expected, the recorded dominant signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage landscape is important for interpreting results from all electrical readout schemes. Finally, initiation of the electrical activity at the distal end of the axon initial segment (AIS) and subsequent spreading into the axon proper and backward through the proximal AIS toward the soma are confirmed. The corresponding extracellular waveforms across different neuronal compartments could be tracked. Close https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201800308 doi:10.1002/adbi.201800308 Close
	Viswam, Vijay; Bounik, Raziyeh; Shadmani, Amir; Dragas, Jelena; Urwyler, Cedar; Boos, Julia Alicia; Obien, Marie Engelene J; Muller, Jan; Chen, Yihui; Hierlemann, Andreas Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System Journal Article IEEE Transactions on Biomedical Circuits and Systems, 12 (6), pp. 1356-1368, 2018, ISSN: 1932-4545. Abstract \| Links \| BibTeX \| Tags: HD-MEA @article{Viswam2018, title = {Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System}, author = {Vijay Viswam and Raziyeh Bounik and Amir Shadmani and Jelena Dragas and Cedar Urwyler and Julia Alicia Boos and Marie Engelene J. Obien and Jan Muller and Yihui Chen and Andreas Hierlemann}, url = {https://ieeexplore.ieee.org/document/8532304}, doi = {10.1109/TBCAS.2018.2881044}, issn = {1932-4545}, year = {2018}, date = {2018-11-12}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {12}, number = {6}, pages = {1356-1368}, abstract = {A monolithic multi-functional CMOS microelectrode array system was developed that enables label-free electrochemical impedance spectroscopy of cells in vitro at high spatiotemporal resolution. The electrode array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 μm. A total of 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen subset of electrodes in the array. A sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, was applied to the reference electrode. The sensing currents through the selected recording electrodes were amplified, demodulated, filtered, and digitized to obtain the magnitude and phase information of the respective impedances. The circuitry consumes only 412 μW at 3.3 V supply voltage and occupies only 0.1 mm 2 , for each channel. The system also included 2048 extracellular action-potential recording channels on the same chip. Proof of concept measurements of electrical impedance imaging and electrophysiology recording of cardiac cells and brain slices are demonstrated in this paper. Optical and impedance images showed a strong correlation.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {article} } Close A monolithic multi-functional CMOS microelectrode array system was developed that enables label-free electrochemical impedance spectroscopy of cells in vitro at high spatiotemporal resolution. The electrode array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 μm. A total of 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen subset of electrodes in the array. A sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, was applied to the reference electrode. The sensing currents through the selected recording electrodes were amplified, demodulated, filtered, and digitized to obtain the magnitude and phase information of the respective impedances. The circuitry consumes only 412 μW at 3.3 V supply voltage and occupies only 0.1 mm 2 , for each channel. The system also included 2048 extracellular action-potential recording channels on the same chip. Proof of concept measurements of electrical impedance imaging and electrophysiology recording of cardiac cells and brain slices are demonstrated in this paper. Optical and impedance images showed a strong correlation. Close https://ieeexplore.ieee.org/document/8532304 doi:10.1109/TBCAS.2018.2881044 Close
	Lewandowska, Marta K; Bogatikov, Evgenii; Hierlemann, Andreas; Punga, Anna Rostedt Long-term high-density extracellular recordings enable studies of muscle cell physiology and pathology Conference Contribution 700.13 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Physiology @conference{Lewandowska2018c, title = {Long-term high-density extracellular recordings enable studies of muscle cell physiology and pathology}, author = {Marta K. Lewandowska and Evgenii Bogatikov and Andreas Hierlemann and Anna Rostedt Punga}, url = {https://abstractsonline.com/pp8/#!/4649/presentation/24936}, year = {2018}, date = {2018-11-07}, volume = {Contribution 700.13}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of defective ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high spatial resolution and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. We present a method, which we used to follow the development of primary skeletal muscle cells from myoblasts into mature contracting myofibers over more than two months. In contrast to most previous studies, the muscles do not detach from the surface but instead form functional networks between the myofibers, whose electrical signals we observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myofibers on a chip that contains an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enables discovery of the origin of possible failure mechanisms in muscle diseases. This system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models.}, keywords = {ETH-CMOS-MEA, Physiology}, pubstate = {published}, tppubtype = {conference} } Close Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of defective ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high spatial resolution and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. We present a method, which we used to follow the development of primary skeletal muscle cells from myoblasts into mature contracting myofibers over more than two months. In contrast to most previous studies, the muscles do not detach from the surface but instead form functional networks between the myofibers, whose electrical signals we observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myofibers on a chip that contains an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enables discovery of the origin of possible failure mechanisms in muscle diseases. This system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models. Close https://abstractsonline.com/pp8/#!/4649/presentation/24936 Close
	Fiscella, Michele; Leary, Noelle; Ronchi, Silvia; Hierlemann, Andreas Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelectrode array Conference Contribution 700.13 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC @conference{Fiscella2018, title = {Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelectrode array}, author = {Michele Fiscella and Noelle Leary and Silvia Ronchi and Andreas Hierlemann }, url = {https://www.abstractsonline.com/pp8/#!/4649/presentation/24924}, year = {2018}, date = {2018-11-07}, volume = {Contribution 700.13}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {High-resolution-microelectrode-array (HD-MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity [1]. We have used this HD-MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural-culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple HD-MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons [2]. Furthermore, we found different axonal-action-potential-velocity-development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular-resolution electrical stimulation. HD-MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing.}, keywords = {HD-MEA, IPSC}, pubstate = {published}, tppubtype = {conference} } Close High-resolution-microelectrode-array (HD-MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity [1]. We have used this HD-MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural-culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple HD-MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons [2]. Furthermore, we found different axonal-action-potential-velocity-development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular-resolution electrical stimulation. HD-MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing. Close https://www.abstractsonline.com/pp8/#!/4649/presentation/24924 Close
	Emmenegger, Vishalini; Bartram, Julian; Sitnikov, Sergey; Hierlemann, Andreas Investigating the analog modulation of action-potential waveforms in axonal arbors of cortical neurons using whole-cell patch-clamp recordings and high-density microelectrode arrays Conference Contribution 203.05 , Society for Neuroscience (SfN) Meeting, San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @conference{Emmenegger2018, title = {Investigating the analog modulation of action-potential waveforms in axonal arbors of cortical neurons using whole-cell patch-clamp recordings and high-density microelectrode arrays}, author = {Vishalini Emmenegger and Julian Bartram and Sergey Sitnikov and Andreas Hierlemann}, url = {https://abstractsonline.com/pp8/#!/4649/presentation/9323}, year = {2018}, date = {2018-11-04}, volume = {Contribution 203.05}, publisher = {Society for Neuroscience (SfN) Meeting}, address = {San Diego, CA, USA}, abstract = {Analog-digital facilitation (ADF) is a type of short-term plasticity, where the subthreshold membrane potential in the presynaptic element enhances the spike-evoked synaptic response. Most cases of ADF have been induced by long (0.3-10 s) subthreshold depolarization of the soma, while in few cases, transient (15-200 ms) hyperpolarization has been evoked immediately before the action potential (AP). In both cases, somatic membrane fluctuations modulate the biophysical properties of voltage-gated ion channels causing changes in the AP waveform, which result in larger release of neurotransmitters. However, it is still unknown, whether the modulation of the AP waveform changes with increasing distance from the soma and differs in different axonal arbors, and whether such modulation affects the velocity of AP propagation. Here, we used CMOS-based high-density microelectrode arrays (HD-MEA) with 26,400 microelectrodes, which enabled unprecedented high-resolution access to investigating axonal signaling at multiple sites simultaneously, thus providing in-depth information on the propagation of AP. The subthreshold depolarization and hyperpolarization of the presynaptic cell was performed using whole-cell patch-clamp recordings from cells in low-density cortical cultures, plated on a HD-MEA that allowed to trace the effects of such manipulations on AP propagation characteristics. Array-wide spike-triggered average signals were computed, and their spatiotemporal distribution was reconstructed. In order to study the changes in extracellular AP waveforms, we first induced pharmacological modulations using dendrotoxin and carbamazepine, which increased AP width and amplitude. As a next step, we evoked AP broadening and amplitude changes by subthreshold depolarization and hyperpolarization. We detected the extracellular AP waveforms directly under the soma and traced them throughout the axon during various time spans and for different holding potentials. We found that changes in AP propagation velocity were correlated to the detected AP broadening. Our preliminary data evidenced changes in AP waveforms with increasing distance from the soma along the axon, but further experiments on synaptically coupled neurons using paired recordings will be performed to better understand the influence of AP modulation on ADF. Information encoding in neuronal circuits is probably contingent on both, temporal spike patterns and spike waveforms. In the light of the latter being typically disregarded in computational models, the study of the analog modulation of AP waveforms will contribute to a better understanding of neuronal information processing.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {conference} } Close Analog-digital facilitation (ADF) is a type of short-term plasticity, where the subthreshold membrane potential in the presynaptic element enhances the spike-evoked synaptic response. Most cases of ADF have been induced by long (0.3-10 s) subthreshold depolarization of the soma, while in few cases, transient (15-200 ms) hyperpolarization has been evoked immediately before the action potential (AP). In both cases, somatic membrane fluctuations modulate the biophysical properties of voltage-gated ion channels causing changes in the AP waveform, which result in larger release of neurotransmitters. However, it is still unknown, whether the modulation of the AP waveform changes with increasing distance from the soma and differs in different axonal arbors, and whether such modulation affects the velocity of AP propagation. Here, we used CMOS-based high-density microelectrode arrays (HD-MEA) with 26,400 microelectrodes, which enabled unprecedented high-resolution access to investigating axonal signaling at multiple sites simultaneously, thus providing in-depth information on the propagation of AP. The subthreshold depolarization and hyperpolarization of the presynaptic cell was performed using whole-cell patch-clamp recordings from cells in low-density cortical cultures, plated on a HD-MEA that allowed to trace the effects of such manipulations on AP propagation characteristics. Array-wide spike-triggered average signals were computed, and their spatiotemporal distribution was reconstructed. In order to study the changes in extracellular AP waveforms, we first induced pharmacological modulations using dendrotoxin and carbamazepine, which increased AP width and amplitude. As a next step, we evoked AP broadening and amplitude changes by subthreshold depolarization and hyperpolarization. We detected the extracellular AP waveforms directly under the soma and traced them throughout the axon during various time spans and for different holding potentials. We found that changes in AP propagation velocity were correlated to the detected AP broadening. Our preliminary data evidenced changes in AP waveforms with increasing distance from the soma along the axon, but further experiments on synaptically coupled neurons using paired recordings will be performed to better understand the influence of AP modulation on ADF. Information encoding in neuronal circuits is probably contingent on both, temporal spike patterns and spike waveforms. In the light of the latter being typically disregarded in computational models, the study of the analog modulation of AP waveforms will contribute to a better understanding of neuronal information processing. Close https://abstractsonline.com/pp8/#!/4649/presentation/9323 Close
	Ronchi, Silvia; Fiscella, Michele; Marchetti, Camilla; Viswam, Vijay; Müller, Jan; Frey, Urs; Hierlemann, Andreas Single-neuron sub-cellular-resolution electrical stimulation with high-density microelectrode arrays Conference Contribution 174.05 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @conference{Ronchi2018, title = {Single-neuron sub-cellular-resolution electrical stimulation with high-density microelectrode arrays}, author = {Silvia Ronchi and Michele Fiscella and Camilla Marchetti and Vijay Viswam and Jan Müller and Urs Frey and Andreas Hierlemann}, url = {https://abstractsonline.com/pp8/#!/4649/presentation/24382}, year = {2018}, date = {2018-11-04}, volume = {Contribution 174.05}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {Non-invasive electrical stimulation is a consolidated technique to study and control neural activity in the brain and peripheral nervous system. It is used, e.g., for controlling Parkinson's disease or to induce sensation in paralyzed patients (Armenta Salas et al., 2018), as well as for attempts to restore vision (Fan et al., 2018; Grosberg et al., 2017) and hearing (Wilson & Dorman, 2008). A common requirement in electrical stimulation is the precise and controlled stimulation of individual targeted neurons. For achieving this purpose, it is necessary that electrodes can stimulate and record extracellular signals at sub-cellular resolution. Furthermore, it is important to design efficient stimulation pulses to be delivered to the neurons. In the present work we used an CMOS-based high-density microelectrode array (HD-MEA) (Ballini et al., 2014), featuring 26’400 bidirectional electrodes with a pitch of 17.5 µm, which was designed for in-vitro applications. This high-resolution was used to test electrical stimulation parameters in vitro, which then could potentially be adapted to elicit single-cell action potentials in vivo. In this work we used different stimulation parameters, such as waveforms, amplitudes and durations (Grosberg et al., 2017; Wagenaar, Pine, & Potter, 2004), using 5x9 µm² electrodes to target sub-cellular structures in single neurons. E-18 Wistar rat cortical neurons were stimulated at days-in-vitro 10, 15, 20 and 25 using randomized voltage and current stimulation modalities. Axon initial segments of individual neurons (Radivojevic et al., 2016) were targeted for stimulation, enabled by the HD-MEA device. We found that voltage biphasic anodic-cathodic waveforms were less efficient than biphasic cathodic-anodic waveforms in eliciting action potentials in a single neuron. Moreover, it was possible to detect action potentials directly at the cell soma, which ensured a reliable confirmation of successful neuron stimulation. Finally, HD-MEA technology enabled to elicit action potentials in single-neurons embedded in high-density cell cultures. The obtained results can be used to optimize in vivo single-cell targeting for stimulation and read-out.}, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {conference} } Close Non-invasive electrical stimulation is a consolidated technique to study and control neural activity in the brain and peripheral nervous system. It is used, e.g., for controlling Parkinson's disease or to induce sensation in paralyzed patients (Armenta Salas et al., 2018), as well as for attempts to restore vision (Fan et al., 2018; Grosberg et al., 2017) and hearing (Wilson & Dorman, 2008). A common requirement in electrical stimulation is the precise and controlled stimulation of individual targeted neurons. For achieving this purpose, it is necessary that electrodes can stimulate and record extracellular signals at sub-cellular resolution. Furthermore, it is important to design efficient stimulation pulses to be delivered to the neurons. In the present work we used an CMOS-based high-density microelectrode array (HD-MEA) (Ballini et al., 2014), featuring 26’400 bidirectional electrodes with a pitch of 17.5 µm, which was designed for in-vitro applications. This high-resolution was used to test electrical stimulation parameters in vitro, which then could potentially be adapted to elicit single-cell action potentials in vivo. In this work we used different stimulation parameters, such as waveforms, amplitudes and durations (Grosberg et al., 2017; Wagenaar, Pine, & Potter, 2004), using 5x9 µm² electrodes to target sub-cellular structures in single neurons. E-18 Wistar rat cortical neurons were stimulated at days-in-vitro 10, 15, 20 and 25 using randomized voltage and current stimulation modalities. Axon initial segments of individual neurons (Radivojevic et al., 2016) were targeted for stimulation, enabled by the HD-MEA device. We found that voltage biphasic anodic-cathodic waveforms were less efficient than biphasic cathodic-anodic waveforms in eliciting action potentials in a single neuron. Moreover, it was possible to detect action potentials directly at the cell soma, which ensured a reliable confirmation of successful neuron stimulation. Finally, HD-MEA technology enabled to elicit action potentials in single-neurons embedded in high-density cell cultures. The obtained results can be used to optimize in vivo single-cell targeting for stimulation and read-out. Close https://abstractsonline.com/pp8/#!/4649/presentation/24382 Close
	Bartram, Julian; Schroter, Manuel; Ronchi, Silvia; Emmenegger, Vishalini; Muller, Jan; Hierlemann, Andreas Mechanisms of homeostatic synaptic plasticity Conference Contribution 037.11 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Bartram2018, title = {Mechanisms of homeostatic synaptic plasticity}, author = {Julian Bartram and Manuel Schroter and Silvia Ronchi and Vishalini Emmenegger and Jan Muller and Andreas Hierlemann}, url = {https://www.abstractsonline.com/pp8/#!/4649/presentation/3968}, year = {2018}, date = {2018-11-03}, volume = {Contribution 037.11}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {Homeostatic plasticity is a crucial set of mechanisms acting at typically slow temporal scales in order to stabilize neuronal spike rates. Despite the functional significance of such processes, revealing the precise induction mechanisms has proven to be difficult, as the roles of postsynaptic spiking and synaptic activity are still debated. For a clearer picture of the induction process to emerge, information about synaptic efficacies of multiple inputs needs to be combined with accurate information about spiking activities of the respective presynaptic cells and the postsynaptic cell during the induction of homeostatic plasticity. In this study, we were able to achieve such measurements by performing combined high-density microelectrode array (HD-MEA) and whole-cell patch-clamp recordings in cultures of primary cortical neurons. Homeostatic plasticity was induced by pharmacological alteration of global network spiking and synaptic transmission with TTX or CNQX. Monosynaptic connections between neurons - here with a focus on excitatory connections between pyramidal cells - were identified by correlating presynaptic spiking activity (HD-MEA recordings) with postsynaptic subthreshold responses (patch current-clamp recordings). Presynaptic spiking was spontaneously observed or could be induced via the stimulation capabilities of the HD-MEA system. This experimental approach enabled us to link changes in synaptic efficacy with the respective pre- and postsynaptic spike patterns, recorded during the induction phase, which sheds new light on the rules and mechanisms of homeostatic synaptic plasticity at excitatory synapses. Financial support through the ERC Advanced Grant 694829 “neuroXscales” is gratefully acknowledged.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close Homeostatic plasticity is a crucial set of mechanisms acting at typically slow temporal scales in order to stabilize neuronal spike rates. Despite the functional significance of such processes, revealing the precise induction mechanisms has proven to be difficult, as the roles of postsynaptic spiking and synaptic activity are still debated. For a clearer picture of the induction process to emerge, information about synaptic efficacies of multiple inputs needs to be combined with accurate information about spiking activities of the respective presynaptic cells and the postsynaptic cell during the induction of homeostatic plasticity. In this study, we were able to achieve such measurements by performing combined high-density microelectrode array (HD-MEA) and whole-cell patch-clamp recordings in cultures of primary cortical neurons. Homeostatic plasticity was induced by pharmacological alteration of global network spiking and synaptic transmission with TTX or CNQX. Monosynaptic connections between neurons - here with a focus on excitatory connections between pyramidal cells - were identified by correlating presynaptic spiking activity (HD-MEA recordings) with postsynaptic subthreshold responses (patch current-clamp recordings). Presynaptic spiking was spontaneously observed or could be induced via the stimulation capabilities of the HD-MEA system. This experimental approach enabled us to link changes in synaptic efficacy with the respective pre- and postsynaptic spike patterns, recorded during the induction phase, which sheds new light on the rules and mechanisms of homeostatic synaptic plasticity at excitatory synapses. Financial support through the ERC Advanced Grant 694829 “neuroXscales” is gratefully acknowledged. Close https://www.abstractsonline.com/pp8/#!/4649/presentation/3968 Close
	Yuan, Xinyue; Emmenegger, Vishalini; Obien, Marie Engelene J; Hierlemann, Andreas; Frey, Urs Dual-Mode Microelectrode Array Featuring 20k Electrodes and High SNR for Extracellular Recording of Neural Networks Conference paper 6065 , IEEE Biomedical Circuits and Systems Conference (BioCAS) Cleveland, Ohio, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @conference{Yuan2018b, title = {Dual-Mode Microelectrode Array Featuring 20k Electrodes and High SNR for Extracellular Recording of Neural Networks}, author = {Xinyue Yuan and Vishalini Emmenegger and Marie Engelene J. Obien and Andreas Hierlemann and Urs Frey}, url = {https://www.epapers.org/biocas2018/ESR/paper_details.php?PHPSESSID=ok076vdjtkiu7kett65d8hk0g0&paper_id=6056}, year = {2018}, date = {2018-10-17}, volume = {paper 6065}, address = {Cleveland, Ohio, USA}, organization = {IEEE Biomedical Circuits and Systems Conference (BioCAS)}, abstract = {In recent electrophysiological studies, CMOS-based high-density microelectrode arrays (HD-MEA) have been widely used for studies of both in-vitro and in-vivo neuronal signals and network behavior. Yet, an open issue in MEA design concerns the tradeoff between signal-to-noise ratio (SNR) and number of readout channels. Here we present a new HD-MEA design in 0.18 μm CMOS technology, consisting of 19,584 electrodes at a pitch of 18.0 μm. By combing two readout structures,namely active-pixel-sensor (APS) and switch-matrix (SM) on a single chip, the dual-mode HD-MEA is capable of recording simultaneously from the entire array and achieving high signal-to-noise-ratio recordings on a subset of electrodes. The APS readout circuits feature a noise level of 10.9 μVrms for the action potential band (300 Hz - 5 kHz), while the noise level for the switch-matrix readout is 3.1 μVrms. }, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {conference} } Close In recent electrophysiological studies, CMOS-based high-density microelectrode arrays (HD-MEA) have been widely used for studies of both in-vitro and in-vivo neuronal signals and network behavior. Yet, an open issue in MEA design concerns the tradeoff between signal-to-noise ratio (SNR) and number of readout channels. Here we present a new HD-MEA design in 0.18 μm CMOS technology, consisting of 19,584 electrodes at a pitch of 18.0 μm. By combing two readout structures,namely active-pixel-sensor (APS) and switch-matrix (SM) on a single chip, the dual-mode HD-MEA is capable of recording simultaneously from the entire array and achieving high signal-to-noise-ratio recordings on a subset of electrodes. The APS readout circuits feature a noise level of 10.9 μVrms for the action potential band (300 Hz - 5 kHz), while the noise level for the switch-matrix readout is 3.1 μVrms. Close https://www.epapers.org/biocas2018/ESR/paper_details.php?PHPSESSID=ok076vdjtkiu7[...] Close
	Lewandowska, Marta K; Bogatikov, Evgenii; Hierlemann, Andreas; Punga, Anna Rostedt Long-Term High-Density Extracellular Recordings Enable Studies of Muscle Cell Physiology Journal Article Frontiers in Physiology, 9 , 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Muscle @article{Lewandowska2018cb, title = {Long-Term High-Density Extracellular Recordings Enable Studies of Muscle Cell Physiology }, author = {Marta K. Lewandowska and Evgenii Bogatikov and Andreas Hierlemann and Anna Rostedt Punga}, url = {https://www.frontiersin.org/article/10.3389/fphys.2018.01424 }, doi = {10.3389/fphys.2018.01424}, year = {2018}, date = {2018-10-09}, journal = {Frontiers in Physiology}, volume = {9}, abstract = {Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high-spatial-resolution measurement techniques and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. Here, we present a method, which allows tracking the development of primary skeletal muscle cells from myoblasts into mature contracting myotubes over more than 2 months. In contrast to most previous studies, the myotubes did not detach from the surface but instead formed functional networks between the myotubes, whose electrical signals were observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myotubes on a chip that contained an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enabled study of skeletal muscle development and kinetics, modes of spiking and spatio-temporal relationships between muscles. The developed system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models. }, keywords = {ETH-CMOS-MEA, Muscle}, pubstate = {published}, tppubtype = {article} } Close Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high-spatial-resolution measurement techniques and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. Here, we present a method, which allows tracking the development of primary skeletal muscle cells from myoblasts into mature contracting myotubes over more than 2 months. In contrast to most previous studies, the myotubes did not detach from the surface but instead formed functional networks between the myotubes, whose electrical signals were observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myotubes on a chip that contained an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enabled study of skeletal muscle development and kinetics, modes of spiking and spatio-temporal relationships between muscles. The developed system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models. Close https://www.frontiersin.org/article/10.3389/fphys.2018.01424 doi:10.3389/fphys.2018.01424 Close
	Diggelmann, Roland; Fiscella, Michele; Hierlemann, Andreas; Franke, Felix Automatic Spike Sorting Algorithm for High-Density Microelectrode Arrays Journal Article Journal of Neurophysiology, 120 (4), 2018. Abstract \| Links \| BibTeX \| Tags: MEA Technology @article{Diggelmann2018, title = {Automatic Spike Sorting Algorithm for High-Density Microelectrode Arrays}, author = {Roland Diggelmann and Michele Fiscella and Andreas Hierlemann and Felix Franke}, url = {https://www.physiology.org/doi/pdf/10.1152/jn.00803.2017}, doi = {10.1152/jn.00803.2017}, year = {2018}, date = {2018-09-12}, journal = {Journal of Neurophysiology}, volume = {120}, number = {4}, abstract = {High-density microelectrode arrays (HD-MEAs) can be used to record extracellular action potentials from hundreds to thousands of neurons simultaneously. Efficient spike-sorters have to be developed to cope with such large data volumes. Most existing spike sorting methods for single electrodes or small multi-electrodes, however, suffer from the "curse of dimensionality", and cannot be directly applied to recordings with hundreds of electrodes. This holds particularly true for the standard reference spike sorting algorithm, principal-component-analysis-based feature extraction, followed by k-means or expectation maximization clustering, against which most spike-sorters are evaluated. We present a spike sorting algorithm that circumvents the dimensionality problem by sorting local groups of electrodes independently using classical spike sorting approaches. It is scalable to any number of recording electrodes and well suited for parallel computing. The combination of data pre-whitening before the principal-component-analysis-based extraction and a parameter-free clustering algorithm obviated the need for parameter adjustments. We evaluated its performance using surrogate data in which we systematically varied spike amplitudes and spike rates and which were generated by inserting template spikes into the voltage traces of real recordings. In a direct comparison, our algorithm could compete with existing state-of-the-art spike sorters in terms of sensitivity and precision, while parameter adjustment or manual cluster curation were not required.}, keywords = {MEA Technology}, pubstate = {published}, tppubtype = {article} } Close High-density microelectrode arrays (HD-MEAs) can be used to record extracellular action potentials from hundreds to thousands of neurons simultaneously. Efficient spike-sorters have to be developed to cope with such large data volumes. Most existing spike sorting methods for single electrodes or small multi-electrodes, however, suffer from the "curse of dimensionality", and cannot be directly applied to recordings with hundreds of electrodes. This holds particularly true for the standard reference spike sorting algorithm, principal-component-analysis-based feature extraction, followed by k-means or expectation maximization clustering, against which most spike-sorters are evaluated. We present a spike sorting algorithm that circumvents the dimensionality problem by sorting local groups of electrodes independently using classical spike sorting approaches. It is scalable to any number of recording electrodes and well suited for parallel computing. The combination of data pre-whitening before the principal-component-analysis-based extraction and a parameter-free clustering algorithm obviated the need for parameter adjustments. We evaluated its performance using surrogate data in which we systematically varied spike amplitudes and spike rates and which were generated by inserting template spikes into the voltage traces of real recordings. In a direct comparison, our algorithm could compete with existing state-of-the-art spike sorters in terms of sensitivity and precision, while parameter adjustment or manual cluster curation were not required. Close https://www.physiology.org/doi/pdf/10.1152/jn.00803.2017 doi:10.1152/jn.00803.2017 Close
	Ronchi, Silvia; Fiscella, Michele; Muller, Jan; Viswam, Vijay; Frey, Urs; Hierlemann, Andreas Single-cell electrical stimulation with CMOS-based high-density microelectrode arrays Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @conference{Ronchi2018b, title = {Single-cell electrical stimulation with CMOS-based high-density microelectrode arrays}, author = {Silvia Ronchi and Michele Fiscella and Jan Muller and Vijay Viswam and Urs Frey and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00086/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00086}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {The main goal of this work was to explore electrical stimulation parameters that reproducibly and precisely elicit action potentials in single neurons (Wagenaar et al. 2004). We compared voltage and current modalities’ and their efficacy in activating single neurons; we also studied the related stimulation artifacts. For our studies, we used a CMOS-based MEA featuring 26400 electrodes at 17.5 µm pitch (Ballini et al. 2014). }, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {conference} } Close The main goal of this work was to explore electrical stimulation parameters that reproducibly and precisely elicit action potentials in single neurons (Wagenaar et al. 2004). We compared voltage and current modalities’ and their efficacy in activating single neurons; we also studied the related stimulation artifacts. For our studies, we used a CMOS-based MEA featuring 26400 electrodes at 17.5 µm pitch (Ballini et al. 2014). Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00086/event_abstract doi:10.3389/conf.fncel.2018.38.00086 Close
	Obien, Marie Engelene J; Zorzi, Giulio; Fiscella, Michele; Leary, Noelle; Hierlemann, Andreas Comparison of axonal-conduction velocity in developing primary cells and human iPSC-derived neurons Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne @conference{Obien2018, title = {Comparison of axonal-conduction velocity in developing primary cells and human iPSC-derived neurons}, author = {Marie Engelene J. Obien and Giulio Zorzi and Michele Fiscella and Noelle Leary and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00095/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00095}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Neurons communicate through action potentials propagating along axons. In developing cell cultures, axonal arbor outgrowth indicates the formation of synaptic connections between neurons, which form networks. As axons regulate the transfer of information, we hypothesize that axonal conduction characteristics, e.g., axonal action potential amplitude and propagation velocity, may be indicative of the maturation state of cells and the strength of interneuronal connections.}, keywords = {ETH-CMOS-MEA, MaxOne}, pubstate = {published}, tppubtype = {conference} } Close Neurons communicate through action potentials propagating along axons. In developing cell cultures, axonal arbor outgrowth indicates the formation of synaptic connections between neurons, which form networks. As axons regulate the transfer of information, we hypothesize that axonal conduction characteristics, e.g., axonal action potential amplitude and propagation velocity, may be indicative of the maturation state of cells and the strength of interneuronal connections. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00095/event_abstract doi:10.3389/conf.fncel.2018.38.00095 Close
	Zorzi, Giulio; Obien, Marie Engelene J; Fiscella, Michele; Leary, Noelle; Hierlemann, Andreas Automatic extraction of axonal arbor morphology applied to h-iPSC-derived neurons Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne @conference{Zorzi2018, title = {Automatic extraction of axonal arbor morphology applied to h-iPSC-derived neurons}, author = {Giulio Zorzi and Marie Engelene J. Obien and Michele Fiscella and Noelle Leary and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00049/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00049}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Neurons derived from human induced pluripotent stem cells (h-iPSCs) offer tremendous opportunities to investigate the mechanisms involved in brain function and to model neurodegenerative diseases. Analyzing the behavior of h-iPSC-derived neurons that represent the phenotypes of human neurological disorders paves the way for the development of physiologically-relevant models and assays for drug discovery. In this framework, we utilize a CMOS-based high-density microelectrode array (HD-MEA, MaxWell Biosystems) to investigate h-iPSC neurons at sub-cellular resolution. Recording extracellular action potentials (EAPs or spikes) of cultured neurons through microelectrode arrays (MEAs) is a well-established technique for extracting valuable features of neuronal function and network connectivity (Obien et al., Frontiers in Neuroscience, 2015). }, keywords = {ETH-CMOS-MEA, MaxOne}, pubstate = {published}, tppubtype = {conference} } Close Neurons derived from human induced pluripotent stem cells (h-iPSCs) offer tremendous opportunities to investigate the mechanisms involved in brain function and to model neurodegenerative diseases. Analyzing the behavior of h-iPSC-derived neurons that represent the phenotypes of human neurological disorders paves the way for the development of physiologically-relevant models and assays for drug discovery. In this framework, we utilize a CMOS-based high-density microelectrode array (HD-MEA, MaxWell Biosystems) to investigate h-iPSC neurons at sub-cellular resolution. Recording extracellular action potentials (EAPs or spikes) of cultured neurons through microelectrode arrays (MEAs) is a well-established technique for extracting valuable features of neuronal function and network connectivity (Obien et al., Frontiers in Neuroscience, 2015). Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00049/event_abstract doi:10.3389/conf.fncel.2018.38.00049 Close
	Bounik, Raziyeh; Gusmaroli, Massimiliano; Viswam, Vijay; Modena, Mario M; Hierlemann, Andreas COMSOL modeling of an integrated impedance sensor in a hanging-drop platform Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Microtissue @conference{Bounik2018, title = {COMSOL modeling of an integrated impedance sensor in a hanging-drop platform}, author = {Raziyeh Bounik and Massimiliano Gusmaroli and Vijay Viswam and Mario M. Modena and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00083/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00083}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Traditional dish-based, two-dimensional cell cultures have limited prediction capability for drug testing, whereas three-dimensional spherical microtissues (spheroids) and organoids much more accurately replicate physiological conditions of cells in the respective tissue [1,2]. Such spheroids can be formed and cultured in microphysiological multi-tissue formats by using the hanging-drop technology as depicted in Fig. 1 [3]. Like most other microfluidic platforms, the hanging-drop platform still requires a microscope for visual inspection and considerable time for doing off-line measurements, as the spheroids/media have to be harvested from the microfluidic device for labeling and chemical analysis. It would be beneficial to have an integrated on-line multi-functional sensor as an additional readout, located directly at the tissue sites in the hanging-drop platform, so that measurements can be performed in situ and without harvesting medium or the tissue and without interrupting the overall culturing process. }, keywords = {ETH-CMOS-MEA, Microtissue}, pubstate = {published}, tppubtype = {conference} } Close Traditional dish-based, two-dimensional cell cultures have limited prediction capability for drug testing, whereas three-dimensional spherical microtissues (spheroids) and organoids much more accurately replicate physiological conditions of cells in the respective tissue [1,2]. Such spheroids can be formed and cultured in microphysiological multi-tissue formats by using the hanging-drop technology as depicted in Fig. 1 [3]. Like most other microfluidic platforms, the hanging-drop platform still requires a microscope for visual inspection and considerable time for doing off-line measurements, as the spheroids/media have to be harvested from the microfluidic device for labeling and chemical analysis. It would be beneficial to have an integrated on-line multi-functional sensor as an additional readout, located directly at the tissue sites in the hanging-drop platform, so that measurements can be performed in situ and without harvesting medium or the tissue and without interrupting the overall culturing process. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00083/event_abstract doi:10.3389/conf.fncel.2018.38.00083 Close
	Yuan, Xinyue; Hierlemann, Andreas; Frey, Urs Dual-mode Microelectrode Array with 20k-electrodes and High SNR for High-Throughput Extracellular Recording and Stimulation Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @conference{Yuan2018, title = {Dual-mode Microelectrode Array with 20k-electrodes and High SNR for High-Throughput Extracellular Recording and Stimulation}, author = {Xinyue Yuan and Andreas Hierlemann and Urs Frey}, url = {https://https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389/conf.fncel.2018.38.00088&eid=5473&sname=MEA_Meeting_2018_%7C_11th_International_Meeting_on_Substrate_Integrated_Microelectrode_Arrays}, doi = {10.3389/conf.fncel.2018.38.00088}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Recording and analysis of neuronal signals can provide much insight into how neurons process information and communicate with each other. Recent advancements of microelectrode-array (MEA) technology provide unprecedented means to study neuronal signals and network behavior in in vitro and in vivo applications [1], [2]. The trade-off between noise performance, power consumption and electrode density, however, remains a major challenge in MEA design. To balance this tradeoff, we designed a Dual-mode (DM) MEA that combines two major types of readout schemes, i.e., the active-pixel-sensor (APS) and switch-matrix (SM) schemes, in order to achieve high electrode density and high signal-to-noise ratio (SNR) at the same time. Based on a previous prototype [3], the new DM-MEA has shown to be a useful tool for in-vitro neuroscience studies, especially for network studies}, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {conference} } Close Recording and analysis of neuronal signals can provide much insight into how neurons process information and communicate with each other. Recent advancements of microelectrode-array (MEA) technology provide unprecedented means to study neuronal signals and network behavior in in vitro and in vivo applications [1], [2]. The trade-off between noise performance, power consumption and electrode density, however, remains a major challenge in MEA design. To balance this tradeoff, we designed a Dual-mode (DM) MEA that combines two major types of readout schemes, i.e., the active-pixel-sensor (APS) and switch-matrix (SM) schemes, in order to achieve high electrode density and high signal-to-noise ratio (SNR) at the same time. Based on a previous prototype [3], the new DM-MEA has shown to be a useful tool for in-vitro neuroscience studies, especially for network studies Close https://https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.33[...] doi:10.3389/conf.fncel.2018.38.00088 Close
	Fiscella, Michele; Leary, Noelle; Ronchi, Silvia; Hierlemann, Andreas Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC @conference{Fiscella2018c, title = {Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays}, author = {Michele Fiscella and Noelle Leary and Silvia Ronchi and Andreas Hierlemann}, url = {https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389/conf.fncel.2018.38.00014&eid=5473&sname=MEA_Meeting_2018_%7C_11th_International_Meeting_on_Substrate_Integrated_Microelectrode_Arrays}, doi = {10.3389/conf.fncel.2018.38.00014}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recording sessions compared to neural cultures without astrocytes. We compared velocities of action potential propagation along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than, for example, in rat primary cortical neurons (Bakkum et. al, Nature Communications, 2013). Furthermore, we found different axonal action-potential-velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-typecell line. Finally, we were able to precisely and reproducibly evoke action potentials in individual single human IPSC-derived neurons through subcellular-resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing.}, keywords = {HD-MEA, IPSC}, pubstate = {published}, tppubtype = {conference} } Close High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recording sessions compared to neural cultures without astrocytes. We compared velocities of action potential propagation along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than, for example, in rat primary cortical neurons (Bakkum et. al, Nature Communications, 2013). Furthermore, we found different axonal action-potential-velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-typecell line. Finally, we were able to precisely and reproducibly evoke action potentials in individual single human IPSC-derived neurons through subcellular-resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing. Close https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389/conf.[...] doi:10.3389/conf.fncel.2018.38.00014 Close
	Urwyler, Cedar; Bounik, Raziyeh; Viswam, Vijay; Hierlemann, Andreas Electrical impedance tomography on high-density microelectrode arrays Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Urwyler2018, title = {Electrical impedance tomography on high-density microelectrode arrays}, author = {Cedar Urwyler and Raziyeh Bounik and Vijay Viswam and Andreas Hierlemann }, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00084/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00084}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Electrical impedance tomography (EIT) is a non-invasive, label-free imaging technique that enables to reconstruct the conductivity distribution in a body from a series of impedance measurements. Impedance measurements can be used to determine the position, morphology, and growth of cells or tissues, as well as pathological signs, e.g., precancerous tissue conditions (Gersing 1999). The newest high-density microelectrode array (MEA) system developed in our group features 59,760 integrated electrodes (Dragas et al. 2017). The chip features a variety of electrophysiological functions: Action-potential recording (2048 channels), cyclic voltammetry (28 channels), local-field-potential recording (32 channels) and extracellular stimulation (16 channels) [Fig 1A]. The chip can also measure impedance through 32 channels, which enables EIT measurements. We were able to establish a proof of concept for EIT (Viswam et al. 2017). The current goal of this project is to develop an impedance measurement protocol and an appropriate reconstruction algorithm that allow for single-cell-resolution impedance imaging.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close Electrical impedance tomography (EIT) is a non-invasive, label-free imaging technique that enables to reconstruct the conductivity distribution in a body from a series of impedance measurements. Impedance measurements can be used to determine the position, morphology, and growth of cells or tissues, as well as pathological signs, e.g., precancerous tissue conditions (Gersing 1999). The newest high-density microelectrode array (MEA) system developed in our group features 59,760 integrated electrodes (Dragas et al. 2017). The chip features a variety of electrophysiological functions: Action-potential recording (2048 channels), cyclic voltammetry (28 channels), local-field-potential recording (32 channels) and extracellular stimulation (16 channels) [Fig 1A]. The chip can also measure impedance through 32 channels, which enables EIT measurements. We were able to establish a proof of concept for EIT (Viswam et al. 2017). The current goal of this project is to develop an impedance measurement protocol and an appropriate reconstruction algorithm that allow for single-cell-resolution impedance imaging. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00084/event_abstract doi:10.3389/conf.fncel.2018.38.00084 Close
	Schroter, Manuel; Girr, Monika; Boos, Julia Alicia; Renner, Magdalena; Gazorpak, Mahshid; Gong, Wei; Bartram, Julian; Muller, Jan; Hierlemann, Andreas Mapping neuronal network dynamics in developing cerebral organoids Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks, Organoids @conference{Schroter2018, title = {Mapping neuronal network dynamics in developing cerebral organoids}, author = {Manuel Schroter and Monika Girr and Julia Alicia Boos and Magdalena Renner and Mahshid Gazorpak and Wei Gong and Julian Bartram and Jan Muller and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00066/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00066}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Cerebral organoids represent an attractive, novel model system to study early brain development in vitro (Di Lullo and Kriegstein, 2017). Although recent evidence shows that cerebral organoids do recapitulate fundamental milestones of early brain morphogenesis (Lancaster and Knoblich, 2014), the emergence and functionality of brain-organoid neuronal connectivity has not been studied systematically yet. In this study, we apply high-density micro-electrode arrays (MEAs) to record from developing mouse cerebral organoids and characterize their spontaneous neuronal activity. Results provide first evidence on the potential of MEAs as a platform to study the role of spontaneous neuronal activity during brain organoid development and formation of functional microcircuits. }, keywords = {Neuronal Networks, Organoids}, pubstate = {published}, tppubtype = {conference} } Close Cerebral organoids represent an attractive, novel model system to study early brain development in vitro (Di Lullo and Kriegstein, 2017). Although recent evidence shows that cerebral organoids do recapitulate fundamental milestones of early brain morphogenesis (Lancaster and Knoblich, 2014), the emergence and functionality of brain-organoid neuronal connectivity has not been studied systematically yet. In this study, we apply high-density micro-electrode arrays (MEAs) to record from developing mouse cerebral organoids and characterize their spontaneous neuronal activity. Results provide first evidence on the potential of MEAs as a platform to study the role of spontaneous neuronal activity during brain organoid development and formation of functional microcircuits. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00066/event_abstract doi:10.3389/conf.fncel.2018.38.00066 Close
	Bartram, Julian; Schroter, Manuel; Ronchi, Silvia; Emmenegger, Vishalini; Muller, Jan; Hierlemann, Andreas Probing synaptic connectivity and function using high-density microelectrode arrays and whole-cell patch-clamp recordings Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Bartram2018b, title = {Probing synaptic connectivity and function using high-density microelectrode arrays and whole-cell patch-clamp recordings}, author = {Julian Bartram and Manuel Schroter and Silvia Ronchi and Vishalini Emmenegger and Jan Muller and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00085/5473/MEA_Meeting_2018_%7C_11th_International_Meeting_on_Substrate_Integrated_Microelectrode_Arrays/all_events/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00085}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Synaptic efficacy and synapse number of monosynaptic connections between neurons are often regulated by the spiking activity of the respective pre- and postsynaptic cell. Progress towards a better understanding of the rules and mechanisms that underlie such modifications has been limited due to the difficulties associated with simultaneously studying plasticity at multiple synaptic inputs. Here, we provide a solution to this problem by combining cutting-edge high-density microelectrode array (HD-MEA) technology with the patch-clamp technique. While the latter allows for accurate measurement of postsynaptic currents or potentials, evoked by individual synaptic activation, the HD-MEA technology provides large-scale information about unit activity and allows for selective stimulation of neurons, including multiple presynaptic cells. The proposed approach has been applied to comprehensively examine forms of homeostatic plasticity – a collection of crucial processes acting at different temporal scales in order to stabilize neuronal firing rates. We report on a characterization of classic synaptic scaling operating in mature cortical networks and propose a novel model for the study of homeostatic plasticity during natural network states. }, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close Synaptic efficacy and synapse number of monosynaptic connections between neurons are often regulated by the spiking activity of the respective pre- and postsynaptic cell. Progress towards a better understanding of the rules and mechanisms that underlie such modifications has been limited due to the difficulties associated with simultaneously studying plasticity at multiple synaptic inputs. Here, we provide a solution to this problem by combining cutting-edge high-density microelectrode array (HD-MEA) technology with the patch-clamp technique. While the latter allows for accurate measurement of postsynaptic currents or potentials, evoked by individual synaptic activation, the HD-MEA technology provides large-scale information about unit activity and allows for selective stimulation of neurons, including multiple presynaptic cells. The proposed approach has been applied to comprehensively examine forms of homeostatic plasticity – a collection of crucial processes acting at different temporal scales in order to stabilize neuronal firing rates. We report on a characterization of classic synaptic scaling operating in mature cortical networks and propose a novel model for the study of homeostatic plasticity during natural network states. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00085/5473/MEA_Meeting_20[...] doi:10.3389/conf.fncel.2018.38.00085 Close
	da Drinnenberg Antonia; Franke, Felix; Morikawa Rei Jüttner; Hillier Daniel; Hantz Peter; Hierlemann Andreas; Azeredo Silveira Rava; Roska Botond K; How diverse retinal functions arise from feedback at the first visual synapse Journal Article Neuron, 99 (1), pp. 117-134, 2018. Abstract \| Links \| BibTeX \| Tags: Retina @article{Drinnenberg2018, title = {How diverse retinal functions arise from feedback at the first visual synapse}, author = {Drinnenberg, Antonia; Franke, Felix; Morikawa, Rei K; Jüttner; Hillier, Daniel; Hantz, Peter; Hierlemann, Andreas; Azeredo da Silveira, Rava; Roska, Botond}, url = {https://www.cell.com/neuron/fulltext/S0896-6273(18)30469-0}, doi = {10.1016/j.neuron.2018.06.001}, year = {2018}, date = {2018-06-21}, journal = {Neuron}, volume = {99}, number = {1}, pages = {117-134}, abstract = {Many brain regions contain local interneurons of distinct types. How does an interneuron type contribute to the input-output transformations of a given brain region? We addressed this question in the mouse retina by chemogenetically perturbing horizontal cells, an interneuron type providing feedback at the first visual synapse, while monitoring the light-driven spiking activity in thousands of ganglion cells, the retinal output neurons. We uncovered six reversible perturbation-induced effects in the response dynamics and response range of ganglion cells. The effects were enhancing or suppressive, occurred in different response epochs, and depended on the ganglion cell type. A computational model of the retinal circuitry reproduced all perturbation-induced effects and led us to assign specific functions to horizontal cells with respect to different ganglion cell types. Our combined experimental and theoretical work reveals how a single interneuron type can differentially shape the dynamical properties of distinct output channels of a brain region.}, keywords = {Retina}, pubstate = {published}, tppubtype = {article} } Close Many brain regions contain local interneurons of distinct types. How does an interneuron type contribute to the input-output transformations of a given brain region? We addressed this question in the mouse retina by chemogenetically perturbing horizontal cells, an interneuron type providing feedback at the first visual synapse, while monitoring the light-driven spiking activity in thousands of ganglion cells, the retinal output neurons. We uncovered six reversible perturbation-induced effects in the response dynamics and response range of ganglion cells. The effects were enhancing or suppressive, occurred in different response epochs, and depended on the ganglion cell type. A computational model of the retinal circuitry reproduced all perturbation-induced effects and led us to assign specific functions to horizontal cells with respect to different ganglion cell types. Our combined experimental and theoretical work reveals how a single interneuron type can differentially shape the dynamical properties of distinct output channels of a brain region. Close https://www.cell.com/neuron/fulltext/S0896-6273(18)30469-0 doi:10.1016/j.neuron.2018.06.001 Close
	Fiscella, Michele; Leary, Noelle; Ronchi, Silvia; Hierlemann, Andreas Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays Conference W-2151 , International Society for Stem Cell Research (ISSCR) Annual Meeting Melbourne, Australia, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC @conference{Fiscella2018b, title = {Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays}, author = {Michele Fiscella and Noelle Leary and Silvia Ronchi and Andreas Hierlemann }, url = {http://www.isscr.org/docs/default-source/2018-melbourne-ann-mtng/66670-isscr-abstracts_with-links.pdf?sfvrsn=4&utm_source=ISSCR-Informz&utm_medium=email&utm_campaign=default}, year = {2018}, date = {2018-06-20}, volume = {W-2151}, address = {Melbourne, Australia}, organization = {International Society for Stem Cell Research (ISSCR) Annual Meeting}, abstract = {High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co- cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons. Furthermore, we found different axonal action potential velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular- resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing.}, keywords = {HD-MEA, IPSC}, pubstate = {published}, tppubtype = {conference} } Close High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co- cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons. Furthermore, we found different axonal action potential velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular- resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing. Close http://www.isscr.org/docs/default-source/2018-melbourne-ann-mtng/66670-isscr-abs[...] Close
	Bakkum Douglas J; Radivojevic, Milos; Obien Marie Engelene; Jaeckel David; Frey Urs; Takahashi Hirokazu; Hierlemann Andreas The axon initial segment drives the neuron's extracellular action potential Journal Article bioRxiv, pp. 1-30, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Bakkum2018, title = {The axon initial segment drives the neuron's extracellular action potential}, author = {Bakkum, Douglas J; Radivojevic, Milos; Obien, Marie Engelene; Jaeckel, David; Frey, Urs; Takahashi, Hirokazu; Hierlemann, Andreas }, url = {https://www.biorxiv.org/content/early/2018/02/16/266734}, doi = {10.1101/266734 }, year = {2018}, date = {2018-02-16}, journal = {bioRxiv}, pages = {1-30}, abstract = {Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology. Close https://www.biorxiv.org/content/early/2018/02/16/266734 doi:10.1101/266734 Close
2017
	Viswam, Vijay; Obien, Marie Engelene J; Frey, Urs; Franke, Felix; Hierlemann, Andreas Acquisition of Bioelectrical Signals with Small Electrodes Conference 2017 IEEE Biomedical Circuits and Systems Conference (BioCAS) Turin, Italy, 2017. Abstract \| Links \| BibTeX \| Tags: Electrodes @conference{Viswam2017, title = {Acquisition of Bioelectrical Signals with Small Electrodes}, author = {Vijay Viswam and Marie Engelene J. Obien and Urs Frey and Felix Franke and Andreas Hierlemann}, url = {https://ieeexplore.ieee.org/document/8325216}, doi = {10.1109/BIOCAS.2017.8325216}, year = {2017}, date = {2017-10-19}, address = {Turin, Italy}, organization = {2017 IEEE Biomedical Circuits and Systems Conference (BioCAS)}, abstract = {Although the mechanisms of recording bioelectrical signals from different types of electrogenic cells (neurons, cardiac cells etc.) by means of planar metal electrodes have been extensively studied, the recording characteristics and conditions for very small electrode sizes are not yet established. Here, we present a combined experimental and computational approach to elucidate, how the electrode size influences the recorded signals, and how inherent properties of the electrode, such as impedance, noise, and transmission characteristics shape the signal. We demonstrate that good quality recordings can be achieved with electrode diameters of less than 10 μm, provided that impedance reduction measures have been implemented and provided that a set of requirements for signal amplification has been met.}, keywords = {Electrodes}, pubstate = {published}, tppubtype = {conference} } Close Although the mechanisms of recording bioelectrical signals from different types of electrogenic cells (neurons, cardiac cells etc.) by means of planar metal electrodes have been extensively studied, the recording characteristics and conditions for very small electrode sizes are not yet established. Here, we present a combined experimental and computational approach to elucidate, how the electrode size influences the recorded signals, and how inherent properties of the electrode, such as impedance, noise, and transmission characteristics shape the signal. We demonstrate that good quality recordings can be achieved with electrode diameters of less than 10 μm, provided that impedance reduction measures have been implemented and provided that a set of requirements for signal amplification has been met. Close https://ieeexplore.ieee.org/document/8325216 doi:10.1109/BIOCAS.2017.8325216 Close
	Radivojevic, Milos; Franke, Felix; Altermatt, Michael; Müller, Jan; Hierlemann, Andreas; Bakkum, Douglas J Tracking individual action potentials throughout mammalian axonal arbors Journal Article eLife, 6 , pp. 1-23, 2017, ISSN: 2050-084X. Abstract \| Links \| BibTeX \| Tags: Data Analysis, ETH-CMOS-MEA, Neuronal Networks, Stimulation @article{Radivojevic2017, title = {Tracking individual action potentials throughout mammalian axonal arbors}, author = {Milos Radivojevic and Felix Franke and Michael Altermatt and Jan Müller and Andreas Hierlemann and Douglas J Bakkum}, url = {https://elifesciences.org/articles/30198}, doi = {10.7554/eLife.30198}, issn = {2050-084X}, year = {2017}, date = {2017-10-09}, journal = {eLife}, volume = {6}, pages = {1-23}, abstract = {Axons are neuronal processes specialized for conduction of action potentials (APs). The timing and temporal precision of APs when they reach each of the synapses are fundamentally important for information processing in the brain. Due to small diameters of axons, direct recording of single AP transmission is challenging. Consequently, most knowledge about axonal conductance derives from modeling studies or indirect measurements. We demonstrate a method to noninvasively and directly record individual APs propagating along millimeter-length axonal arbors in cortical cultures with hundreds of microelectrodes at microsecond temporal resolution. We find that cortical axons conduct single APs with high temporal precision (~100 µs arrival time jitter per mm length) and reliability: in more than 8,000,000 recorded APs, we did not observe any conduction or branch-point failures. Upon high-frequency stimulation at 100 Hz, successive became slower, and their arrival time precision decreased by 20% and 12% for the 100th AP, respectively.}, keywords = {Data Analysis, ETH-CMOS-MEA, Neuronal Networks, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Axons are neuronal processes specialized for conduction of action potentials (APs). The timing and temporal precision of APs when they reach each of the synapses are fundamentally important for information processing in the brain. Due to small diameters of axons, direct recording of single AP transmission is challenging. Consequently, most knowledge about axonal conductance derives from modeling studies or indirect measurements. We demonstrate a method to noninvasively and directly record individual APs propagating along millimeter-length axonal arbors in cortical cultures with hundreds of microelectrodes at microsecond temporal resolution. We find that cortical axons conduct single APs with high temporal precision (~100 µs arrival time jitter per mm length) and reliability: in more than 8,000,000 recorded APs, we did not observe any conduction or branch-point failures. Upon high-frequency stimulation at 100 Hz, successive became slower, and their arrival time precision decreased by 20% and 12% for the 100th AP, respectively. Close https://elifesciences.org/articles/30198 doi:10.7554/eLife.30198 Close
	Tajima Satohiro; Mita, Takeshi; Bakkum Douglas Takahashi Hirokazu; Toyoizumi Taro J; Locally embedded presages of global network bursts Journal Article National Academy of Sciences, pp. 1-6, 2017, ISSN: 0027-8424. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks @article{Tajima2017, title = {Locally embedded presages of global network bursts}, author = {Tajima, Satohiro; Mita, Takeshi; Bakkum, Douglas J; Takahashi, Hirokazu; Toyoizumi, Taro}, editor = {Sejnowski, Terrence J}, url = {http://www.pnas.org/content/114/36/9517}, doi = {10.1073/pnas.1705981114 }, issn = {0027-8424}, year = {2017}, date = {2017-08-18}, journal = {National Academy of Sciences}, pages = {1-6}, abstract = {Spontaneous, synchronous bursting of neural population is a widely observed phenomenon in nervous networks, which is considered important for functions and dysfunctions of the brain. However, how the global synchrony across a large number of neurons emerges from an initially nonbursting network state is not fully understood. In this study, we develop a state-space reconstruction method combined with high-resolution recordings of cultured neurons. This method extracts deterministic signatures of upcoming global bursts in “local” dynamics of individual neurons during nonbursting periods. We find that local information within a single-cell time series can compare with or even outperform the global mean-field activity for predicting future global bursts. Moreover, the intercell variability in the burst predictability is found to reflect the network structure realized in the nonbursting periods. These findings suggest that deterministic local dynamics can predict seemingly stochastic global events in self-organized networks, implying the potential applications of the present methodology to detecting locally concentrated early warnings of spontaneous seizure occurrence in the brain.}, keywords = {Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Spontaneous, synchronous bursting of neural population is a widely observed phenomenon in nervous networks, which is considered important for functions and dysfunctions of the brain. However, how the global synchrony across a large number of neurons emerges from an initially nonbursting network state is not fully understood. In this study, we develop a state-space reconstruction method combined with high-resolution recordings of cultured neurons. This method extracts deterministic signatures of upcoming global bursts in “local” dynamics of individual neurons during nonbursting periods. We find that local information within a single-cell time series can compare with or even outperform the global mean-field activity for predicting future global bursts. Moreover, the intercell variability in the burst predictability is found to reflect the network structure realized in the nonbursting periods. These findings suggest that deterministic local dynamics can predict seemingly stochastic global events in self-organized networks, implying the potential applications of the present methodology to detecting locally concentrated early warnings of spontaneous seizure occurrence in the brain. Close http://www.pnas.org/content/114/36/9517 doi:10.1073/pnas.1705981114 Close
	Shein-Idelson, Mark; Pammer, Lorenz; Hemberger, Mike; Laurent, Gilles Large-scale mapping of cortical synaptic projections with extracellular electrode arrays Journal Article Nature Methods, 14 (9), pp. 882–889, 2017, ISSN: 1548-7091. Abstract \| Links \| BibTeX \| Tags: Brain Slice, MaxOne, Neuronal Networks @article{Shein-Idelson2017, title = {Large-scale mapping of cortical synaptic projections with extracellular electrode arrays}, author = {Mark Shein-Idelson and Lorenz Pammer and Mike Hemberger and Gilles Laurent}, url = {http://www.nature.com/doifinder/10.1038/nmeth.4393}, doi = {10.1038/nmeth.4393}, issn = {1548-7091}, year = {2017}, date = {2017-08-14}, journal = {Nature Methods}, volume = {14}, number = {9}, pages = {882--889}, abstract = {Understanding circuit computation in the nervous system requires sampling activity over large neural populations and maximizing the number of features that can be extracted. By combining planar arrays of extracellular electrodes with the three-layered cortex of turtles, we show that synaptic signals induced along individual axons as well as action potentials can be easily captured. Two types of information can be extracted from these signals, the neuronal subtype (inhibitory or excitatory)—whose identification is more reliable than with traditional measures such as action potential width—and a (partial) spatial map of functional axonal projections from individual neurons. Because our approach is algorithmic, it can be carried out in parallel on hundreds of simultaneously recorded neurons. Combining our approach with soma triangulation, we reveal an axonal projection bias among a population of pyramidal neurons in turtle cortex and confirm this bias through anatomical reconstructions.}, keywords = {Brain Slice, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Understanding circuit computation in the nervous system requires sampling activity over large neural populations and maximizing the number of features that can be extracted. By combining planar arrays of extracellular electrodes with the three-layered cortex of turtles, we show that synaptic signals induced along individual axons as well as action potentials can be easily captured. Two types of information can be extracted from these signals, the neuronal subtype (inhibitory or excitatory)—whose identification is more reliable than with traditional measures such as action potential width—and a (partial) spatial map of functional axonal projections from individual neurons. Because our approach is algorithmic, it can be carried out in parallel on hundreds of simultaneously recorded neurons. Combining our approach with soma triangulation, we reveal an axonal projection bias among a population of pyramidal neurons in turtle cortex and confirm this bias through anatomical reconstructions. Close http://www.nature.com/doifinder/10.1038/nmeth.4393 doi:10.1038/nmeth.4393 Close
	Obien, Marie Engelene J; Zorzi, Giulio; Hierlemann, Andreas Mapping neuron cluster development based on axonal action potential propagation Conference The 40th Annual Meeting of the Japan Neuroscience Society Chiba, Japan, 2017. BibTeX \| Tags: Action Potential, Neuronal Networks @conference{Obien2017, title = {Mapping neuron cluster development based on axonal action potential propagation}, author = {Marie Engelene J. Obien and Giulio Zorzi and Andreas Hierlemann}, year = {2017}, date = {2017-07-20}, address = {Chiba, Japan}, organization = {The 40th Annual Meeting of the Japan Neuroscience Society}, keywords = {Action Potential, Neuronal Networks}, pubstate = {published}, tppubtype = {conference} } Close
	Diggelmann, Roland; Fiscella, Michele; Hierlemann, Andreas; Franke, Felix Pre-whitening as a means to improve dimensionality reduction and simplify clustering in spike-sorters for multi-electrode recordings Conference 26th Annual Computational Neuroscience Meeting (CNS2017) Antwerp, Belgium , 2017. Abstract \| Links \| BibTeX \| Tags: Spike Sorting @conference{Diggelmann2017, title = {Pre-whitening as a means to improve dimensionality reduction and simplify clustering in spike-sorters for multi-electrode recordings}, author = {Roland Diggelmann and Michele Fiscella and Andreas Hierlemann and Felix Franke}, url = {https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0371-2}, year = {2017}, date = {2017-07-15}, address = {Antwerp, Belgium }, organization = {26th Annual Computational Neuroscience Meeting (CNS2017)}, abstract = {Spike sorting is the process to extract single neuronal activity from extracellular recordings. It makes use of the fact that spikes from a single neuron feature highly similar waveforms, whereas spikes from different neurons have different waveforms. Clustering algorithms are used to find groups of similar spikes that putatively originated from the same neuron. However, since spike waveforms especially in multi-electrode recordings can have a high dimensionality, their dimensionality needs to be reduced before clustering. Principal component analysis (PCA) is one of the most commonly employed dimensionality reduction methods for this purpose [1]. It reduces the dimensions to those where the variance of the data was highest, presumably those along which the waveforms of separate neurons differ most strongly, However, if the noise is not uniform in all dimensions, high variability can also mean high noise, which would render a dimension useless for discrimination. We, therefore, propose an additional pre-whitening step before PCA and discuss two beneficial effects on the subsequent clustering. We illustrate these effects by using spikes from retinal ganglion cells recorded with high-density multi-electrode arrays (HD-MEA).}, keywords = {Spike Sorting}, pubstate = {published}, tppubtype = {conference} } Close Spike sorting is the process to extract single neuronal activity from extracellular recordings. It makes use of the fact that spikes from a single neuron feature highly similar waveforms, whereas spikes from different neurons have different waveforms. Clustering algorithms are used to find groups of similar spikes that putatively originated from the same neuron. However, since spike waveforms especially in multi-electrode recordings can have a high dimensionality, their dimensionality needs to be reduced before clustering. Principal component analysis (PCA) is one of the most commonly employed dimensionality reduction methods for this purpose [1]. It reduces the dimensions to those where the variance of the data was highest, presumably those along which the waveforms of separate neurons differ most strongly, However, if the noise is not uniform in all dimensions, high variability can also mean high noise, which would render a dimension useless for discrimination. We, therefore, propose an additional pre-whitening step before PCA and discuss two beneficial effects on the subsequent clustering. We illustrate these effects by using spikes from retinal ganglion cells recorded with high-density multi-electrode arrays (HD-MEA). Close https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0371-2 Close
	Viswam, Vijay; Bounik, Raziyeh; Shadmani, Amir; Dragas, Jelena; Obien, Marie Engelene J; Muller, Jan; Chen, Yihui; Hierlemann, Andreas High-density Mapping of Brain Slices Using a Large Multi-functional High-density CMOS Microelectrode Array System Conference 19th International Conference on Solid-State Sensors, Actuators and Microsystems (TRANSDUCERS) Kaohsiung, Taiwan, 2017, ISSN: 2167-0021. Abstract \| Links \| BibTeX \| Tags: Brain Slice, ETH-CMOS-MEA, HD-MEA @conference{Viswam2017b, title = {High-density Mapping of Brain Slices Using a Large Multi-functional High-density CMOS Microelectrode Array System}, author = {Vijay Viswam and Raziyeh Bounik and Amir Shadmani and Jelena Dragas and Marie Engelene J. Obien and Jan Muller and Yihui Chen and Andreas Hierlemann }, url = {https://ieeexplore.ieee.org/abstract/document/7994006}, doi = {10.1109/TRANSDUCERS.2017.7994006}, issn = {2167-0021}, year = {2017}, date = {2017-06-18}, pages = {135-138}, address = {Kaohsiung, Taiwan}, organization = {19th International Conference on Solid-State Sensors, Actuators and Microsystems (TRANSDUCERS)}, abstract = {We present a CMOS-based high-density microelectrode array (HD-MEA) system that enables high-density mapping of brain slices in-vitro with multiple readout modalities. The 4.48×2.43 mm 2 array consists of 59,760 micro-electrodes at 13.5 μm pitch (5487 electrodes/mm 2 ). The overall system features 2048 action-potential, 32 local-field-potential and 32 current recording channels, 32 impedance-measurement and 28 neurotransmitter-detection channels and 16 voltage/current stimulation channels. The system enables real-time and label-free monitoring of position, size, morphology and electrical activity of brain slices.}, keywords = {Brain Slice, ETH-CMOS-MEA, HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close We present a CMOS-based high-density microelectrode array (HD-MEA) system that enables high-density mapping of brain slices in-vitro with multiple readout modalities. The 4.48×2.43 mm 2 array consists of 59,760 micro-electrodes at 13.5 μm pitch (5487 electrodes/mm 2 ). The overall system features 2048 action-potential, 32 local-field-potential and 32 current recording channels, 32 impedance-measurement and 28 neurotransmitter-detection channels and 16 voltage/current stimulation channels. The system enables real-time and label-free monitoring of position, size, morphology and electrical activity of brain slices. Close https://ieeexplore.ieee.org/abstract/document/7994006 doi:10.1109/TRANSDUCERS.2017.7994006 Close
	Frey, Urs; Obien, Marie Engelene J; Muller, Jan; Hierlemann, Andreas Technology Trends and Commercialization of High-density Microelectrode Arrays for Advanced In-vitro Electrophysiology Conference IEEE International Symposium on Circuits and Systems (ISCAS Baltimore, MD, USA, 2017, ISSN: 2379-447X. Abstract \| Links \| BibTeX \| Tags: HD-MEA, In-Vitro @conference{Frey2017, title = {Technology Trends and Commercialization of High-density Microelectrode Arrays for Advanced In-vitro Electrophysiology}, author = {Urs Frey and Marie Engelene J. Obien and Jan Muller and Andreas Hierlemann}, url = {https://ieeexplore.ieee.org/document/8050215/}, doi = {10.1109/ISCAS.2017.8050215}, issn = {2379-447X}, year = {2017}, date = {2017-05-28}, address = {Baltimore, MD, USA}, organization = {IEEE International Symposium on Circuits and Systems (ISCAS}, abstract = {Microelectrode arrays (MEAs) enable fast and high-throughput readout of cell's electrical signals. MEAs are currently used for phenotype characterization and drug toxicity/efficacy testing with iPSC-derived neurons and cardiomyocytes. A key advantage of MEAs is the capability to record and stimulate individual neurons at multiple sites simultaneously. We will present ongoing advancements of MEA technology, with a focus on achieving higher quality recordings by means of monolithic co-integration of circuitry on chip by using CMOS technology [1]. Such high-density MEAs with more than 3000 electrodes per mm2 are a suitable tool for capturing neuronal activity across various scales, including axons, somas, dendrites, entire neurons, and networks.}, keywords = {HD-MEA, In-Vitro}, pubstate = {published}, tppubtype = {conference} } Close Microelectrode arrays (MEAs) enable fast and high-throughput readout of cell's electrical signals. MEAs are currently used for phenotype characterization and drug toxicity/efficacy testing with iPSC-derived neurons and cardiomyocytes. A key advantage of MEAs is the capability to record and stimulate individual neurons at multiple sites simultaneously. We will present ongoing advancements of MEA technology, with a focus on achieving higher quality recordings by means of monolithic co-integration of circuitry on chip by using CMOS technology [1]. Such high-density MEAs with more than 3000 electrodes per mm2 are a suitable tool for capturing neuronal activity across various scales, including axons, somas, dendrites, entire neurons, and networks. Close https://ieeexplore.ieee.org/document/8050215/ doi:10.1109/ISCAS.2017.8050215 Close
	Hillier, Daniel; Fiscella, Michele; Drinnenberg, Antonia; Trenholm, Stuart; Rompani, Santiago B; Raics, Zoltan; Katona, Gergely; Jüttner, Josephine; Hierlemann, Andreas; Rozsa, Balazs; Roska, Botond Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex Journal Article Nature Neuroscience, 20 (7), pp. 960–968, 2017, ISSN: 1097-6256. Abstract \| Links \| BibTeX \| Tags: MaxOne, Retina @article{Hillier2017, title = {Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex}, author = {Daniel Hillier and Michele Fiscella and Antonia Drinnenberg and Stuart Trenholm and Santiago B Rompani and Zoltan Raics and Gergely Katona and Josephine Jüttner and Andreas Hierlemann and Balazs Rozsa and Botond Roska}, url = {http://www.nature.com/doifinder/10.1038/nn.4566}, doi = {10.1038/nn.4566}, issn = {1097-6256}, year = {2017}, date = {2017-05-22}, journal = {Nature Neuroscience}, volume = {20}, number = {7}, pages = {960--968}, abstract = {How neuronal computations in the sensory periphery contribute to computations in the cortex is not well understood. We examined this question in the context of visual-motion processing in the retina and primary visual cortex (V1) of mice. We disrupted retinal direction selectivity, either exclusively along the horizontal axis using FRMD7 mutants or along all directions by ablating starburst amacrine cells, and monitored neuronal activity in layer 2/3 of V1 during stimulation with visual motion. In control mice, we found an over-representation of cortical cells preferring posterior visual motion, the dominant motion direction an animal experiences when it moves forward. In mice with disrupted retinal direction selectivity, the over-representation of posterior-motion-preferring cortical cells disappeared, and their responses at higher stimulus speeds were reduced. This work reveals the existence of two functionally distinct, sensory-periphery-dependent and -independent computations of visual motion in the cortex.}, keywords = {MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close How neuronal computations in the sensory periphery contribute to computations in the cortex is not well understood. We examined this question in the context of visual-motion processing in the retina and primary visual cortex (V1) of mice. We disrupted retinal direction selectivity, either exclusively along the horizontal axis using FRMD7 mutants or along all directions by ablating starburst amacrine cells, and monitored neuronal activity in layer 2/3 of V1 during stimulation with visual motion. In control mice, we found an over-representation of cortical cells preferring posterior visual motion, the dominant motion direction an animal experiences when it moves forward. In mice with disrupted retinal direction selectivity, the over-representation of posterior-motion-preferring cortical cells disappeared, and their responses at higher stimulus speeds were reduced. This work reveals the existence of two functionally distinct, sensory-periphery-dependent and -independent computations of visual motion in the cortex. Close http://www.nature.com/doifinder/10.1038/nn.4566 doi:10.1038/nn.4566 Close
	Bullmann Torsten; Radivojevic, Milos; Huber Stefan Deligkaris Kosmas; Hierlemann Andreas; Frey Urs T: Network Analysis Of High-Density Microelectrode Recordings Journal Article bioRxiv , (139436), pp. 1-23, 2017. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Bullmann2017, title = {Network Analysis Of High-Density Microelectrode Recordings}, author = {Bullmann, Torsten; Radivojevic, Milos; Huber, Stefan T: Deligkaris, Kosmas; Hierlemann, Andreas; Frey, Urs }, url = {https://www.biorxiv.org/content/early/2017/05/18/139436 }, doi = {10.1101/139436}, year = {2017}, date = {2017-05-18}, journal = {bioRxiv }, number = {139436}, pages = {1-23}, abstract = {Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology. Close https://www.biorxiv.org/content/early/2017/05/18/139436 doi:10.1101/139436 Close
	Dragas, Jelena; Viswam, Vijay; Shadmani, Amir; Chen, Yihui; Bounik, Raziyeh; Stettler, Alexander; Radivojevic, Milos; Geissler, Sydney; Obien, Marie Engelene J; Müller, Jan; Hierlemann, Andreas A Multi-Functional Microelectrode Array Featuring 59760 Electrodes, 2048 Electrophysiology Channels, Stimulation, Impedance Measurement and Neurotransmitter Detection Channels Journal Article IEEE journal of solid-state circuits, 52 (6), pp. 1576-1590, 2017, ISSN: 0018-9200. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MEA Technology @article{Dragas2017, title = {A Multi-Functional Microelectrode Array Featuring 59760 Electrodes, 2048 Electrophysiology Channels, Stimulation, Impedance Measurement and Neurotransmitter Detection Channels}, author = {Jelena Dragas and Vijay Viswam and Amir Shadmani and Yihui Chen and Raziyeh Bounik and Alexander Stettler and Milos Radivojevic and Sydney Geissler and Marie Engelene J Obien and Jan Müller and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/7913669/}, doi = {10.1109/JSSC.2017.2686580}, issn = {0018-9200}, year = {2017}, date = {2017-04-27}, journal = {IEEE journal of solid-state circuits}, volume = {52}, number = {6}, pages = {1576-1590}, abstract = {Biological cells are characterized by highly complex phenomena and processes that are, to a great extent, interdependent. To gain detailed insights, devices designed to study cellular phenomena need to enable tracking and manipulation of multiple cell parameters in parallel; they have to provide high signal quality and high spatiotemporal resolution. To this end, we have developed a CMOS-based microelectrode array system that integrates six measurement and stimulation functions, the largest number to date. Moreover, the system features the largest active electrode array area to date (4.48×2.43 mm(2)) to accommodate 59,760 electrodes, while its power consumption, noise characteristics, and spatial resolution (13.5 mum electrode pitch) are comparable to the best state-of-the-art devices. The system includes: 2,048 action-potential (AP, bandwidth: 300 Hz to 10 kHz) recording units, 32 local-field-potential (LFP, bandwidth: 1 Hz to 300 Hz) recording units, 32 current recording units, 32 impedance measurement units, and 28 neurotransmitter detection units, in addition to the 16 dual-mode voltage-only or current/voltage-controlled stimulation units. The electrode array architecture is based on a switch matrix, which allows for connecting any measurement/stimulation unit to any electrode in the array and for performing different measurement/stimulation functions in parallel.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Biological cells are characterized by highly complex phenomena and processes that are, to a great extent, interdependent. To gain detailed insights, devices designed to study cellular phenomena need to enable tracking and manipulation of multiple cell parameters in parallel; they have to provide high signal quality and high spatiotemporal resolution. To this end, we have developed a CMOS-based microelectrode array system that integrates six measurement and stimulation functions, the largest number to date. Moreover, the system features the largest active electrode array area to date (4.48×2.43 mm(2)) to accommodate 59,760 electrodes, while its power consumption, noise characteristics, and spatial resolution (13.5 mum electrode pitch) are comparable to the best state-of-the-art devices. The system includes: 2,048 action-potential (AP, bandwidth: 300 Hz to 10 kHz) recording units, 32 local-field-potential (LFP, bandwidth: 1 Hz to 300 Hz) recording units, 32 current recording units, 32 impedance measurement units, and 28 neurotransmitter detection units, in addition to the 16 dual-mode voltage-only or current/voltage-controlled stimulation units. The electrode array architecture is based on a switch matrix, which allows for connecting any measurement/stimulation unit to any electrode in the array and for performing different measurement/stimulation functions in parallel. Close http://ieeexplore.ieee.org/document/7913669/ doi:10.1109/JSSC.2017.2686580 Close

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2020
	Bandarabadi, Mojtaba; Vassalli, Anne; Tafti, Mehdi Sleep as a default state of cortical and subcortical networks Journal Article Current Opinion in Physiology, 15 , pp. 60-67, 2020. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks, Review, Sleep @article{Bandarabadi2020, title = {Sleep as a default state of cortical and subcortical networks}, author = {Mojtaba Bandarabadi and Anne Vassalli and Mehdi Tafti}, url = {https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub}, doi = {10.1016/j.cophys.2019.12.004}, year = {2020}, date = {2020-06-20}, journal = {Current Opinion in Physiology}, volume = {15}, pages = {60-67}, abstract = {Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field.}, keywords = {Neuronal Networks, Review, Sleep}, pubstate = {published}, tppubtype = {article} } Close Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field. Close https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub doi:10.1016/j.cophys.2019.12.004 Close
	Masumori, Atsushi; Sinapayen, Lana; Maruyama, Norihiro; Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Takahashi, Hirokazu; Ikegami, Takashi Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks Journal Article Artificial Life, 26 (1), pp. 130-151, 2020, ISSN: 1064-5462. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks @article{Masumori2020, title = {Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks}, author = {Atsushi Masumori and Lana Sinapayen and Norihiro Maruyama and Takeshi Mita and Douglas J. Bakkum and Urs Frey and Hirokazu Takahashi and Takashi Ikegami}, url = {https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314}, doi = {10.1162/artl_a_00314}, issn = {1064-5462}, year = {2020}, date = {2020-04-28}, journal = {Artificial Life}, volume = {26}, number = {1}, pages = {130-151}, abstract = {Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance.}, keywords = {Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance. Close https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314 doi:10.1162/artl_a_00314 Close
	Idrees, Saad; Baumann, Matthias P; Franke, Felix; Münch, Thomas A; Hafed, Ziad M Perceptual saccadic suppression starts in the retina Journal Article Nature Communications, 11 (1977), 2020. Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne, Retina @article{Idrees2020, title = {Perceptual saccadic suppression starts in the retina}, author = {Saad Idrees and Matthias P. Baumann and Felix Franke and Thomas A. Münch and Ziad M. Hafed}, url = {https://www.nature.com/articles/s41467-020-15890-w}, doi = {10.1038/s41467-020-15890-w}, year = {2020}, date = {2020-04-24}, journal = {Nature Communications}, volume = {11}, number = {1977}, keywords = {ETH-CMOS-MEA, MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close https://www.nature.com/articles/s41467-020-15890-w doi:10.1038/s41467-020-15890-w Close
	Obaid, Abdulmalik; Hanna, Mina-Elrahb; Wu, Yu-Wei; Kollo, Mihaly; Racz, Romeo; Angle, Matthew R; Muller, Jan; Brackbill, Nora; Wray, William; Franke, Felix; Chichilnski, E J; Hierlemann, Andreas; Ding, Jun B; Schaefer, Andreas T; Melosh, Nicholas A Massively parallel microwire arrays integrated withCMOS chips for neural recording Journal Article Science Advances, 2020. Abstract \| Links \| BibTeX \| Tags: Electrodes, ETH-CMOS-MEA @article{Obaid2020, title = {Massively parallel microwire arrays integrated withCMOS chips for neural recording}, author = {Abdulmalik Obaid and Mina-Elrahb Hanna and Yu-Wei Wu and Mihaly Kollo and Romeo Racz and Matthew R Angle and Jan Muller and Nora Brackbill and William Wray and Felix Franke and E J Chichilnski and Andreas Hierlemann and Jun B. Ding and Andreas T. Schaefer and Nicholas A. Melosh}, url = {https://advances.sciencemag.org/content/6/12/eaay2789}, doi = {10.1126/sciadv.aay2789}, year = {2020}, date = {2020-03-20}, journal = {Science Advances}, abstract = {Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface.}, keywords = {Electrodes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface. Close https://advances.sciencemag.org/content/6/12/eaay2789 doi:10.1126/sciadv.aay2789 Close
	Kajiwara, Motoki; Nomura, Ritsuki; Goetze, Felix; Akutsu, Tatsuya; Shimono, Masanori Inhibitory neurons are a Central Controlling regulator in the effective cortical microconnectome Journal Article bioRxiv , 2020. Abstract \| Links \| BibTeX \| Tags: Inhibitory Neurons @article{Kajiwara2020, title = {Inhibitory neurons are a Central Controlling regulator in the effective cortical microconnectome}, author = {Motoki Kajiwara and Ritsuki Nomura and Felix Goetze and Tatsuya Akutsu and Masanori Shimono}, url = {https://www.biorxiv.org/content/10.1101/2020.02.18.954016v1}, doi = {10.1101/2020.02.18.954016}, year = {2020}, date = {2020-02-18}, journal = {bioRxiv }, abstract = {The brain is a network system in which excitatory and inhibitory neurons keep the activity balanced in the highly non-uniform connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neurons. So, in general, how the inhibitory neurons can keep the balance with the surrounding excitatory neurons is an important question. We observed effective networks, reflecting causal interactions, of ~1000 neurons in cortical acute slices. Surprisingly, we found that inhibitory neurons are not only located at more central positions than excitatory neurons but also have stronger controlling ability of other neurons than excitatory neurons. Besides, we found that the precedence in centrality and controlling ability of inhibitory neurons are well observed in deep cortical layers by comparing with distribution of neurons coloured by NeuN immunostaining data. Preceding the observation, we also found that inhibitory neurons show higher firing rate than excitatory neurons, and that their firing rate also closely obey a log-normal distribution as previously known about excitatory neurons. Additionally, their connectivity strengths also obeyed a log-normal distribution. In summary, within the network interaction of huge numbers of neurons, inhibitory neurons seem to produce a central controlling system that sustains the homeostatic behavior of the brain. A similar evaluation in different life stages and in disease states etc. will not only provide deeper understandings in the homeostasis of the brain, but also will provide a selective and effective way to stimulate individual neurons to modulate neuropsychiatry or neurodegeneration disease states.}, keywords = {Inhibitory Neurons}, pubstate = {published}, tppubtype = {article} } Close The brain is a network system in which excitatory and inhibitory neurons keep the activity balanced in the highly non-uniform connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neurons. So, in general, how the inhibitory neurons can keep the balance with the surrounding excitatory neurons is an important question. We observed effective networks, reflecting causal interactions, of ~1000 neurons in cortical acute slices. Surprisingly, we found that inhibitory neurons are not only located at more central positions than excitatory neurons but also have stronger controlling ability of other neurons than excitatory neurons. Besides, we found that the precedence in centrality and controlling ability of inhibitory neurons are well observed in deep cortical layers by comparing with distribution of neurons coloured by NeuN immunostaining data. Preceding the observation, we also found that inhibitory neurons show higher firing rate than excitatory neurons, and that their firing rate also closely obey a log-normal distribution as previously known about excitatory neurons. Additionally, their connectivity strengths also obeyed a log-normal distribution. In summary, within the network interaction of huge numbers of neurons, inhibitory neurons seem to produce a central controlling system that sustains the homeostatic behavior of the brain. A similar evaluation in different life stages and in disease states etc. will not only provide deeper understandings in the homeostasis of the brain, but also will provide a selective and effective way to stimulate individual neurons to modulate neuropsychiatry or neurodegeneration disease states. Close https://www.biorxiv.org/content/10.1101/2020.02.18.954016v1 doi:10.1101/2020.02.18.954016 Close
2019
	Shimba, Kenta; Asahina, Takahiro; Sakai, Koji; JImbo, Yasuhiko; Kotani, Kiyoshi Evaluation of Conduction Properties of Sensory Axons with High-Density Microelectrode Array Conference 2019. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Shimba2019, title = {Evaluation of Conduction Properties of Sensory Axons with High-Density Microelectrode Array}, author = {Kenta Shimba and Takahiro Asahina and Koji Sakai and Yasuhiko JImbo and Kiyoshi Kotani}, url = {https://ieeexplore.ieee.org/abstract/document/8990233}, doi = {10.1109/BMEiCON47515.2019.8990233}, year = {2019}, date = {2019-11-20}, abstract = {In vitro modeling of neurodegenerative disorder is a promising method for developing new treatment. However, little is known about myelination and subsequent increase of conduction velocity in vitro. Here, we aim to develop a new method for evaluating salutatory conduction from myelinated sensory axons. First, sensory neurons and Schwann cells were cultured on high-density microelectrode array chips. Myelin sheath formation was confirmed with immunocytochemistry. Axonal signal was detected, and instantaneous conduction velocity was evaluated. As a result, we observed that relatively fast conduction sites between slow conduction sites. Our method is suitable for evaluating conduction properties of sensory axons.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close In vitro modeling of neurodegenerative disorder is a promising method for developing new treatment. However, little is known about myelination and subsequent increase of conduction velocity in vitro. Here, we aim to develop a new method for evaluating salutatory conduction from myelinated sensory axons. First, sensory neurons and Schwann cells were cultured on high-density microelectrode array chips. Myelin sheath formation was confirmed with immunocytochemistry. Axonal signal was detected, and instantaneous conduction velocity was evaluated. As a result, we observed that relatively fast conduction sites between slow conduction sites. Our method is suitable for evaluating conduction properties of sensory axons. Close https://ieeexplore.ieee.org/abstract/document/8990233 doi:10.1109/BMEiCON47515.2019.8990233 Close
	Kubota, Tomoyuki; Nakajima, Kohei; Takahashi, Hirokazu Echo State Property of Neuronal Cell Cultures Book Chapter 11731 , Springer, 2019, ISBN: 978-3-030-30493-5. Abstract \| Links \| BibTeX \| Tags: Action Potential, MaxOne, Neuronal cell culture @inbook{Kubota2019b, title = {Echo State Property of Neuronal Cell Cultures}, author = {Tomoyuki Kubota and Kohei Nakajima and Hirokazu Takahashi }, url = {https://link.springer.com/chapter/10.1007%2F978-3-030-30493-5_13}, doi = {10.1007/978-3-030-30493-5_13}, isbn = {978-3-030-30493-5}, year = {2019}, date = {2019-09-09}, volume = {11731}, publisher = {Springer}, abstract = {Physical reservoir computing (PRC) utilizes the nonlinear dynamics of physical systems, which is called a reservoir, as a computational resource. The prerequisite for physical dynamics to be a successful reservoir is to have the echo state property (ESP), asymptotic properties of transient trajectory to driving signals, with some memory held in the system. In this study, the prerequisites in dissociate cultures of cortical neuronal cells are estimated. With a state-of-the-art measuring system of high-dense CMOS array, our experiments demonstrated that each neuron exhibited reproducible spike trains in response to identical driving stimulus. Additionally, the memory function was estimated, which found that input information in the dynamics of neuronal activities in the culture up to at least 20 ms was retrieved. These results supported the notion that the cultures had ESP and could thereby serve as PRC.}, keywords = {Action Potential, MaxOne, Neuronal cell culture}, pubstate = {published}, tppubtype = {inbook} } Close Physical reservoir computing (PRC) utilizes the nonlinear dynamics of physical systems, which is called a reservoir, as a computational resource. The prerequisite for physical dynamics to be a successful reservoir is to have the echo state property (ESP), asymptotic properties of transient trajectory to driving signals, with some memory held in the system. In this study, the prerequisites in dissociate cultures of cortical neuronal cells are estimated. With a state-of-the-art measuring system of high-dense CMOS array, our experiments demonstrated that each neuron exhibited reproducible spike trains in response to identical driving stimulus. Additionally, the memory function was estimated, which found that input information in the dynamics of neuronal activities in the culture up to at least 20 ms was retrieved. These results supported the notion that the cultures had ESP and could thereby serve as PRC. Close https://link.springer.com/chapter/10.1007%2F978-3-030-30493-5_13 doi:10.1007/978-3-030-30493-5_13 Close
	Bullmann Torsten; Radivojevic, Milos; Huber Stefan Deligkaris Kosmas; Hierlemann Andreas; Frey Urs T: Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays Journal Article Frontiers in Cellular Neuroscience , 13 , 2019, ISSN: 1662-5102. Abstract \| Links \| BibTeX \| Tags: Axonal Arbors, HD-MEA @article{Bullmann2019, title = {Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays}, author = {Bullmann, Torsten; Radivojevic, Milos; Huber, Stefan T: Deligkaris, Kosmas; Hierlemann, Andreas; Frey, Urs}, url = {https://www.frontiersin.org/articles/10.3389/fncel.2019.00404/full}, doi = {10.3389/fncel.2019.00404}, issn = {1662-5102}, year = {2019}, date = {2019-09-06}, journal = {Frontiers in Cellular Neuroscience }, volume = {13}, abstract = {Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours.}, keywords = {Axonal Arbors, HD-MEA}, pubstate = {published}, tppubtype = {article} } Close Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours. Close https://www.frontiersin.org/articles/10.3389/fncel.2019.00404/full doi:10.3389/fncel.2019.00404 Close
	Obien, Marie Engelene J; Frey, Urs Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks Book Chapter Springer, 2019. Abstract \| Links \| BibTeX \| Tags: In-Vitro, Neuronal Networks @inbook{Obien2019b, title = {Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks}, author = {Marie Engelene J Obien and Urs Frey}, url = {https://link.springer.com/book/10.1007%2F978-3-030-11135-9#about}, doi = {10.1007/978-3-030-11135-9}, year = {2019}, date = {2019-05-20}, publisher = {Springer}, abstract = {This book provides a comprehensive overview of the incredible advances achieved in the study of in vitro neuronal networks for use in basic and applied research. These cultures of dissociated neurons offer a perfect trade-off between complex experimental models and theoretical modeling approaches giving new opportunities for experimental design but also providing new challenges in data management and interpretation. Topics include culturing methodologies, neuroengineering techniques, stem cell derived neuronal networks, techniques for measuring network activity, and recent improvements in large-scale data analysis. The book ends with a series of case studies examining potential applications of these technologies.}, keywords = {In-Vitro, Neuronal Networks}, pubstate = {published}, tppubtype = {inbook} } Close This book provides a comprehensive overview of the incredible advances achieved in the study of in vitro neuronal networks for use in basic and applied research. These cultures of dissociated neurons offer a perfect trade-off between complex experimental models and theoretical modeling approaches giving new opportunities for experimental design but also providing new challenges in data management and interpretation. Topics include culturing methodologies, neuroengineering techniques, stem cell derived neuronal networks, techniques for measuring network activity, and recent improvements in large-scale data analysis. The book ends with a series of case studies examining potential applications of these technologies. Close https://link.springer.com/book/10.1007%2F978-3-030-11135-9#about doi:10.1007/978-3-030-11135-9 Close
	Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Hierlemann, Andreas; Kanzaki, Ryohei; Takahashi, Hirokazu Classification of Inhibitory and Excitatory Neurons of Dissociated Cultures Based on Action Potential Waveforms on High-density CMOS Microelectrode Arrays Journal Article IEEJ Transactions on Electronics, Information and Systems, 139 (5), pp. 615-624, 2019, ISSN: 1348-8155. Abstract \| Links \| BibTeX \| Tags: Action Potential, HD-MEA @article{Mita2019, title = {Classification of Inhibitory and Excitatory Neurons of Dissociated Cultures Based on Action Potential Waveforms on High-density CMOS Microelectrode Arrays}, author = {Takeshi Mita and Douglas J. Bakkum and Urs Frey and Andreas Hierlemann and Ryohei Kanzaki and Hirokazu Takahashi }, url = {https://www.jstage.jst.go.jp/article/ieejeiss/139/5/139_615/_article/-char/en}, doi = {10.1541/ieejeiss.139.615}, issn = {1348-8155}, year = {2019}, date = {2019-05-01}, journal = {IEEJ Transactions on Electronics, Information and Systems}, volume = {139}, number = {5}, pages = {615-624}, abstract = {Electrophysiological data from in vivo and slice preparations show that inhibitory neurons had shorter duration action potentials (AP) than excitatory neurons. However, this criterion has not yet been established in dissociated cultured neurons. In the present study, we used a high-density CMOS microelectrode array to extracellularly investigate neural signals in primary dissociated cultures of rat neocortex, and we characterized AP waveforms to discriminate excitatory and inhibitory neurons. The CMOS array offers the possibility to acquire comprehensive spatio-temporal neural activity patterns with 11,011 electrodes in about 2×1.75 mm2 area at 20-kHz sampling rate. The waveforms of APs were investigated around cell bodies of neurons, which were classified into either excitatory neurons or inhibitory neurons on the basis of MAP2 and GABA immunostaining images. Consistent with previous in vivo and slice studies, we demonstrated that AP waveforms of inhibitory neurons had shorter durations and recovery time than those of excitatory neurons. The discrimination accuracy was around 0.9 in the receiver-operating characteristics (ROC) analyses. Additionally, taking advantage of non-invasive CMOS recording, we investigated AP waveforms throughout development of cultures. We confirmed that APs were classified into two classes, i.e., putative excitatory and inhibitory neurons, regardless of developmental stages, and found that the duration and recovery time of AP shortened in matured cultures. Thus, AP waveforms have rich information about cell types and developmental stages, which are of worth to elucidate underlying mechanisms of neuronal dynamics in spatio-temporal patterns.}, keywords = {Action Potential, HD-MEA}, pubstate = {published}, tppubtype = {article} } Close Electrophysiological data from in vivo and slice preparations show that inhibitory neurons had shorter duration action potentials (AP) than excitatory neurons. However, this criterion has not yet been established in dissociated cultured neurons. In the present study, we used a high-density CMOS microelectrode array to extracellularly investigate neural signals in primary dissociated cultures of rat neocortex, and we characterized AP waveforms to discriminate excitatory and inhibitory neurons. The CMOS array offers the possibility to acquire comprehensive spatio-temporal neural activity patterns with 11,011 electrodes in about 2×1.75 mm2 area at 20-kHz sampling rate. The waveforms of APs were investigated around cell bodies of neurons, which were classified into either excitatory neurons or inhibitory neurons on the basis of MAP2 and GABA immunostaining images. Consistent with previous in vivo and slice studies, we demonstrated that AP waveforms of inhibitory neurons had shorter durations and recovery time than those of excitatory neurons. The discrimination accuracy was around 0.9 in the receiver-operating characteristics (ROC) analyses. Additionally, taking advantage of non-invasive CMOS recording, we investigated AP waveforms throughout development of cultures. We confirmed that APs were classified into two classes, i.e., putative excitatory and inhibitory neurons, regardless of developmental stages, and found that the duration and recovery time of AP shortened in matured cultures. Thus, AP waveforms have rich information about cell types and developmental stages, which are of worth to elucidate underlying mechanisms of neuronal dynamics in spatio-temporal patterns. Close https://www.jstage.jst.go.jp/article/ieejeiss/139/5/139_615/_article/-char/en doi:10.1541/ieejeiss.139.615 Close
	Emmenegger, Vishalini; Obien, Marie Engelene J; Franke, Felix; Hierlemann, Andreas Technologies to Study Action Potential Propagation With a Focus on HD-MEAs Journal Article Frontiers in Cellular Neuroscience, 13 , pp. 1-11, 2019, ISSN: 1662-5102 . Abstract \| Links \| BibTeX \| Tags: Action Potential, HD-MEA @article{Emmenegger2019, title = {Technologies to Study Action Potential Propagation With a Focus on HD-MEAs}, author = {Vishalini Emmenegger and Marie Engelene J. Obien and Felix Franke and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fncel.2019.00159/full}, doi = {10.3389/fncel.2019.00159 }, issn = {1662-5102 }, year = {2019}, date = {2019-04-26}, journal = {Frontiers in Cellular Neuroscience}, volume = {13}, pages = {1-11}, abstract = {Axons convey information in neuronal circuits via reliable conduction of action potentials from the axon initial segment to the presynaptic terminals. Recent experimental findings increasingly evidence that the axonal function is not limited to the simple transmission of action potentials. Advances in subcellular-resolution recording techniques have shown that axons display activity-dependent modulation in spike shape and conduction velocity, which influence synaptic strength and latency. We briefly review, here, how recent methodological developments facilitate the understanding of the axon physiology. We included the three most common methods, i.e. genetically encoded voltage imaging, subcellular patch-clamp and high-density microelectrode arrays (HD-MEAs). We then describe the potential of using HD-MEAs in studying axonal physiology in more detail. Due to their robustness, amenability to high-throughput and high spatiotemporal resolution, HD-MEAs can provide a direct functional electrical readout of single cells and cellular ensembles at subcellular resolution. HD-MEAs can, therefore, be employed in investigating axonal pathologies, the effects of large-scale genomic interventions (e.g., with RNAi or CRISPR) or in compound screenings. A combination of extracellular microelectrode arrays, intracellular microelectrodes and optical imaging may potentially reveal yet unexplored repertoires of axonal functions.}, keywords = {Action Potential, HD-MEA}, pubstate = {published}, tppubtype = {article} } Close Axons convey information in neuronal circuits via reliable conduction of action potentials from the axon initial segment to the presynaptic terminals. Recent experimental findings increasingly evidence that the axonal function is not limited to the simple transmission of action potentials. Advances in subcellular-resolution recording techniques have shown that axons display activity-dependent modulation in spike shape and conduction velocity, which influence synaptic strength and latency. We briefly review, here, how recent methodological developments facilitate the understanding of the axon physiology. We included the three most common methods, i.e. genetically encoded voltage imaging, subcellular patch-clamp and high-density microelectrode arrays (HD-MEAs). We then describe the potential of using HD-MEAs in studying axonal physiology in more detail. Due to their robustness, amenability to high-throughput and high spatiotemporal resolution, HD-MEAs can provide a direct functional electrical readout of single cells and cellular ensembles at subcellular resolution. HD-MEAs can, therefore, be employed in investigating axonal pathologies, the effects of large-scale genomic interventions (e.g., with RNAi or CRISPR) or in compound screenings. A combination of extracellular microelectrode arrays, intracellular microelectrodes and optical imaging may potentially reveal yet unexplored repertoires of axonal functions. Close https://www.frontiersin.org/articles/10.3389/fncel.2019.00159/full doi:10.3389/fncel.2019.00159 Close
	Viswam, Vijay; Obien, Marie Engelene J; Franke, Felix; Frey, Urs; Hierlemann, Andreas Optimal Electrode Size for Multi-Scale Extracellular-Potential Recording From Neuronal Assemblies Journal Article Frontiers in Neuroscience, 13 , 2019, ISSN: 1662-453X. Abstract \| Links \| BibTeX \| Tags: Neuronal Assemblies @article{Viswam2019, title = {Optimal Electrode Size for Multi-Scale Extracellular-Potential Recording From Neuronal Assemblies}, author = {Vijay Viswam and Marie Engelene J. Obien and Felix Franke and Urs Frey and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2019.00385/full}, doi = {10.3389/fnins.2019.00385}, issn = {1662-453X}, year = {2019}, date = {2019-04-26}, journal = {Frontiers in Neuroscience}, volume = {13}, abstract = {Advances in microfabrication technology have enabled the production of devices containing arrays of thousands of closely spaced recording electrodes, which afford subcellular resolution of electrical signals in neurons and neuronal networks. Rationalizing the electrode size and configuration in such arrays demands consideration of application-specific requirements and inherent features of the electrodes. Tradeoffs among size, spatial density, sensitivity, noise, attenuation, and other factors are inevitable. Although recording extracellular signals from neurons with planar metal electrodes is fairly well established, the effects of the electrode characteristics on the quality and utility of recorded signals, especially for small, densely packed electrodes, have yet to be fully characterized. Here, we present a combined experimental and computational approach to elucidating how electrode size, and size-dependent parameters, such as impedance, baseline noise, and transmission characteristics, influence recorded neuronal signals. Using arrays containing platinum electrodes of different sizes, we experimentally evaluated the electrode performance in the recording of local-field-potentials (LFPs) and extracellular-action-potentials (EAPs) from the following cell preparations: acute brain slices, dissociated cell cultures, and organotypic slice cultures. Moreover, we simulated the potential spatial decay of point-current sources to investigate signal averaging using known signal sources. We demonstrated that the noise and signal attenuation depend more on the electrode impedance than on electrode size, per se, especially for electrodes < 10 µm in width or diameter to achieve high-spatial-resolution readout. By minimizing electrode impedance in small electrodes (< 10 µm), via surface modification, we could maximize the signal-to-noise ratio to electrically visualize the propagation of axonal EAPs and to isolate single-unit spikes. Due to the large amplitude of LFP signals, recording quality was high and nearly independent of electrode size. These findings should be of value in configuring in vitro and in vivo microelectrode arrays for extracellular recordings with high spatial resolution in various applications.}, keywords = {Neuronal Assemblies}, pubstate = {published}, tppubtype = {article} } Close Advances in microfabrication technology have enabled the production of devices containing arrays of thousands of closely spaced recording electrodes, which afford subcellular resolution of electrical signals in neurons and neuronal networks. Rationalizing the electrode size and configuration in such arrays demands consideration of application-specific requirements and inherent features of the electrodes. Tradeoffs among size, spatial density, sensitivity, noise, attenuation, and other factors are inevitable. Although recording extracellular signals from neurons with planar metal electrodes is fairly well established, the effects of the electrode characteristics on the quality and utility of recorded signals, especially for small, densely packed electrodes, have yet to be fully characterized. Here, we present a combined experimental and computational approach to elucidating how electrode size, and size-dependent parameters, such as impedance, baseline noise, and transmission characteristics, influence recorded neuronal signals. Using arrays containing platinum electrodes of different sizes, we experimentally evaluated the electrode performance in the recording of local-field-potentials (LFPs) and extracellular-action-potentials (EAPs) from the following cell preparations: acute brain slices, dissociated cell cultures, and organotypic slice cultures. Moreover, we simulated the potential spatial decay of point-current sources to investigate signal averaging using known signal sources. We demonstrated that the noise and signal attenuation depend more on the electrode impedance than on electrode size, per se, especially for electrodes < 10 µm in width or diameter to achieve high-spatial-resolution readout. By minimizing electrode impedance in small electrodes (< 10 µm), via surface modification, we could maximize the signal-to-noise ratio to electrically visualize the propagation of axonal EAPs and to isolate single-unit spikes. Due to the large amplitude of LFP signals, recording quality was high and nearly independent of electrode size. These findings should be of value in configuring in vitro and in vivo microelectrode arrays for extracellular recordings with high spatial resolution in various applications. Close https://www.frontiersin.org/articles/10.3389/fnins.2019.00385/full doi:10.3389/fnins.2019.00385 Close
	Russell, Thomas L; Zhang, Jichang; Okoniewksi, Michal; Franke, Felix; Bichet, Sandrine; Hierlemann, Andreas Medullary Respiratory Circuit Is Reorganized by a Seasonally-Induced Program in Preparation for Hibernation Journal Article Frontiers in Neuroscience , 13 , 2019, ISSN: 1662-453X. Abstract \| Links \| BibTeX \| Tags: Respiratory Circuit @article{Russell2019, title = {Medullary Respiratory Circuit Is Reorganized by a Seasonally-Induced Program in Preparation for Hibernation }, author = {Thomas L. Russell and Jichang Zhang and Michal Okoniewksi and Felix Franke and Sandrine Bichet and Andreas Hierlemann}, url = {https://www.frontiersin.org/article/10.3389/fnins.2019.00376}, doi = {10.3389/fnins.2019.00376 }, issn = {1662-453X}, year = {2019}, date = {2019-04-26}, journal = {Frontiers in Neuroscience }, volume = {13}, abstract = {Deep hibernators go through several cycles of profound drops in body temperature during the winter season, with core temperatures sometimes reaching near freezing. Yet unlike non-hibernating mammals, they can sustain breathing rhythms. The physiological processes that make this possible are still not understood. In this study, we focused on the medullary Ventral Respiratory Column of a facultative hibernator, the Syrian hamster. Using shortened day-lengths, we induced a "winter-adapted" physiological state, which is a prerequisite for hibernation. When recording electrophysiological signals from acute slices in the winter-adapted pre-Bötzinger complex, spike trains showed higher spike rates, amplitudes, complexity, as well as higher temperature sensitivity, suggesting an increase in connectivity and/or synaptic strength during the winter season. We further examined action potential waveforms and found that the depolarization integral, as measured by the area under the curve, is selectively enhanced in winter-adapted animals. This suggests that a shift in the ion handling kinetics is also being induced by the winter-adaptation program. RNA sequencing of respiratory pre-motor neurons, followed by gene set enrichment analysis, revealed differential regulation and splicing in structural, synaptic, and ion handling genes. Splice junction analysis suggested that differential exon usage is occurring in a select subset of ion handling subunits (ATP1A3, KCNC3, SCN1B), and synaptic structure genes (SNCB, SNCG, RAB3A). Our findings show that the hamster respiratory center undergoes a seasonally-cued alteration in electrophysiological properties, likely protecting against respiratory failure at low temperatures.}, keywords = {Respiratory Circuit}, pubstate = {published}, tppubtype = {article} } Close Deep hibernators go through several cycles of profound drops in body temperature during the winter season, with core temperatures sometimes reaching near freezing. Yet unlike non-hibernating mammals, they can sustain breathing rhythms. The physiological processes that make this possible are still not understood. In this study, we focused on the medullary Ventral Respiratory Column of a facultative hibernator, the Syrian hamster. Using shortened day-lengths, we induced a "winter-adapted" physiological state, which is a prerequisite for hibernation. When recording electrophysiological signals from acute slices in the winter-adapted pre-Bötzinger complex, spike trains showed higher spike rates, amplitudes, complexity, as well as higher temperature sensitivity, suggesting an increase in connectivity and/or synaptic strength during the winter season. We further examined action potential waveforms and found that the depolarization integral, as measured by the area under the curve, is selectively enhanced in winter-adapted animals. This suggests that a shift in the ion handling kinetics is also being induced by the winter-adaptation program. RNA sequencing of respiratory pre-motor neurons, followed by gene set enrichment analysis, revealed differential regulation and splicing in structural, synaptic, and ion handling genes. Splice junction analysis suggested that differential exon usage is occurring in a select subset of ion handling subunits (ATP1A3, KCNC3, SCN1B), and synaptic structure genes (SNCB, SNCG, RAB3A). Our findings show that the hamster respiratory center undergoes a seasonally-cued alteration in electrophysiological properties, likely protecting against respiratory failure at low temperatures. Close https://www.frontiersin.org/article/10.3389/fnins.2019.00376 doi:10.3389/fnins.2019.00376 Close
	Ronchi, Silvia; Fiscella, Michele; Marchetti, Camilla; Viswam, Vijay; Muller, Jan; Frey, Urs; Hierlemann, Andreas Single-Cell Electrical Stimulation Using CMOS-Based High-Density Microelectrode Arrays Journal Article Frontiers in Neuroscience, 13 , 2019, ISSN: 1662-453X . Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @article{Ronchi2019, title = {Single-Cell Electrical Stimulation Using CMOS-Based High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Michele Fiscella and Camilla Marchetti and Vijay Viswam and Jan Muller and Urs Frey and Andreas Hierlemann}, url = {https://www.frontiersin.org/article/10.3389/fnins.2019.00208 }, doi = {10.3389/fnins.2019.00208 }, issn = {1662-453X }, year = {2019}, date = {2019-03-13}, journal = {Frontiers in Neuroscience}, volume = {13}, abstract = {Non-invasive electrical stimulation can be used to study and control neural activity in the brain or to alleviate somatosensory dysfunctions. One intriguing prospect is to precisely stimulate individual targeted neurons. Here, we investigated single-neuron current and voltage stimulation in vitro using high-density microelectrode arrays featuring 26’400 bidirectional electrodes at a pitch of 17.5 µm and an electrode area of 5 × 9 µm². We determined optimal waveforms, amplitudes and durations for both stimulation modes. Owing to the high spatial resolution of our arrays and the close proximity of the electrodes to the respective neurons, we were able to stimulate the axon initial segments (AIS) with charges of less than 2 picoCoulombs. This resulted in minimal artifact production and reliable readout of stimulation efficiency directly at the soma of the stimulated cell. Stimulation signals as low as 70 mV or 100 nA,with pulse durations as short as 18 µs, yielded measurable action potential initiation and propagation. We found that the required stimulation signal amplitudes decreased with cell growth and development and that stimulation efficiency did not improve at higher electric fields generated by simultaneous multi-electrode stimulation.}, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Non-invasive electrical stimulation can be used to study and control neural activity in the brain or to alleviate somatosensory dysfunctions. One intriguing prospect is to precisely stimulate individual targeted neurons. Here, we investigated single-neuron current and voltage stimulation in vitro using high-density microelectrode arrays featuring 26’400 bidirectional electrodes at a pitch of 17.5 µm and an electrode area of 5 × 9 µm². We determined optimal waveforms, amplitudes and durations for both stimulation modes. Owing to the high spatial resolution of our arrays and the close proximity of the electrodes to the respective neurons, we were able to stimulate the axon initial segments (AIS) with charges of less than 2 picoCoulombs. This resulted in minimal artifact production and reliable readout of stimulation efficiency directly at the soma of the stimulated cell. Stimulation signals as low as 70 mV or 100 nA,with pulse durations as short as 18 µs, yielded measurable action potential initiation and propagation. We found that the required stimulation signal amplitudes decreased with cell growth and development and that stimulation efficiency did not improve at higher electric fields generated by simultaneous multi-electrode stimulation. Close https://www.frontiersin.org/article/10.3389/fnins.2019.00208 doi:10.3389/fnins.2019.00208 Close
	Obien, Marie Engelene J; Hierlemann, Andreas; Frey, Urs Accurate signal-source localization in brain slices by means of high-density microelectrode arrays Journal Article Scientific Reports, 9 (788), 2019. Abstract \| Links \| BibTeX \| Tags: Brain Slice @article{Obien2019, title = {Accurate signal-source localization in brain slices by means of high-density microelectrode arrays}, author = {Marie Engelene J. Obien and Andreas Hierlemann and Urs Frey}, url = {https://www.nature.com/articles/s41598-018-36895-y}, doi = {10.1038/s41598-018-36895-y}, year = {2019}, date = {2019-01-28}, journal = {Scientific Reports}, volume = {9}, number = {788}, abstract = {Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 μm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 μm systematic mean error, compared to 22.0 μm obtained with MoI. These results suggest that the medium volume or “saline height”, the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 μm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation.}, keywords = {Brain Slice}, pubstate = {published}, tppubtype = {article} } Close Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 μm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 μm systematic mean error, compared to 22.0 μm obtained with MoI. These results suggest that the medium volume or “saline height”, the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 μm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation. Close https://www.nature.com/articles/s41598-018-36895-y doi:10.1038/s41598-018-36895-y Close
	Dudina, Alexandra; Seichepine, Florent; Chen, Yihui; and Stettler, Alexander; Hierlemann, Andreas; and Frey, Urs Monolithic CMOS sensor platform featuring an array of 9’216 carbon-nanotube-sensor elements and low-noise, wide-bandwidth and wide-dynamic-range readout circuitry Journal Article Sensors and Actuators B: Chemical, 279 , pp. 255-266, 2019. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Dudina2019, title = {Monolithic CMOS sensor platform featuring an array of 9’216 carbon-nanotube-sensor elements and low-noise, wide-bandwidth and wide-dynamic-range readout circuitry}, author = {Alexandra Dudina and Florent Seichepine and Yihui Chen and and Alexander Stettler and Andreas Hierlemann and and Urs Frey}, url = {https://www.sciencedirect.com/science/article/pii/S0925400518317672?via%3Dihub}, doi = {10.1016/j.snb.2018.10.004}, year = {2019}, date = {2019-01-15}, journal = {Sensors and Actuators B: Chemical}, volume = {279}, pages = {255-266}, abstract = {We present the design and characterization of a monolithic complementary metal–oxide–semiconductor (CMOS) biosensor platform comprising of a switch-matrix-based array of 9′216 carbon nanotube field-effect transistors (CNTFETs) and associated readout circuitry. The switch-matrix allows for flexible selection and simultaneous routing of 96 sensor elements to the corresponding readout channels. A low-noise, wide-bandwidth, wide-dynamic-range transimpedance continuous-time amplifier architecture has been implemented to facilitate resistance measurements in the range between 50 kΩ and 1 GΩ at a bandwidth of up to 1 MHz. The achieved accuracy of the resistance measurements over the whole range is 4%. The system has been successfully fabricated and tested and shows a noise performance equal to 2.14 pArms at a bandwidth of 1 kHz and 0.84 nArms at a bandwidth of 1 MHz. A batch integration of the CNTFETs has been achieved by using a dielectrophoresis (DEP)–based manipulation technique. The current-voltage curves of CNTFETs have been acquired, and the sensing capabilities of the system have been demonstrated by recording resistance changes of CNTFETs upon exposure to solutions with different pH values and different concentrations of NaCl. The smallest resolvable concentrations for the respective analytes were estimated to amount to 0.025 pH-units and 4 mM NaCl.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close We present the design and characterization of a monolithic complementary metal–oxide–semiconductor (CMOS) biosensor platform comprising of a switch-matrix-based array of 9′216 carbon nanotube field-effect transistors (CNTFETs) and associated readout circuitry. The switch-matrix allows for flexible selection and simultaneous routing of 96 sensor elements to the corresponding readout channels. A low-noise, wide-bandwidth, wide-dynamic-range transimpedance continuous-time amplifier architecture has been implemented to facilitate resistance measurements in the range between 50 kΩ and 1 GΩ at a bandwidth of up to 1 MHz. The achieved accuracy of the resistance measurements over the whole range is 4%. The system has been successfully fabricated and tested and shows a noise performance equal to 2.14 pArms at a bandwidth of 1 kHz and 0.84 nArms at a bandwidth of 1 MHz. A batch integration of the CNTFETs has been achieved by using a dielectrophoresis (DEP)–based manipulation technique. The current-voltage curves of CNTFETs have been acquired, and the sensing capabilities of the system have been demonstrated by recording resistance changes of CNTFETs upon exposure to solutions with different pH values and different concentrations of NaCl. The smallest resolvable concentrations for the respective analytes were estimated to amount to 0.025 pH-units and 4 mM NaCl. Close https://www.sciencedirect.com/science/article/pii/S0925400518317672?via%3Dihub doi:10.1016/j.snb.2018.10.004 Close
	Shadmani, Amir; Viswam, Vijay; Chen, Yihui; Bounik, Raziyeh; Dragas, Jelena; Radivojevic, Milos; Geissler, Sydney; Sitnikov, Sergey; Muller, Jan; Hierlemann, Andreas Stimulation and Artifact-suppression Techniques for in-vitro High-density Microelectrode Array Systems. Journal Article IEEE Transactions on Biomedical Engineering, 2019. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Shadmani2019b, title = {Stimulation and Artifact-suppression Techniques for in-vitro High-density Microelectrode Array Systems.}, author = {Amir Shadmani and Vijay Viswam and Yihui Chen and Raziyeh Bounik and Jelena Dragas and Milos Radivojevic and Sydney Geissler and Sergey Sitnikov and Jan Muller and Andreas Hierlemann }, url = {https://ieeexplore.ieee.org/document/8599003}, doi = {10.1109/TBME.2018.2890530}, year = {2019}, date = {2019-01-01}, journal = {IEEE Transactions on Biomedical Engineering}, abstract = {We present novel voltage stimulation buffers with controlled output current, along with recording circuits featuring adjustable high-pass cut-off filtering to perform efficient stimulation while actively suppressing stimulation artifacts in high-density microelectrode arrays. Owing to the dense packing and close proximity of the electrodes in such systems, a stimulation through one electrode can cause large electrical artifacts on neighboring electrodes that easily saturate the corresponding recording amplifiers. To suppress such artifacts, the high-pass corner frequencies of all available 2048 recording channels can be raised from several Hz to several kHz by applying a "soft-reset" or pole-shifting technique. With the implemented artifact suppression technique, the saturation time of the recording circuits, connected to electrodes in immediate vicinity to the stimulation site, could be reduced to less than 150μs. For the stimulation buffer, we developed a circuit, which can operate in two modes: either control of only the stimulation voltage, or control of current and voltage during stimulation. The voltage-only controlled mode employs a local common-mode feedback operational transconductance amplifier with a near rail-to-rail input/output range, suitable for driving high capacitive loads. The current/voltage controlled mode is based on a positive current conveyor generating adjustable output currents, while its upper and lower output voltages are limited by two feedback loops. The current/voltage controlled circuit can generate stimulation pulses up to 30 μA with less than ±0.1% linearity error in the low-current mode, and up to 300 μA with less than ±0.2% linearity error in the high-current mode.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close We present novel voltage stimulation buffers with controlled output current, along with recording circuits featuring adjustable high-pass cut-off filtering to perform efficient stimulation while actively suppressing stimulation artifacts in high-density microelectrode arrays. Owing to the dense packing and close proximity of the electrodes in such systems, a stimulation through one electrode can cause large electrical artifacts on neighboring electrodes that easily saturate the corresponding recording amplifiers. To suppress such artifacts, the high-pass corner frequencies of all available 2048 recording channels can be raised from several Hz to several kHz by applying a "soft-reset" or pole-shifting technique. With the implemented artifact suppression technique, the saturation time of the recording circuits, connected to electrodes in immediate vicinity to the stimulation site, could be reduced to less than 150μs. For the stimulation buffer, we developed a circuit, which can operate in two modes: either control of only the stimulation voltage, or control of current and voltage during stimulation. The voltage-only controlled mode employs a local common-mode feedback operational transconductance amplifier with a near rail-to-rail input/output range, suitable for driving high capacitive loads. The current/voltage controlled mode is based on a positive current conveyor generating adjustable output currents, while its upper and lower output voltages are limited by two feedback loops. The current/voltage controlled circuit can generate stimulation pulses up to 30 μA with less than ±0.1% linearity error in the low-current mode, and up to 300 μA with less than ±0.2% linearity error in the high-current mode. Close https://ieeexplore.ieee.org/document/8599003 doi:10.1109/TBME.2018.2890530 Close
2018
	Bakkum, Douglas J; Obien, Marie Engelene J; Radivojevic, Milos; Jäckel, David; Frey, Urs; Takahashi, Hirokazu; Hierlemann, Andreas The Axon Initial Segment is the Dominant Contributor to the Neuron's Extracellular Electrical Potential Landscape Journal Article Advanced Biosystems, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Bakkum2018b, title = {The Axon Initial Segment is the Dominant Contributor to the Neuron's Extracellular Electrical Potential Landscape}, author = {Douglas J. Bakkum and Marie Engelene J. Obien and Milos Radivojevic and David Jäckel and Urs Frey and Hirokazu Takahashi and Andreas Hierlemann}, url = {https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201800308}, doi = {10.1002/adbi.201800308}, year = {2018}, date = {2018-11-29}, journal = {Advanced Biosystems}, abstract = {Extracellular voltage fields, produced by a neuron's action potentials, provide a widely used means for studying neuronal and neuronal‐network function. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP) landscape, while the axon's contribution is usually considered less important. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices through hundreds of densely packed electrodes, it is found, instead, that the axon initial segment dominates the measured EAP landscape, and, surprisingly, the soma only contributes to a minor extent. As expected, the recorded dominant signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage landscape is important for interpreting results from all electrical readout schemes. Finally, initiation of the electrical activity at the distal end of the axon initial segment (AIS) and subsequent spreading into the axon proper and backward through the proximal AIS toward the soma are confirmed. The corresponding extracellular waveforms across different neuronal compartments could be tracked.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Extracellular voltage fields, produced by a neuron's action potentials, provide a widely used means for studying neuronal and neuronal‐network function. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP) landscape, while the axon's contribution is usually considered less important. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices through hundreds of densely packed electrodes, it is found, instead, that the axon initial segment dominates the measured EAP landscape, and, surprisingly, the soma only contributes to a minor extent. As expected, the recorded dominant signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage landscape is important for interpreting results from all electrical readout schemes. Finally, initiation of the electrical activity at the distal end of the axon initial segment (AIS) and subsequent spreading into the axon proper and backward through the proximal AIS toward the soma are confirmed. The corresponding extracellular waveforms across different neuronal compartments could be tracked. Close https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201800308 doi:10.1002/adbi.201800308 Close
	Viswam, Vijay; Bounik, Raziyeh; Shadmani, Amir; Dragas, Jelena; Urwyler, Cedar; Boos, Julia Alicia; Obien, Marie Engelene J; Muller, Jan; Chen, Yihui; Hierlemann, Andreas Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System Journal Article IEEE Transactions on Biomedical Circuits and Systems, 12 (6), pp. 1356-1368, 2018, ISSN: 1932-4545. Abstract \| Links \| BibTeX \| Tags: HD-MEA @article{Viswam2018, title = {Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System}, author = {Vijay Viswam and Raziyeh Bounik and Amir Shadmani and Jelena Dragas and Cedar Urwyler and Julia Alicia Boos and Marie Engelene J. Obien and Jan Muller and Yihui Chen and Andreas Hierlemann}, url = {https://ieeexplore.ieee.org/document/8532304}, doi = {10.1109/TBCAS.2018.2881044}, issn = {1932-4545}, year = {2018}, date = {2018-11-12}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {12}, number = {6}, pages = {1356-1368}, abstract = {A monolithic multi-functional CMOS microelectrode array system was developed that enables label-free electrochemical impedance spectroscopy of cells in vitro at high spatiotemporal resolution. The electrode array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 μm. A total of 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen subset of electrodes in the array. A sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, was applied to the reference electrode. The sensing currents through the selected recording electrodes were amplified, demodulated, filtered, and digitized to obtain the magnitude and phase information of the respective impedances. The circuitry consumes only 412 μW at 3.3 V supply voltage and occupies only 0.1 mm 2 , for each channel. The system also included 2048 extracellular action-potential recording channels on the same chip. Proof of concept measurements of electrical impedance imaging and electrophysiology recording of cardiac cells and brain slices are demonstrated in this paper. Optical and impedance images showed a strong correlation.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {article} } Close A monolithic multi-functional CMOS microelectrode array system was developed that enables label-free electrochemical impedance spectroscopy of cells in vitro at high spatiotemporal resolution. The electrode array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 μm. A total of 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen subset of electrodes in the array. A sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, was applied to the reference electrode. The sensing currents through the selected recording electrodes were amplified, demodulated, filtered, and digitized to obtain the magnitude and phase information of the respective impedances. The circuitry consumes only 412 μW at 3.3 V supply voltage and occupies only 0.1 mm 2 , for each channel. The system also included 2048 extracellular action-potential recording channels on the same chip. Proof of concept measurements of electrical impedance imaging and electrophysiology recording of cardiac cells and brain slices are demonstrated in this paper. Optical and impedance images showed a strong correlation. Close https://ieeexplore.ieee.org/document/8532304 doi:10.1109/TBCAS.2018.2881044 Close
	Lewandowska, Marta K; Bogatikov, Evgenii; Hierlemann, Andreas; Punga, Anna Rostedt Long-term high-density extracellular recordings enable studies of muscle cell physiology and pathology Conference Contribution 700.13 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Physiology @conference{Lewandowska2018c, title = {Long-term high-density extracellular recordings enable studies of muscle cell physiology and pathology}, author = {Marta K. Lewandowska and Evgenii Bogatikov and Andreas Hierlemann and Anna Rostedt Punga}, url = {https://abstractsonline.com/pp8/#!/4649/presentation/24936}, year = {2018}, date = {2018-11-07}, volume = {Contribution 700.13}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of defective ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high spatial resolution and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. We present a method, which we used to follow the development of primary skeletal muscle cells from myoblasts into mature contracting myofibers over more than two months. In contrast to most previous studies, the muscles do not detach from the surface but instead form functional networks between the myofibers, whose electrical signals we observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myofibers on a chip that contains an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enables discovery of the origin of possible failure mechanisms in muscle diseases. This system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models.}, keywords = {ETH-CMOS-MEA, Physiology}, pubstate = {published}, tppubtype = {conference} } Close Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of defective ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high spatial resolution and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. We present a method, which we used to follow the development of primary skeletal muscle cells from myoblasts into mature contracting myofibers over more than two months. In contrast to most previous studies, the muscles do not detach from the surface but instead form functional networks between the myofibers, whose electrical signals we observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myofibers on a chip that contains an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enables discovery of the origin of possible failure mechanisms in muscle diseases. This system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models. Close https://abstractsonline.com/pp8/#!/4649/presentation/24936 Close
	Fiscella, Michele; Leary, Noelle; Ronchi, Silvia; Hierlemann, Andreas Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelectrode array Conference Contribution 700.13 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC @conference{Fiscella2018, title = {Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelectrode array}, author = {Michele Fiscella and Noelle Leary and Silvia Ronchi and Andreas Hierlemann }, url = {https://www.abstractsonline.com/pp8/#!/4649/presentation/24924}, year = {2018}, date = {2018-11-07}, volume = {Contribution 700.13}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {High-resolution-microelectrode-array (HD-MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity [1]. We have used this HD-MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural-culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple HD-MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons [2]. Furthermore, we found different axonal-action-potential-velocity-development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular-resolution electrical stimulation. HD-MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing.}, keywords = {HD-MEA, IPSC}, pubstate = {published}, tppubtype = {conference} } Close High-resolution-microelectrode-array (HD-MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity [1]. We have used this HD-MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural-culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple HD-MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons [2]. Furthermore, we found different axonal-action-potential-velocity-development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular-resolution electrical stimulation. HD-MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing. Close https://www.abstractsonline.com/pp8/#!/4649/presentation/24924 Close
	Emmenegger, Vishalini; Bartram, Julian; Sitnikov, Sergey; Hierlemann, Andreas Investigating the analog modulation of action-potential waveforms in axonal arbors of cortical neurons using whole-cell patch-clamp recordings and high-density microelectrode arrays Conference Contribution 203.05 , Society for Neuroscience (SfN) Meeting, San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @conference{Emmenegger2018, title = {Investigating the analog modulation of action-potential waveforms in axonal arbors of cortical neurons using whole-cell patch-clamp recordings and high-density microelectrode arrays}, author = {Vishalini Emmenegger and Julian Bartram and Sergey Sitnikov and Andreas Hierlemann}, url = {https://abstractsonline.com/pp8/#!/4649/presentation/9323}, year = {2018}, date = {2018-11-04}, volume = {Contribution 203.05}, publisher = {Society for Neuroscience (SfN) Meeting}, address = {San Diego, CA, USA}, abstract = {Analog-digital facilitation (ADF) is a type of short-term plasticity, where the subthreshold membrane potential in the presynaptic element enhances the spike-evoked synaptic response. Most cases of ADF have been induced by long (0.3-10 s) subthreshold depolarization of the soma, while in few cases, transient (15-200 ms) hyperpolarization has been evoked immediately before the action potential (AP). In both cases, somatic membrane fluctuations modulate the biophysical properties of voltage-gated ion channels causing changes in the AP waveform, which result in larger release of neurotransmitters. However, it is still unknown, whether the modulation of the AP waveform changes with increasing distance from the soma and differs in different axonal arbors, and whether such modulation affects the velocity of AP propagation. Here, we used CMOS-based high-density microelectrode arrays (HD-MEA) with 26,400 microelectrodes, which enabled unprecedented high-resolution access to investigating axonal signaling at multiple sites simultaneously, thus providing in-depth information on the propagation of AP. The subthreshold depolarization and hyperpolarization of the presynaptic cell was performed using whole-cell patch-clamp recordings from cells in low-density cortical cultures, plated on a HD-MEA that allowed to trace the effects of such manipulations on AP propagation characteristics. Array-wide spike-triggered average signals were computed, and their spatiotemporal distribution was reconstructed. In order to study the changes in extracellular AP waveforms, we first induced pharmacological modulations using dendrotoxin and carbamazepine, which increased AP width and amplitude. As a next step, we evoked AP broadening and amplitude changes by subthreshold depolarization and hyperpolarization. We detected the extracellular AP waveforms directly under the soma and traced them throughout the axon during various time spans and for different holding potentials. We found that changes in AP propagation velocity were correlated to the detected AP broadening. Our preliminary data evidenced changes in AP waveforms with increasing distance from the soma along the axon, but further experiments on synaptically coupled neurons using paired recordings will be performed to better understand the influence of AP modulation on ADF. Information encoding in neuronal circuits is probably contingent on both, temporal spike patterns and spike waveforms. In the light of the latter being typically disregarded in computational models, the study of the analog modulation of AP waveforms will contribute to a better understanding of neuronal information processing.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {conference} } Close Analog-digital facilitation (ADF) is a type of short-term plasticity, where the subthreshold membrane potential in the presynaptic element enhances the spike-evoked synaptic response. Most cases of ADF have been induced by long (0.3-10 s) subthreshold depolarization of the soma, while in few cases, transient (15-200 ms) hyperpolarization has been evoked immediately before the action potential (AP). In both cases, somatic membrane fluctuations modulate the biophysical properties of voltage-gated ion channels causing changes in the AP waveform, which result in larger release of neurotransmitters. However, it is still unknown, whether the modulation of the AP waveform changes with increasing distance from the soma and differs in different axonal arbors, and whether such modulation affects the velocity of AP propagation. Here, we used CMOS-based high-density microelectrode arrays (HD-MEA) with 26,400 microelectrodes, which enabled unprecedented high-resolution access to investigating axonal signaling at multiple sites simultaneously, thus providing in-depth information on the propagation of AP. The subthreshold depolarization and hyperpolarization of the presynaptic cell was performed using whole-cell patch-clamp recordings from cells in low-density cortical cultures, plated on a HD-MEA that allowed to trace the effects of such manipulations on AP propagation characteristics. Array-wide spike-triggered average signals were computed, and their spatiotemporal distribution was reconstructed. In order to study the changes in extracellular AP waveforms, we first induced pharmacological modulations using dendrotoxin and carbamazepine, which increased AP width and amplitude. As a next step, we evoked AP broadening and amplitude changes by subthreshold depolarization and hyperpolarization. We detected the extracellular AP waveforms directly under the soma and traced them throughout the axon during various time spans and for different holding potentials. We found that changes in AP propagation velocity were correlated to the detected AP broadening. Our preliminary data evidenced changes in AP waveforms with increasing distance from the soma along the axon, but further experiments on synaptically coupled neurons using paired recordings will be performed to better understand the influence of AP modulation on ADF. Information encoding in neuronal circuits is probably contingent on both, temporal spike patterns and spike waveforms. In the light of the latter being typically disregarded in computational models, the study of the analog modulation of AP waveforms will contribute to a better understanding of neuronal information processing. Close https://abstractsonline.com/pp8/#!/4649/presentation/9323 Close
	Ronchi, Silvia; Fiscella, Michele; Marchetti, Camilla; Viswam, Vijay; Müller, Jan; Frey, Urs; Hierlemann, Andreas Single-neuron sub-cellular-resolution electrical stimulation with high-density microelectrode arrays Conference Contribution 174.05 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @conference{Ronchi2018, title = {Single-neuron sub-cellular-resolution electrical stimulation with high-density microelectrode arrays}, author = {Silvia Ronchi and Michele Fiscella and Camilla Marchetti and Vijay Viswam and Jan Müller and Urs Frey and Andreas Hierlemann}, url = {https://abstractsonline.com/pp8/#!/4649/presentation/24382}, year = {2018}, date = {2018-11-04}, volume = {Contribution 174.05}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {Non-invasive electrical stimulation is a consolidated technique to study and control neural activity in the brain and peripheral nervous system. It is used, e.g., for controlling Parkinson's disease or to induce sensation in paralyzed patients (Armenta Salas et al., 2018), as well as for attempts to restore vision (Fan et al., 2018; Grosberg et al., 2017) and hearing (Wilson & Dorman, 2008). A common requirement in electrical stimulation is the precise and controlled stimulation of individual targeted neurons. For achieving this purpose, it is necessary that electrodes can stimulate and record extracellular signals at sub-cellular resolution. Furthermore, it is important to design efficient stimulation pulses to be delivered to the neurons. In the present work we used an CMOS-based high-density microelectrode array (HD-MEA) (Ballini et al., 2014), featuring 26’400 bidirectional electrodes with a pitch of 17.5 µm, which was designed for in-vitro applications. This high-resolution was used to test electrical stimulation parameters in vitro, which then could potentially be adapted to elicit single-cell action potentials in vivo. In this work we used different stimulation parameters, such as waveforms, amplitudes and durations (Grosberg et al., 2017; Wagenaar, Pine, & Potter, 2004), using 5x9 µm² electrodes to target sub-cellular structures in single neurons. E-18 Wistar rat cortical neurons were stimulated at days-in-vitro 10, 15, 20 and 25 using randomized voltage and current stimulation modalities. Axon initial segments of individual neurons (Radivojevic et al., 2016) were targeted for stimulation, enabled by the HD-MEA device. We found that voltage biphasic anodic-cathodic waveforms were less efficient than biphasic cathodic-anodic waveforms in eliciting action potentials in a single neuron. Moreover, it was possible to detect action potentials directly at the cell soma, which ensured a reliable confirmation of successful neuron stimulation. Finally, HD-MEA technology enabled to elicit action potentials in single-neurons embedded in high-density cell cultures. The obtained results can be used to optimize in vivo single-cell targeting for stimulation and read-out.}, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {conference} } Close Non-invasive electrical stimulation is a consolidated technique to study and control neural activity in the brain and peripheral nervous system. It is used, e.g., for controlling Parkinson's disease or to induce sensation in paralyzed patients (Armenta Salas et al., 2018), as well as for attempts to restore vision (Fan et al., 2018; Grosberg et al., 2017) and hearing (Wilson & Dorman, 2008). A common requirement in electrical stimulation is the precise and controlled stimulation of individual targeted neurons. For achieving this purpose, it is necessary that electrodes can stimulate and record extracellular signals at sub-cellular resolution. Furthermore, it is important to design efficient stimulation pulses to be delivered to the neurons. In the present work we used an CMOS-based high-density microelectrode array (HD-MEA) (Ballini et al., 2014), featuring 26’400 bidirectional electrodes with a pitch of 17.5 µm, which was designed for in-vitro applications. This high-resolution was used to test electrical stimulation parameters in vitro, which then could potentially be adapted to elicit single-cell action potentials in vivo. In this work we used different stimulation parameters, such as waveforms, amplitudes and durations (Grosberg et al., 2017; Wagenaar, Pine, & Potter, 2004), using 5x9 µm² electrodes to target sub-cellular structures in single neurons. E-18 Wistar rat cortical neurons were stimulated at days-in-vitro 10, 15, 20 and 25 using randomized voltage and current stimulation modalities. Axon initial segments of individual neurons (Radivojevic et al., 2016) were targeted for stimulation, enabled by the HD-MEA device. We found that voltage biphasic anodic-cathodic waveforms were less efficient than biphasic cathodic-anodic waveforms in eliciting action potentials in a single neuron. Moreover, it was possible to detect action potentials directly at the cell soma, which ensured a reliable confirmation of successful neuron stimulation. Finally, HD-MEA technology enabled to elicit action potentials in single-neurons embedded in high-density cell cultures. The obtained results can be used to optimize in vivo single-cell targeting for stimulation and read-out. Close https://abstractsonline.com/pp8/#!/4649/presentation/24382 Close
	Bartram, Julian; Schroter, Manuel; Ronchi, Silvia; Emmenegger, Vishalini; Muller, Jan; Hierlemann, Andreas Mechanisms of homeostatic synaptic plasticity Conference Contribution 037.11 , Society for Neuroscience (SfN) Meeting San Diego, CA, USA, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Bartram2018, title = {Mechanisms of homeostatic synaptic plasticity}, author = {Julian Bartram and Manuel Schroter and Silvia Ronchi and Vishalini Emmenegger and Jan Muller and Andreas Hierlemann}, url = {https://www.abstractsonline.com/pp8/#!/4649/presentation/3968}, year = {2018}, date = {2018-11-03}, volume = {Contribution 037.11}, address = {San Diego, CA, USA}, organization = {Society for Neuroscience (SfN) Meeting}, abstract = {Homeostatic plasticity is a crucial set of mechanisms acting at typically slow temporal scales in order to stabilize neuronal spike rates. Despite the functional significance of such processes, revealing the precise induction mechanisms has proven to be difficult, as the roles of postsynaptic spiking and synaptic activity are still debated. For a clearer picture of the induction process to emerge, information about synaptic efficacies of multiple inputs needs to be combined with accurate information about spiking activities of the respective presynaptic cells and the postsynaptic cell during the induction of homeostatic plasticity. In this study, we were able to achieve such measurements by performing combined high-density microelectrode array (HD-MEA) and whole-cell patch-clamp recordings in cultures of primary cortical neurons. Homeostatic plasticity was induced by pharmacological alteration of global network spiking and synaptic transmission with TTX or CNQX. Monosynaptic connections between neurons - here with a focus on excitatory connections between pyramidal cells - were identified by correlating presynaptic spiking activity (HD-MEA recordings) with postsynaptic subthreshold responses (patch current-clamp recordings). Presynaptic spiking was spontaneously observed or could be induced via the stimulation capabilities of the HD-MEA system. This experimental approach enabled us to link changes in synaptic efficacy with the respective pre- and postsynaptic spike patterns, recorded during the induction phase, which sheds new light on the rules and mechanisms of homeostatic synaptic plasticity at excitatory synapses. Financial support through the ERC Advanced Grant 694829 “neuroXscales” is gratefully acknowledged.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close Homeostatic plasticity is a crucial set of mechanisms acting at typically slow temporal scales in order to stabilize neuronal spike rates. Despite the functional significance of such processes, revealing the precise induction mechanisms has proven to be difficult, as the roles of postsynaptic spiking and synaptic activity are still debated. For a clearer picture of the induction process to emerge, information about synaptic efficacies of multiple inputs needs to be combined with accurate information about spiking activities of the respective presynaptic cells and the postsynaptic cell during the induction of homeostatic plasticity. In this study, we were able to achieve such measurements by performing combined high-density microelectrode array (HD-MEA) and whole-cell patch-clamp recordings in cultures of primary cortical neurons. Homeostatic plasticity was induced by pharmacological alteration of global network spiking and synaptic transmission with TTX or CNQX. Monosynaptic connections between neurons - here with a focus on excitatory connections between pyramidal cells - were identified by correlating presynaptic spiking activity (HD-MEA recordings) with postsynaptic subthreshold responses (patch current-clamp recordings). Presynaptic spiking was spontaneously observed or could be induced via the stimulation capabilities of the HD-MEA system. This experimental approach enabled us to link changes in synaptic efficacy with the respective pre- and postsynaptic spike patterns, recorded during the induction phase, which sheds new light on the rules and mechanisms of homeostatic synaptic plasticity at excitatory synapses. Financial support through the ERC Advanced Grant 694829 “neuroXscales” is gratefully acknowledged. Close https://www.abstractsonline.com/pp8/#!/4649/presentation/3968 Close
	Yuan, Xinyue; Emmenegger, Vishalini; Obien, Marie Engelene J; Hierlemann, Andreas; Frey, Urs Dual-Mode Microelectrode Array Featuring 20k Electrodes and High SNR for Extracellular Recording of Neural Networks Conference paper 6065 , IEEE Biomedical Circuits and Systems Conference (BioCAS) Cleveland, Ohio, USA, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @conference{Yuan2018b, title = {Dual-Mode Microelectrode Array Featuring 20k Electrodes and High SNR for Extracellular Recording of Neural Networks}, author = {Xinyue Yuan and Vishalini Emmenegger and Marie Engelene J. Obien and Andreas Hierlemann and Urs Frey}, url = {https://www.epapers.org/biocas2018/ESR/paper_details.php?PHPSESSID=ok076vdjtkiu7kett65d8hk0g0&paper_id=6056}, year = {2018}, date = {2018-10-17}, volume = {paper 6065}, address = {Cleveland, Ohio, USA}, organization = {IEEE Biomedical Circuits and Systems Conference (BioCAS)}, abstract = {In recent electrophysiological studies, CMOS-based high-density microelectrode arrays (HD-MEA) have been widely used for studies of both in-vitro and in-vivo neuronal signals and network behavior. Yet, an open issue in MEA design concerns the tradeoff between signal-to-noise ratio (SNR) and number of readout channels. Here we present a new HD-MEA design in 0.18 μm CMOS technology, consisting of 19,584 electrodes at a pitch of 18.0 μm. By combing two readout structures,namely active-pixel-sensor (APS) and switch-matrix (SM) on a single chip, the dual-mode HD-MEA is capable of recording simultaneously from the entire array and achieving high signal-to-noise-ratio recordings on a subset of electrodes. The APS readout circuits feature a noise level of 10.9 μVrms for the action potential band (300 Hz - 5 kHz), while the noise level for the switch-matrix readout is 3.1 μVrms. }, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {conference} } Close In recent electrophysiological studies, CMOS-based high-density microelectrode arrays (HD-MEA) have been widely used for studies of both in-vitro and in-vivo neuronal signals and network behavior. Yet, an open issue in MEA design concerns the tradeoff between signal-to-noise ratio (SNR) and number of readout channels. Here we present a new HD-MEA design in 0.18 μm CMOS technology, consisting of 19,584 electrodes at a pitch of 18.0 μm. By combing two readout structures,namely active-pixel-sensor (APS) and switch-matrix (SM) on a single chip, the dual-mode HD-MEA is capable of recording simultaneously from the entire array and achieving high signal-to-noise-ratio recordings on a subset of electrodes. The APS readout circuits feature a noise level of 10.9 μVrms for the action potential band (300 Hz - 5 kHz), while the noise level for the switch-matrix readout is 3.1 μVrms. Close https://www.epapers.org/biocas2018/ESR/paper_details.php?PHPSESSID=ok076vdjtkiu7[...] Close
	Lewandowska, Marta K; Bogatikov, Evgenii; Hierlemann, Andreas; Punga, Anna Rostedt Long-Term High-Density Extracellular Recordings Enable Studies of Muscle Cell Physiology Journal Article Frontiers in Physiology, 9 , 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Muscle @article{Lewandowska2018cb, title = {Long-Term High-Density Extracellular Recordings Enable Studies of Muscle Cell Physiology }, author = {Marta K. Lewandowska and Evgenii Bogatikov and Andreas Hierlemann and Anna Rostedt Punga}, url = {https://www.frontiersin.org/article/10.3389/fphys.2018.01424 }, doi = {10.3389/fphys.2018.01424}, year = {2018}, date = {2018-10-09}, journal = {Frontiers in Physiology}, volume = {9}, abstract = {Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high-spatial-resolution measurement techniques and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. Here, we present a method, which allows tracking the development of primary skeletal muscle cells from myoblasts into mature contracting myotubes over more than 2 months. In contrast to most previous studies, the myotubes did not detach from the surface but instead formed functional networks between the myotubes, whose electrical signals were observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myotubes on a chip that contained an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enabled study of skeletal muscle development and kinetics, modes of spiking and spatio-temporal relationships between muscles. The developed system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models. }, keywords = {ETH-CMOS-MEA, Muscle}, pubstate = {published}, tppubtype = {article} } Close Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high-spatial-resolution measurement techniques and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. Here, we present a method, which allows tracking the development of primary skeletal muscle cells from myoblasts into mature contracting myotubes over more than 2 months. In contrast to most previous studies, the myotubes did not detach from the surface but instead formed functional networks between the myotubes, whose electrical signals were observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myotubes on a chip that contained an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm2. Our ability to track extracellular action potentials at subcellular resolution enabled study of skeletal muscle development and kinetics, modes of spiking and spatio-temporal relationships between muscles. The developed system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models. Close https://www.frontiersin.org/article/10.3389/fphys.2018.01424 doi:10.3389/fphys.2018.01424 Close
	Diggelmann, Roland; Fiscella, Michele; Hierlemann, Andreas; Franke, Felix Automatic Spike Sorting Algorithm for High-Density Microelectrode Arrays Journal Article Journal of Neurophysiology, 120 (4), 2018. Abstract \| Links \| BibTeX \| Tags: MEA Technology @article{Diggelmann2018, title = {Automatic Spike Sorting Algorithm for High-Density Microelectrode Arrays}, author = {Roland Diggelmann and Michele Fiscella and Andreas Hierlemann and Felix Franke}, url = {https://www.physiology.org/doi/pdf/10.1152/jn.00803.2017}, doi = {10.1152/jn.00803.2017}, year = {2018}, date = {2018-09-12}, journal = {Journal of Neurophysiology}, volume = {120}, number = {4}, abstract = {High-density microelectrode arrays (HD-MEAs) can be used to record extracellular action potentials from hundreds to thousands of neurons simultaneously. Efficient spike-sorters have to be developed to cope with such large data volumes. Most existing spike sorting methods for single electrodes or small multi-electrodes, however, suffer from the "curse of dimensionality", and cannot be directly applied to recordings with hundreds of electrodes. This holds particularly true for the standard reference spike sorting algorithm, principal-component-analysis-based feature extraction, followed by k-means or expectation maximization clustering, against which most spike-sorters are evaluated. We present a spike sorting algorithm that circumvents the dimensionality problem by sorting local groups of electrodes independently using classical spike sorting approaches. It is scalable to any number of recording electrodes and well suited for parallel computing. The combination of data pre-whitening before the principal-component-analysis-based extraction and a parameter-free clustering algorithm obviated the need for parameter adjustments. We evaluated its performance using surrogate data in which we systematically varied spike amplitudes and spike rates and which were generated by inserting template spikes into the voltage traces of real recordings. In a direct comparison, our algorithm could compete with existing state-of-the-art spike sorters in terms of sensitivity and precision, while parameter adjustment or manual cluster curation were not required.}, keywords = {MEA Technology}, pubstate = {published}, tppubtype = {article} } Close High-density microelectrode arrays (HD-MEAs) can be used to record extracellular action potentials from hundreds to thousands of neurons simultaneously. Efficient spike-sorters have to be developed to cope with such large data volumes. Most existing spike sorting methods for single electrodes or small multi-electrodes, however, suffer from the "curse of dimensionality", and cannot be directly applied to recordings with hundreds of electrodes. This holds particularly true for the standard reference spike sorting algorithm, principal-component-analysis-based feature extraction, followed by k-means or expectation maximization clustering, against which most spike-sorters are evaluated. We present a spike sorting algorithm that circumvents the dimensionality problem by sorting local groups of electrodes independently using classical spike sorting approaches. It is scalable to any number of recording electrodes and well suited for parallel computing. The combination of data pre-whitening before the principal-component-analysis-based extraction and a parameter-free clustering algorithm obviated the need for parameter adjustments. We evaluated its performance using surrogate data in which we systematically varied spike amplitudes and spike rates and which were generated by inserting template spikes into the voltage traces of real recordings. In a direct comparison, our algorithm could compete with existing state-of-the-art spike sorters in terms of sensitivity and precision, while parameter adjustment or manual cluster curation were not required. Close https://www.physiology.org/doi/pdf/10.1152/jn.00803.2017 doi:10.1152/jn.00803.2017 Close
	Ronchi, Silvia; Fiscella, Michele; Muller, Jan; Viswam, Vijay; Frey, Urs; Hierlemann, Andreas Single-cell electrical stimulation with CMOS-based high-density microelectrode arrays Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @conference{Ronchi2018b, title = {Single-cell electrical stimulation with CMOS-based high-density microelectrode arrays}, author = {Silvia Ronchi and Michele Fiscella and Jan Muller and Vijay Viswam and Urs Frey and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00086/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00086}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {The main goal of this work was to explore electrical stimulation parameters that reproducibly and precisely elicit action potentials in single neurons (Wagenaar et al. 2004). We compared voltage and current modalities’ and their efficacy in activating single neurons; we also studied the related stimulation artifacts. For our studies, we used a CMOS-based MEA featuring 26400 electrodes at 17.5 µm pitch (Ballini et al. 2014). }, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {conference} } Close The main goal of this work was to explore electrical stimulation parameters that reproducibly and precisely elicit action potentials in single neurons (Wagenaar et al. 2004). We compared voltage and current modalities’ and their efficacy in activating single neurons; we also studied the related stimulation artifacts. For our studies, we used a CMOS-based MEA featuring 26400 electrodes at 17.5 µm pitch (Ballini et al. 2014). Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00086/event_abstract doi:10.3389/conf.fncel.2018.38.00086 Close
	Obien, Marie Engelene J; Zorzi, Giulio; Fiscella, Michele; Leary, Noelle; Hierlemann, Andreas Comparison of axonal-conduction velocity in developing primary cells and human iPSC-derived neurons Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne @conference{Obien2018, title = {Comparison of axonal-conduction velocity in developing primary cells and human iPSC-derived neurons}, author = {Marie Engelene J. Obien and Giulio Zorzi and Michele Fiscella and Noelle Leary and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00095/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00095}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Neurons communicate through action potentials propagating along axons. In developing cell cultures, axonal arbor outgrowth indicates the formation of synaptic connections between neurons, which form networks. As axons regulate the transfer of information, we hypothesize that axonal conduction characteristics, e.g., axonal action potential amplitude and propagation velocity, may be indicative of the maturation state of cells and the strength of interneuronal connections.}, keywords = {ETH-CMOS-MEA, MaxOne}, pubstate = {published}, tppubtype = {conference} } Close Neurons communicate through action potentials propagating along axons. In developing cell cultures, axonal arbor outgrowth indicates the formation of synaptic connections between neurons, which form networks. As axons regulate the transfer of information, we hypothesize that axonal conduction characteristics, e.g., axonal action potential amplitude and propagation velocity, may be indicative of the maturation state of cells and the strength of interneuronal connections. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00095/event_abstract doi:10.3389/conf.fncel.2018.38.00095 Close
	Zorzi, Giulio; Obien, Marie Engelene J; Fiscella, Michele; Leary, Noelle; Hierlemann, Andreas Automatic extraction of axonal arbor morphology applied to h-iPSC-derived neurons Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne @conference{Zorzi2018, title = {Automatic extraction of axonal arbor morphology applied to h-iPSC-derived neurons}, author = {Giulio Zorzi and Marie Engelene J. Obien and Michele Fiscella and Noelle Leary and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00049/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00049}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Neurons derived from human induced pluripotent stem cells (h-iPSCs) offer tremendous opportunities to investigate the mechanisms involved in brain function and to model neurodegenerative diseases. Analyzing the behavior of h-iPSC-derived neurons that represent the phenotypes of human neurological disorders paves the way for the development of physiologically-relevant models and assays for drug discovery. In this framework, we utilize a CMOS-based high-density microelectrode array (HD-MEA, MaxWell Biosystems) to investigate h-iPSC neurons at sub-cellular resolution. Recording extracellular action potentials (EAPs or spikes) of cultured neurons through microelectrode arrays (MEAs) is a well-established technique for extracting valuable features of neuronal function and network connectivity (Obien et al., Frontiers in Neuroscience, 2015). }, keywords = {ETH-CMOS-MEA, MaxOne}, pubstate = {published}, tppubtype = {conference} } Close Neurons derived from human induced pluripotent stem cells (h-iPSCs) offer tremendous opportunities to investigate the mechanisms involved in brain function and to model neurodegenerative diseases. Analyzing the behavior of h-iPSC-derived neurons that represent the phenotypes of human neurological disorders paves the way for the development of physiologically-relevant models and assays for drug discovery. In this framework, we utilize a CMOS-based high-density microelectrode array (HD-MEA, MaxWell Biosystems) to investigate h-iPSC neurons at sub-cellular resolution. Recording extracellular action potentials (EAPs or spikes) of cultured neurons through microelectrode arrays (MEAs) is a well-established technique for extracting valuable features of neuronal function and network connectivity (Obien et al., Frontiers in Neuroscience, 2015). Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00049/event_abstract doi:10.3389/conf.fncel.2018.38.00049 Close
	Bounik, Raziyeh; Gusmaroli, Massimiliano; Viswam, Vijay; Modena, Mario M; Hierlemann, Andreas COMSOL modeling of an integrated impedance sensor in a hanging-drop platform Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Microtissue @conference{Bounik2018, title = {COMSOL modeling of an integrated impedance sensor in a hanging-drop platform}, author = {Raziyeh Bounik and Massimiliano Gusmaroli and Vijay Viswam and Mario M. Modena and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00083/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00083}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Traditional dish-based, two-dimensional cell cultures have limited prediction capability for drug testing, whereas three-dimensional spherical microtissues (spheroids) and organoids much more accurately replicate physiological conditions of cells in the respective tissue [1,2]. Such spheroids can be formed and cultured in microphysiological multi-tissue formats by using the hanging-drop technology as depicted in Fig. 1 [3]. Like most other microfluidic platforms, the hanging-drop platform still requires a microscope for visual inspection and considerable time for doing off-line measurements, as the spheroids/media have to be harvested from the microfluidic device for labeling and chemical analysis. It would be beneficial to have an integrated on-line multi-functional sensor as an additional readout, located directly at the tissue sites in the hanging-drop platform, so that measurements can be performed in situ and without harvesting medium or the tissue and without interrupting the overall culturing process. }, keywords = {ETH-CMOS-MEA, Microtissue}, pubstate = {published}, tppubtype = {conference} } Close Traditional dish-based, two-dimensional cell cultures have limited prediction capability for drug testing, whereas three-dimensional spherical microtissues (spheroids) and organoids much more accurately replicate physiological conditions of cells in the respective tissue [1,2]. Such spheroids can be formed and cultured in microphysiological multi-tissue formats by using the hanging-drop technology as depicted in Fig. 1 [3]. Like most other microfluidic platforms, the hanging-drop platform still requires a microscope for visual inspection and considerable time for doing off-line measurements, as the spheroids/media have to be harvested from the microfluidic device for labeling and chemical analysis. It would be beneficial to have an integrated on-line multi-functional sensor as an additional readout, located directly at the tissue sites in the hanging-drop platform, so that measurements can be performed in situ and without harvesting medium or the tissue and without interrupting the overall culturing process. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00083/event_abstract doi:10.3389/conf.fncel.2018.38.00083 Close
	Yuan, Xinyue; Hierlemann, Andreas; Frey, Urs Dual-mode Microelectrode Array with 20k-electrodes and High SNR for High-Throughput Extracellular Recording and Stimulation Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Stimulation @conference{Yuan2018, title = {Dual-mode Microelectrode Array with 20k-electrodes and High SNR for High-Throughput Extracellular Recording and Stimulation}, author = {Xinyue Yuan and Andreas Hierlemann and Urs Frey}, url = {https://https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389/conf.fncel.2018.38.00088&eid=5473&sname=MEA_Meeting_2018_%7C_11th_International_Meeting_on_Substrate_Integrated_Microelectrode_Arrays}, doi = {10.3389/conf.fncel.2018.38.00088}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Recording and analysis of neuronal signals can provide much insight into how neurons process information and communicate with each other. Recent advancements of microelectrode-array (MEA) technology provide unprecedented means to study neuronal signals and network behavior in in vitro and in vivo applications [1], [2]. The trade-off between noise performance, power consumption and electrode density, however, remains a major challenge in MEA design. To balance this tradeoff, we designed a Dual-mode (DM) MEA that combines two major types of readout schemes, i.e., the active-pixel-sensor (APS) and switch-matrix (SM) schemes, in order to achieve high electrode density and high signal-to-noise ratio (SNR) at the same time. Based on a previous prototype [3], the new DM-MEA has shown to be a useful tool for in-vitro neuroscience studies, especially for network studies}, keywords = {ETH-CMOS-MEA, Stimulation}, pubstate = {published}, tppubtype = {conference} } Close Recording and analysis of neuronal signals can provide much insight into how neurons process information and communicate with each other. Recent advancements of microelectrode-array (MEA) technology provide unprecedented means to study neuronal signals and network behavior in in vitro and in vivo applications [1], [2]. The trade-off between noise performance, power consumption and electrode density, however, remains a major challenge in MEA design. To balance this tradeoff, we designed a Dual-mode (DM) MEA that combines two major types of readout schemes, i.e., the active-pixel-sensor (APS) and switch-matrix (SM) schemes, in order to achieve high electrode density and high signal-to-noise ratio (SNR) at the same time. Based on a previous prototype [3], the new DM-MEA has shown to be a useful tool for in-vitro neuroscience studies, especially for network studies Close https://https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.33[...] doi:10.3389/conf.fncel.2018.38.00088 Close
	Fiscella, Michele; Leary, Noelle; Ronchi, Silvia; Hierlemann, Andreas Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC @conference{Fiscella2018c, title = {Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays}, author = {Michele Fiscella and Noelle Leary and Silvia Ronchi and Andreas Hierlemann}, url = {https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389/conf.fncel.2018.38.00014&eid=5473&sname=MEA_Meeting_2018_%7C_11th_International_Meeting_on_Substrate_Integrated_Microelectrode_Arrays}, doi = {10.3389/conf.fncel.2018.38.00014}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recording sessions compared to neural cultures without astrocytes. We compared velocities of action potential propagation along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than, for example, in rat primary cortical neurons (Bakkum et. al, Nature Communications, 2013). Furthermore, we found different axonal action-potential-velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-typecell line. Finally, we were able to precisely and reproducibly evoke action potentials in individual single human IPSC-derived neurons through subcellular-resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing.}, keywords = {HD-MEA, IPSC}, pubstate = {published}, tppubtype = {conference} } Close High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co-cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recording sessions compared to neural cultures without astrocytes. We compared velocities of action potential propagation along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease-model neurons, axonal action potential propagation velocities were lower than, for example, in rat primary cortical neurons (Bakkum et. al, Nature Communications, 2013). Furthermore, we found different axonal action-potential-velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-typecell line. Finally, we were able to precisely and reproducibly evoke action potentials in individual single human IPSC-derived neurons through subcellular-resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing. Close https://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389/conf.[...] doi:10.3389/conf.fncel.2018.38.00014 Close
	Urwyler, Cedar; Bounik, Raziyeh; Viswam, Vijay; Hierlemann, Andreas Electrical impedance tomography on high-density microelectrode arrays Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Urwyler2018, title = {Electrical impedance tomography on high-density microelectrode arrays}, author = {Cedar Urwyler and Raziyeh Bounik and Vijay Viswam and Andreas Hierlemann }, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00084/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00084}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Electrical impedance tomography (EIT) is a non-invasive, label-free imaging technique that enables to reconstruct the conductivity distribution in a body from a series of impedance measurements. Impedance measurements can be used to determine the position, morphology, and growth of cells or tissues, as well as pathological signs, e.g., precancerous tissue conditions (Gersing 1999). The newest high-density microelectrode array (MEA) system developed in our group features 59,760 integrated electrodes (Dragas et al. 2017). The chip features a variety of electrophysiological functions: Action-potential recording (2048 channels), cyclic voltammetry (28 channels), local-field-potential recording (32 channels) and extracellular stimulation (16 channels) [Fig 1A]. The chip can also measure impedance through 32 channels, which enables EIT measurements. We were able to establish a proof of concept for EIT (Viswam et al. 2017). The current goal of this project is to develop an impedance measurement protocol and an appropriate reconstruction algorithm that allow for single-cell-resolution impedance imaging.}, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close Electrical impedance tomography (EIT) is a non-invasive, label-free imaging technique that enables to reconstruct the conductivity distribution in a body from a series of impedance measurements. Impedance measurements can be used to determine the position, morphology, and growth of cells or tissues, as well as pathological signs, e.g., precancerous tissue conditions (Gersing 1999). The newest high-density microelectrode array (MEA) system developed in our group features 59,760 integrated electrodes (Dragas et al. 2017). The chip features a variety of electrophysiological functions: Action-potential recording (2048 channels), cyclic voltammetry (28 channels), local-field-potential recording (32 channels) and extracellular stimulation (16 channels) [Fig 1A]. The chip can also measure impedance through 32 channels, which enables EIT measurements. We were able to establish a proof of concept for EIT (Viswam et al. 2017). The current goal of this project is to develop an impedance measurement protocol and an appropriate reconstruction algorithm that allow for single-cell-resolution impedance imaging. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00084/event_abstract doi:10.3389/conf.fncel.2018.38.00084 Close
	Schroter, Manuel; Girr, Monika; Boos, Julia Alicia; Renner, Magdalena; Gazorpak, Mahshid; Gong, Wei; Bartram, Julian; Muller, Jan; Hierlemann, Andreas Mapping neuronal network dynamics in developing cerebral organoids Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks, Organoids @conference{Schroter2018, title = {Mapping neuronal network dynamics in developing cerebral organoids}, author = {Manuel Schroter and Monika Girr and Julia Alicia Boos and Magdalena Renner and Mahshid Gazorpak and Wei Gong and Julian Bartram and Jan Muller and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00066/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00066}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Cerebral organoids represent an attractive, novel model system to study early brain development in vitro (Di Lullo and Kriegstein, 2017). Although recent evidence shows that cerebral organoids do recapitulate fundamental milestones of early brain morphogenesis (Lancaster and Knoblich, 2014), the emergence and functionality of brain-organoid neuronal connectivity has not been studied systematically yet. In this study, we apply high-density micro-electrode arrays (MEAs) to record from developing mouse cerebral organoids and characterize their spontaneous neuronal activity. Results provide first evidence on the potential of MEAs as a platform to study the role of spontaneous neuronal activity during brain organoid development and formation of functional microcircuits. }, keywords = {Neuronal Networks, Organoids}, pubstate = {published}, tppubtype = {conference} } Close Cerebral organoids represent an attractive, novel model system to study early brain development in vitro (Di Lullo and Kriegstein, 2017). Although recent evidence shows that cerebral organoids do recapitulate fundamental milestones of early brain morphogenesis (Lancaster and Knoblich, 2014), the emergence and functionality of brain-organoid neuronal connectivity has not been studied systematically yet. In this study, we apply high-density micro-electrode arrays (MEAs) to record from developing mouse cerebral organoids and characterize their spontaneous neuronal activity. Results provide first evidence on the potential of MEAs as a platform to study the role of spontaneous neuronal activity during brain organoid development and formation of functional microcircuits. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00066/event_abstract doi:10.3389/conf.fncel.2018.38.00066 Close
	Bartram, Julian; Schroter, Manuel; Ronchi, Silvia; Emmenegger, Vishalini; Muller, Jan; Hierlemann, Andreas Probing synaptic connectivity and function using high-density microelectrode arrays and whole-cell patch-clamp recordings Conference 11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting) Reutlingen, Germany, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA @conference{Bartram2018b, title = {Probing synaptic connectivity and function using high-density microelectrode arrays and whole-cell patch-clamp recordings}, author = {Julian Bartram and Manuel Schroter and Silvia Ronchi and Vishalini Emmenegger and Jan Muller and Andreas Hierlemann}, url = {https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00085/5473/MEA_Meeting_2018_%7C_11th_International_Meeting_on_Substrate_Integrated_Microelectrode_Arrays/all_events/event_abstract}, doi = {10.3389/conf.fncel.2018.38.00085}, year = {2018}, date = {2018-07-04}, address = {Reutlingen, Germany}, organization = {11th International Meeting on Substrate Integrated Microelectrode Arrays (MEA Meeting)}, abstract = {Synaptic efficacy and synapse number of monosynaptic connections between neurons are often regulated by the spiking activity of the respective pre- and postsynaptic cell. Progress towards a better understanding of the rules and mechanisms that underlie such modifications has been limited due to the difficulties associated with simultaneously studying plasticity at multiple synaptic inputs. Here, we provide a solution to this problem by combining cutting-edge high-density microelectrode array (HD-MEA) technology with the patch-clamp technique. While the latter allows for accurate measurement of postsynaptic currents or potentials, evoked by individual synaptic activation, the HD-MEA technology provides large-scale information about unit activity and allows for selective stimulation of neurons, including multiple presynaptic cells. The proposed approach has been applied to comprehensively examine forms of homeostatic plasticity – a collection of crucial processes acting at different temporal scales in order to stabilize neuronal firing rates. We report on a characterization of classic synaptic scaling operating in mature cortical networks and propose a novel model for the study of homeostatic plasticity during natural network states. }, keywords = {HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close Synaptic efficacy and synapse number of monosynaptic connections between neurons are often regulated by the spiking activity of the respective pre- and postsynaptic cell. Progress towards a better understanding of the rules and mechanisms that underlie such modifications has been limited due to the difficulties associated with simultaneously studying plasticity at multiple synaptic inputs. Here, we provide a solution to this problem by combining cutting-edge high-density microelectrode array (HD-MEA) technology with the patch-clamp technique. While the latter allows for accurate measurement of postsynaptic currents or potentials, evoked by individual synaptic activation, the HD-MEA technology provides large-scale information about unit activity and allows for selective stimulation of neurons, including multiple presynaptic cells. The proposed approach has been applied to comprehensively examine forms of homeostatic plasticity – a collection of crucial processes acting at different temporal scales in order to stabilize neuronal firing rates. We report on a characterization of classic synaptic scaling operating in mature cortical networks and propose a novel model for the study of homeostatic plasticity during natural network states. Close https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00085/5473/MEA_Meeting_20[...] doi:10.3389/conf.fncel.2018.38.00085 Close
	da Drinnenberg Antonia; Franke, Felix; Morikawa Rei Jüttner; Hillier Daniel; Hantz Peter; Hierlemann Andreas; Azeredo Silveira Rava; Roska Botond K; How diverse retinal functions arise from feedback at the first visual synapse Journal Article Neuron, 99 (1), pp. 117-134, 2018. Abstract \| Links \| BibTeX \| Tags: Retina @article{Drinnenberg2018, title = {How diverse retinal functions arise from feedback at the first visual synapse}, author = {Drinnenberg, Antonia; Franke, Felix; Morikawa, Rei K; Jüttner; Hillier, Daniel; Hantz, Peter; Hierlemann, Andreas; Azeredo da Silveira, Rava; Roska, Botond}, url = {https://www.cell.com/neuron/fulltext/S0896-6273(18)30469-0}, doi = {10.1016/j.neuron.2018.06.001}, year = {2018}, date = {2018-06-21}, journal = {Neuron}, volume = {99}, number = {1}, pages = {117-134}, abstract = {Many brain regions contain local interneurons of distinct types. How does an interneuron type contribute to the input-output transformations of a given brain region? We addressed this question in the mouse retina by chemogenetically perturbing horizontal cells, an interneuron type providing feedback at the first visual synapse, while monitoring the light-driven spiking activity in thousands of ganglion cells, the retinal output neurons. We uncovered six reversible perturbation-induced effects in the response dynamics and response range of ganglion cells. The effects were enhancing or suppressive, occurred in different response epochs, and depended on the ganglion cell type. A computational model of the retinal circuitry reproduced all perturbation-induced effects and led us to assign specific functions to horizontal cells with respect to different ganglion cell types. Our combined experimental and theoretical work reveals how a single interneuron type can differentially shape the dynamical properties of distinct output channels of a brain region.}, keywords = {Retina}, pubstate = {published}, tppubtype = {article} } Close Many brain regions contain local interneurons of distinct types. How does an interneuron type contribute to the input-output transformations of a given brain region? We addressed this question in the mouse retina by chemogenetically perturbing horizontal cells, an interneuron type providing feedback at the first visual synapse, while monitoring the light-driven spiking activity in thousands of ganglion cells, the retinal output neurons. We uncovered six reversible perturbation-induced effects in the response dynamics and response range of ganglion cells. The effects were enhancing or suppressive, occurred in different response epochs, and depended on the ganglion cell type. A computational model of the retinal circuitry reproduced all perturbation-induced effects and led us to assign specific functions to horizontal cells with respect to different ganglion cell types. Our combined experimental and theoretical work reveals how a single interneuron type can differentially shape the dynamical properties of distinct output channels of a brain region. Close https://www.cell.com/neuron/fulltext/S0896-6273(18)30469-0 doi:10.1016/j.neuron.2018.06.001 Close
	Fiscella, Michele; Leary, Noelle; Ronchi, Silvia; Hierlemann, Andreas Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays Conference W-2151 , International Society for Stem Cell Research (ISSCR) Annual Meeting Melbourne, Australia, 2018. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC @conference{Fiscella2018b, title = {Electrophysiological phenotype characterization of human iPSC-derived dopaminergic neuronal lines by means of high-resolution microelelectrode arrays}, author = {Michele Fiscella and Noelle Leary and Silvia Ronchi and Andreas Hierlemann }, url = {http://www.isscr.org/docs/default-source/2018-melbourne-ann-mtng/66670-isscr-abstracts_with-links.pdf?sfvrsn=4&utm_source=ISSCR-Informz&utm_medium=email&utm_campaign=default}, year = {2018}, date = {2018-06-20}, volume = {W-2151}, address = {Melbourne, Australia}, organization = {International Society for Stem Cell Research (ISSCR) Annual Meeting}, abstract = {High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co- cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons. Furthermore, we found different axonal action potential velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular- resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing.}, keywords = {HD-MEA, IPSC}, pubstate = {published}, tppubtype = {conference} } Close High-resolution-microelectrode-array (MEA) technology enables to study neuronal dynamics at different scales, ranging from axonal physiology to network connectivity (Müller et. al, Lab on a Chip, 2015). We have used this MEA technology to characterize and compare the electrical phenotypes of commercially available human dopaminergic neurons (iCell DopaNeurons, MyCell DopaNeurons A53T α-synuclein, Cellular Dynamics International, Madison, WI, US). Furthermore, we have studied the effect of human astrocytes (iCell Astrocytes, Cellular Dynamics International, Madison, WI, US) on neural culture development. Astrocyte/neuron co- cultures showed higher signal amplitudes and higher firing rates than neural cultures without astrocytes. Adding astrocytes to neural cultures changed the whole culture morphology by promoting cell clustering. Interestingly, astrocyte/neuron co-cultures showed a lower sample-to-sample variability across multiple MEA recordings compared to neural cultures without astrocytes. We compared action potential propagation velocities along axons between dopaminergic A53T α-synuclein neurons and the wild-type isogenic control cell line. We found that in both, wild-type and disease model neurons, axonal action potential propagation velocities were lower than in rat primary cortical neurons. Furthermore, we found different axonal action potential velocity development profiles of A53T α-synuclein dopaminergic neurons and the wild-type counterpart. Finally, we were able to precisely evoke action potentials in individual single human neurons by subcellular- resolution electrical stimulation. High-resolution MEA systems enable to access novel electrophysiological parameters of iPSC-derived neurons, which can be potentially used as biomarkers for phenotype screening and drug testing. Close http://www.isscr.org/docs/default-source/2018-melbourne-ann-mtng/66670-isscr-abs[...] Close
	Bakkum Douglas J; Radivojevic, Milos; Obien Marie Engelene; Jaeckel David; Frey Urs; Takahashi Hirokazu; Hierlemann Andreas The axon initial segment drives the neuron's extracellular action potential Journal Article bioRxiv, pp. 1-30, 2018. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Bakkum2018, title = {The axon initial segment drives the neuron's extracellular action potential}, author = {Bakkum, Douglas J; Radivojevic, Milos; Obien, Marie Engelene; Jaeckel, David; Frey, Urs; Takahashi, Hirokazu; Hierlemann, Andreas }, url = {https://www.biorxiv.org/content/early/2018/02/16/266734}, doi = {10.1101/266734 }, year = {2018}, date = {2018-02-16}, journal = {bioRxiv}, pages = {1-30}, abstract = {Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology. Close https://www.biorxiv.org/content/early/2018/02/16/266734 doi:10.1101/266734 Close
2017
	Viswam, Vijay; Obien, Marie Engelene J; Frey, Urs; Franke, Felix; Hierlemann, Andreas Acquisition of Bioelectrical Signals with Small Electrodes Conference 2017 IEEE Biomedical Circuits and Systems Conference (BioCAS) Turin, Italy, 2017. Abstract \| Links \| BibTeX \| Tags: Electrodes @conference{Viswam2017, title = {Acquisition of Bioelectrical Signals with Small Electrodes}, author = {Vijay Viswam and Marie Engelene J. Obien and Urs Frey and Felix Franke and Andreas Hierlemann}, url = {https://ieeexplore.ieee.org/document/8325216}, doi = {10.1109/BIOCAS.2017.8325216}, year = {2017}, date = {2017-10-19}, address = {Turin, Italy}, organization = {2017 IEEE Biomedical Circuits and Systems Conference (BioCAS)}, abstract = {Although the mechanisms of recording bioelectrical signals from different types of electrogenic cells (neurons, cardiac cells etc.) by means of planar metal electrodes have been extensively studied, the recording characteristics and conditions for very small electrode sizes are not yet established. Here, we present a combined experimental and computational approach to elucidate, how the electrode size influences the recorded signals, and how inherent properties of the electrode, such as impedance, noise, and transmission characteristics shape the signal. We demonstrate that good quality recordings can be achieved with electrode diameters of less than 10 μm, provided that impedance reduction measures have been implemented and provided that a set of requirements for signal amplification has been met.}, keywords = {Electrodes}, pubstate = {published}, tppubtype = {conference} } Close Although the mechanisms of recording bioelectrical signals from different types of electrogenic cells (neurons, cardiac cells etc.) by means of planar metal electrodes have been extensively studied, the recording characteristics and conditions for very small electrode sizes are not yet established. Here, we present a combined experimental and computational approach to elucidate, how the electrode size influences the recorded signals, and how inherent properties of the electrode, such as impedance, noise, and transmission characteristics shape the signal. We demonstrate that good quality recordings can be achieved with electrode diameters of less than 10 μm, provided that impedance reduction measures have been implemented and provided that a set of requirements for signal amplification has been met. Close https://ieeexplore.ieee.org/document/8325216 doi:10.1109/BIOCAS.2017.8325216 Close
	Radivojevic, Milos; Franke, Felix; Altermatt, Michael; Müller, Jan; Hierlemann, Andreas; Bakkum, Douglas J Tracking individual action potentials throughout mammalian axonal arbors Journal Article eLife, 6 , pp. 1-23, 2017, ISSN: 2050-084X. Abstract \| Links \| BibTeX \| Tags: Data Analysis, ETH-CMOS-MEA, Neuronal Networks, Stimulation @article{Radivojevic2017, title = {Tracking individual action potentials throughout mammalian axonal arbors}, author = {Milos Radivojevic and Felix Franke and Michael Altermatt and Jan Müller and Andreas Hierlemann and Douglas J Bakkum}, url = {https://elifesciences.org/articles/30198}, doi = {10.7554/eLife.30198}, issn = {2050-084X}, year = {2017}, date = {2017-10-09}, journal = {eLife}, volume = {6}, pages = {1-23}, abstract = {Axons are neuronal processes specialized for conduction of action potentials (APs). The timing and temporal precision of APs when they reach each of the synapses are fundamentally important for information processing in the brain. Due to small diameters of axons, direct recording of single AP transmission is challenging. Consequently, most knowledge about axonal conductance derives from modeling studies or indirect measurements. We demonstrate a method to noninvasively and directly record individual APs propagating along millimeter-length axonal arbors in cortical cultures with hundreds of microelectrodes at microsecond temporal resolution. We find that cortical axons conduct single APs with high temporal precision (~100 µs arrival time jitter per mm length) and reliability: in more than 8,000,000 recorded APs, we did not observe any conduction or branch-point failures. Upon high-frequency stimulation at 100 Hz, successive became slower, and their arrival time precision decreased by 20% and 12% for the 100th AP, respectively.}, keywords = {Data Analysis, ETH-CMOS-MEA, Neuronal Networks, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Axons are neuronal processes specialized for conduction of action potentials (APs). The timing and temporal precision of APs when they reach each of the synapses are fundamentally important for information processing in the brain. Due to small diameters of axons, direct recording of single AP transmission is challenging. Consequently, most knowledge about axonal conductance derives from modeling studies or indirect measurements. We demonstrate a method to noninvasively and directly record individual APs propagating along millimeter-length axonal arbors in cortical cultures with hundreds of microelectrodes at microsecond temporal resolution. We find that cortical axons conduct single APs with high temporal precision (~100 µs arrival time jitter per mm length) and reliability: in more than 8,000,000 recorded APs, we did not observe any conduction or branch-point failures. Upon high-frequency stimulation at 100 Hz, successive became slower, and their arrival time precision decreased by 20% and 12% for the 100th AP, respectively. Close https://elifesciences.org/articles/30198 doi:10.7554/eLife.30198 Close
	Tajima Satohiro; Mita, Takeshi; Bakkum Douglas Takahashi Hirokazu; Toyoizumi Taro J; Locally embedded presages of global network bursts Journal Article National Academy of Sciences, pp. 1-6, 2017, ISSN: 0027-8424. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks @article{Tajima2017, title = {Locally embedded presages of global network bursts}, author = {Tajima, Satohiro; Mita, Takeshi; Bakkum, Douglas J; Takahashi, Hirokazu; Toyoizumi, Taro}, editor = {Sejnowski, Terrence J}, url = {http://www.pnas.org/content/114/36/9517}, doi = {10.1073/pnas.1705981114 }, issn = {0027-8424}, year = {2017}, date = {2017-08-18}, journal = {National Academy of Sciences}, pages = {1-6}, abstract = {Spontaneous, synchronous bursting of neural population is a widely observed phenomenon in nervous networks, which is considered important for functions and dysfunctions of the brain. However, how the global synchrony across a large number of neurons emerges from an initially nonbursting network state is not fully understood. In this study, we develop a state-space reconstruction method combined with high-resolution recordings of cultured neurons. This method extracts deterministic signatures of upcoming global bursts in “local” dynamics of individual neurons during nonbursting periods. We find that local information within a single-cell time series can compare with or even outperform the global mean-field activity for predicting future global bursts. Moreover, the intercell variability in the burst predictability is found to reflect the network structure realized in the nonbursting periods. These findings suggest that deterministic local dynamics can predict seemingly stochastic global events in self-organized networks, implying the potential applications of the present methodology to detecting locally concentrated early warnings of spontaneous seizure occurrence in the brain.}, keywords = {Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Spontaneous, synchronous bursting of neural population is a widely observed phenomenon in nervous networks, which is considered important for functions and dysfunctions of the brain. However, how the global synchrony across a large number of neurons emerges from an initially nonbursting network state is not fully understood. In this study, we develop a state-space reconstruction method combined with high-resolution recordings of cultured neurons. This method extracts deterministic signatures of upcoming global bursts in “local” dynamics of individual neurons during nonbursting periods. We find that local information within a single-cell time series can compare with or even outperform the global mean-field activity for predicting future global bursts. Moreover, the intercell variability in the burst predictability is found to reflect the network structure realized in the nonbursting periods. These findings suggest that deterministic local dynamics can predict seemingly stochastic global events in self-organized networks, implying the potential applications of the present methodology to detecting locally concentrated early warnings of spontaneous seizure occurrence in the brain. Close http://www.pnas.org/content/114/36/9517 doi:10.1073/pnas.1705981114 Close
	Shein-Idelson, Mark; Pammer, Lorenz; Hemberger, Mike; Laurent, Gilles Large-scale mapping of cortical synaptic projections with extracellular electrode arrays Journal Article Nature Methods, 14 (9), pp. 882–889, 2017, ISSN: 1548-7091. Abstract \| Links \| BibTeX \| Tags: Brain Slice, MaxOne, Neuronal Networks @article{Shein-Idelson2017, title = {Large-scale mapping of cortical synaptic projections with extracellular electrode arrays}, author = {Mark Shein-Idelson and Lorenz Pammer and Mike Hemberger and Gilles Laurent}, url = {http://www.nature.com/doifinder/10.1038/nmeth.4393}, doi = {10.1038/nmeth.4393}, issn = {1548-7091}, year = {2017}, date = {2017-08-14}, journal = {Nature Methods}, volume = {14}, number = {9}, pages = {882--889}, abstract = {Understanding circuit computation in the nervous system requires sampling activity over large neural populations and maximizing the number of features that can be extracted. By combining planar arrays of extracellular electrodes with the three-layered cortex of turtles, we show that synaptic signals induced along individual axons as well as action potentials can be easily captured. Two types of information can be extracted from these signals, the neuronal subtype (inhibitory or excitatory)—whose identification is more reliable than with traditional measures such as action potential width—and a (partial) spatial map of functional axonal projections from individual neurons. Because our approach is algorithmic, it can be carried out in parallel on hundreds of simultaneously recorded neurons. Combining our approach with soma triangulation, we reveal an axonal projection bias among a population of pyramidal neurons in turtle cortex and confirm this bias through anatomical reconstructions.}, keywords = {Brain Slice, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Understanding circuit computation in the nervous system requires sampling activity over large neural populations and maximizing the number of features that can be extracted. By combining planar arrays of extracellular electrodes with the three-layered cortex of turtles, we show that synaptic signals induced along individual axons as well as action potentials can be easily captured. Two types of information can be extracted from these signals, the neuronal subtype (inhibitory or excitatory)—whose identification is more reliable than with traditional measures such as action potential width—and a (partial) spatial map of functional axonal projections from individual neurons. Because our approach is algorithmic, it can be carried out in parallel on hundreds of simultaneously recorded neurons. Combining our approach with soma triangulation, we reveal an axonal projection bias among a population of pyramidal neurons in turtle cortex and confirm this bias through anatomical reconstructions. Close http://www.nature.com/doifinder/10.1038/nmeth.4393 doi:10.1038/nmeth.4393 Close
	Obien, Marie Engelene J; Zorzi, Giulio; Hierlemann, Andreas Mapping neuron cluster development based on axonal action potential propagation Conference The 40th Annual Meeting of the Japan Neuroscience Society Chiba, Japan, 2017. BibTeX \| Tags: Action Potential, Neuronal Networks @conference{Obien2017, title = {Mapping neuron cluster development based on axonal action potential propagation}, author = {Marie Engelene J. Obien and Giulio Zorzi and Andreas Hierlemann}, year = {2017}, date = {2017-07-20}, address = {Chiba, Japan}, organization = {The 40th Annual Meeting of the Japan Neuroscience Society}, keywords = {Action Potential, Neuronal Networks}, pubstate = {published}, tppubtype = {conference} } Close
	Diggelmann, Roland; Fiscella, Michele; Hierlemann, Andreas; Franke, Felix Pre-whitening as a means to improve dimensionality reduction and simplify clustering in spike-sorters for multi-electrode recordings Conference 26th Annual Computational Neuroscience Meeting (CNS2017) Antwerp, Belgium , 2017. Abstract \| Links \| BibTeX \| Tags: Spike Sorting @conference{Diggelmann2017, title = {Pre-whitening as a means to improve dimensionality reduction and simplify clustering in spike-sorters for multi-electrode recordings}, author = {Roland Diggelmann and Michele Fiscella and Andreas Hierlemann and Felix Franke}, url = {https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0371-2}, year = {2017}, date = {2017-07-15}, address = {Antwerp, Belgium }, organization = {26th Annual Computational Neuroscience Meeting (CNS2017)}, abstract = {Spike sorting is the process to extract single neuronal activity from extracellular recordings. It makes use of the fact that spikes from a single neuron feature highly similar waveforms, whereas spikes from different neurons have different waveforms. Clustering algorithms are used to find groups of similar spikes that putatively originated from the same neuron. However, since spike waveforms especially in multi-electrode recordings can have a high dimensionality, their dimensionality needs to be reduced before clustering. Principal component analysis (PCA) is one of the most commonly employed dimensionality reduction methods for this purpose [1]. It reduces the dimensions to those where the variance of the data was highest, presumably those along which the waveforms of separate neurons differ most strongly, However, if the noise is not uniform in all dimensions, high variability can also mean high noise, which would render a dimension useless for discrimination. We, therefore, propose an additional pre-whitening step before PCA and discuss two beneficial effects on the subsequent clustering. We illustrate these effects by using spikes from retinal ganglion cells recorded with high-density multi-electrode arrays (HD-MEA).}, keywords = {Spike Sorting}, pubstate = {published}, tppubtype = {conference} } Close Spike sorting is the process to extract single neuronal activity from extracellular recordings. It makes use of the fact that spikes from a single neuron feature highly similar waveforms, whereas spikes from different neurons have different waveforms. Clustering algorithms are used to find groups of similar spikes that putatively originated from the same neuron. However, since spike waveforms especially in multi-electrode recordings can have a high dimensionality, their dimensionality needs to be reduced before clustering. Principal component analysis (PCA) is one of the most commonly employed dimensionality reduction methods for this purpose [1]. It reduces the dimensions to those where the variance of the data was highest, presumably those along which the waveforms of separate neurons differ most strongly, However, if the noise is not uniform in all dimensions, high variability can also mean high noise, which would render a dimension useless for discrimination. We, therefore, propose an additional pre-whitening step before PCA and discuss two beneficial effects on the subsequent clustering. We illustrate these effects by using spikes from retinal ganglion cells recorded with high-density multi-electrode arrays (HD-MEA). Close https://bmcneurosci.biomedcentral.com/articles/10.1186/s12868-017-0371-2 Close
	Viswam, Vijay; Bounik, Raziyeh; Shadmani, Amir; Dragas, Jelena; Obien, Marie Engelene J; Muller, Jan; Chen, Yihui; Hierlemann, Andreas High-density Mapping of Brain Slices Using a Large Multi-functional High-density CMOS Microelectrode Array System Conference 19th International Conference on Solid-State Sensors, Actuators and Microsystems (TRANSDUCERS) Kaohsiung, Taiwan, 2017, ISSN: 2167-0021. Abstract \| Links \| BibTeX \| Tags: Brain Slice, ETH-CMOS-MEA, HD-MEA @conference{Viswam2017b, title = {High-density Mapping of Brain Slices Using a Large Multi-functional High-density CMOS Microelectrode Array System}, author = {Vijay Viswam and Raziyeh Bounik and Amir Shadmani and Jelena Dragas and Marie Engelene J. Obien and Jan Muller and Yihui Chen and Andreas Hierlemann }, url = {https://ieeexplore.ieee.org/abstract/document/7994006}, doi = {10.1109/TRANSDUCERS.2017.7994006}, issn = {2167-0021}, year = {2017}, date = {2017-06-18}, pages = {135-138}, address = {Kaohsiung, Taiwan}, organization = {19th International Conference on Solid-State Sensors, Actuators and Microsystems (TRANSDUCERS)}, abstract = {We present a CMOS-based high-density microelectrode array (HD-MEA) system that enables high-density mapping of brain slices in-vitro with multiple readout modalities. The 4.48×2.43 mm 2 array consists of 59,760 micro-electrodes at 13.5 μm pitch (5487 electrodes/mm 2 ). The overall system features 2048 action-potential, 32 local-field-potential and 32 current recording channels, 32 impedance-measurement and 28 neurotransmitter-detection channels and 16 voltage/current stimulation channels. The system enables real-time and label-free monitoring of position, size, morphology and electrical activity of brain slices.}, keywords = {Brain Slice, ETH-CMOS-MEA, HD-MEA}, pubstate = {published}, tppubtype = {conference} } Close We present a CMOS-based high-density microelectrode array (HD-MEA) system that enables high-density mapping of brain slices in-vitro with multiple readout modalities. The 4.48×2.43 mm 2 array consists of 59,760 micro-electrodes at 13.5 μm pitch (5487 electrodes/mm 2 ). The overall system features 2048 action-potential, 32 local-field-potential and 32 current recording channels, 32 impedance-measurement and 28 neurotransmitter-detection channels and 16 voltage/current stimulation channels. The system enables real-time and label-free monitoring of position, size, morphology and electrical activity of brain slices. Close https://ieeexplore.ieee.org/abstract/document/7994006 doi:10.1109/TRANSDUCERS.2017.7994006 Close
	Frey, Urs; Obien, Marie Engelene J; Muller, Jan; Hierlemann, Andreas Technology Trends and Commercialization of High-density Microelectrode Arrays for Advanced In-vitro Electrophysiology Conference IEEE International Symposium on Circuits and Systems (ISCAS Baltimore, MD, USA, 2017, ISSN: 2379-447X. Abstract \| Links \| BibTeX \| Tags: HD-MEA, In-Vitro @conference{Frey2017, title = {Technology Trends and Commercialization of High-density Microelectrode Arrays for Advanced In-vitro Electrophysiology}, author = {Urs Frey and Marie Engelene J. Obien and Jan Muller and Andreas Hierlemann}, url = {https://ieeexplore.ieee.org/document/8050215/}, doi = {10.1109/ISCAS.2017.8050215}, issn = {2379-447X}, year = {2017}, date = {2017-05-28}, address = {Baltimore, MD, USA}, organization = {IEEE International Symposium on Circuits and Systems (ISCAS}, abstract = {Microelectrode arrays (MEAs) enable fast and high-throughput readout of cell's electrical signals. MEAs are currently used for phenotype characterization and drug toxicity/efficacy testing with iPSC-derived neurons and cardiomyocytes. A key advantage of MEAs is the capability to record and stimulate individual neurons at multiple sites simultaneously. We will present ongoing advancements of MEA technology, with a focus on achieving higher quality recordings by means of monolithic co-integration of circuitry on chip by using CMOS technology [1]. Such high-density MEAs with more than 3000 electrodes per mm2 are a suitable tool for capturing neuronal activity across various scales, including axons, somas, dendrites, entire neurons, and networks.}, keywords = {HD-MEA, In-Vitro}, pubstate = {published}, tppubtype = {conference} } Close Microelectrode arrays (MEAs) enable fast and high-throughput readout of cell's electrical signals. MEAs are currently used for phenotype characterization and drug toxicity/efficacy testing with iPSC-derived neurons and cardiomyocytes. A key advantage of MEAs is the capability to record and stimulate individual neurons at multiple sites simultaneously. We will present ongoing advancements of MEA technology, with a focus on achieving higher quality recordings by means of monolithic co-integration of circuitry on chip by using CMOS technology [1]. Such high-density MEAs with more than 3000 electrodes per mm2 are a suitable tool for capturing neuronal activity across various scales, including axons, somas, dendrites, entire neurons, and networks. Close https://ieeexplore.ieee.org/document/8050215/ doi:10.1109/ISCAS.2017.8050215 Close
	Hillier, Daniel; Fiscella, Michele; Drinnenberg, Antonia; Trenholm, Stuart; Rompani, Santiago B; Raics, Zoltan; Katona, Gergely; Jüttner, Josephine; Hierlemann, Andreas; Rozsa, Balazs; Roska, Botond Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex Journal Article Nature Neuroscience, 20 (7), pp. 960–968, 2017, ISSN: 1097-6256. Abstract \| Links \| BibTeX \| Tags: MaxOne, Retina @article{Hillier2017, title = {Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex}, author = {Daniel Hillier and Michele Fiscella and Antonia Drinnenberg and Stuart Trenholm and Santiago B Rompani and Zoltan Raics and Gergely Katona and Josephine Jüttner and Andreas Hierlemann and Balazs Rozsa and Botond Roska}, url = {http://www.nature.com/doifinder/10.1038/nn.4566}, doi = {10.1038/nn.4566}, issn = {1097-6256}, year = {2017}, date = {2017-05-22}, journal = {Nature Neuroscience}, volume = {20}, number = {7}, pages = {960--968}, abstract = {How neuronal computations in the sensory periphery contribute to computations in the cortex is not well understood. We examined this question in the context of visual-motion processing in the retina and primary visual cortex (V1) of mice. We disrupted retinal direction selectivity, either exclusively along the horizontal axis using FRMD7 mutants or along all directions by ablating starburst amacrine cells, and monitored neuronal activity in layer 2/3 of V1 during stimulation with visual motion. In control mice, we found an over-representation of cortical cells preferring posterior visual motion, the dominant motion direction an animal experiences when it moves forward. In mice with disrupted retinal direction selectivity, the over-representation of posterior-motion-preferring cortical cells disappeared, and their responses at higher stimulus speeds were reduced. This work reveals the existence of two functionally distinct, sensory-periphery-dependent and -independent computations of visual motion in the cortex.}, keywords = {MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close How neuronal computations in the sensory periphery contribute to computations in the cortex is not well understood. We examined this question in the context of visual-motion processing in the retina and primary visual cortex (V1) of mice. We disrupted retinal direction selectivity, either exclusively along the horizontal axis using FRMD7 mutants or along all directions by ablating starburst amacrine cells, and monitored neuronal activity in layer 2/3 of V1 during stimulation with visual motion. In control mice, we found an over-representation of cortical cells preferring posterior visual motion, the dominant motion direction an animal experiences when it moves forward. In mice with disrupted retinal direction selectivity, the over-representation of posterior-motion-preferring cortical cells disappeared, and their responses at higher stimulus speeds were reduced. This work reveals the existence of two functionally distinct, sensory-periphery-dependent and -independent computations of visual motion in the cortex. Close http://www.nature.com/doifinder/10.1038/nn.4566 doi:10.1038/nn.4566 Close
	Bullmann Torsten; Radivojevic, Milos; Huber Stefan Deligkaris Kosmas; Hierlemann Andreas; Frey Urs T: Network Analysis Of High-Density Microelectrode Recordings Journal Article bioRxiv , (139436), pp. 1-23, 2017. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA @article{Bullmann2017, title = {Network Analysis Of High-Density Microelectrode Recordings}, author = {Bullmann, Torsten; Radivojevic, Milos; Huber, Stefan T: Deligkaris, Kosmas; Hierlemann, Andreas; Frey, Urs }, url = {https://www.biorxiv.org/content/early/2017/05/18/139436 }, doi = {10.1101/139436}, year = {2017}, date = {2017-05-18}, journal = {bioRxiv }, number = {139436}, pages = {1-23}, abstract = {Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology.}, keywords = {ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Extracellular voltage fields produced by a neuron's action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology. Close https://www.biorxiv.org/content/early/2017/05/18/139436 doi:10.1101/139436 Close
	Dragas, Jelena; Viswam, Vijay; Shadmani, Amir; Chen, Yihui; Bounik, Raziyeh; Stettler, Alexander; Radivojevic, Milos; Geissler, Sydney; Obien, Marie Engelene J; Müller, Jan; Hierlemann, Andreas A Multi-Functional Microelectrode Array Featuring 59760 Electrodes, 2048 Electrophysiology Channels, Stimulation, Impedance Measurement and Neurotransmitter Detection Channels Journal Article IEEE journal of solid-state circuits, 52 (6), pp. 1576-1590, 2017, ISSN: 0018-9200. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MEA Technology @article{Dragas2017, title = {A Multi-Functional Microelectrode Array Featuring 59760 Electrodes, 2048 Electrophysiology Channels, Stimulation, Impedance Measurement and Neurotransmitter Detection Channels}, author = {Jelena Dragas and Vijay Viswam and Amir Shadmani and Yihui Chen and Raziyeh Bounik and Alexander Stettler and Milos Radivojevic and Sydney Geissler and Marie Engelene J Obien and Jan Müller and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/7913669/}, doi = {10.1109/JSSC.2017.2686580}, issn = {0018-9200}, year = {2017}, date = {2017-04-27}, journal = {IEEE journal of solid-state circuits}, volume = {52}, number = {6}, pages = {1576-1590}, abstract = {Biological cells are characterized by highly complex phenomena and processes that are, to a great extent, interdependent. To gain detailed insights, devices designed to study cellular phenomena need to enable tracking and manipulation of multiple cell parameters in parallel; they have to provide high signal quality and high spatiotemporal resolution. To this end, we have developed a CMOS-based microelectrode array system that integrates six measurement and stimulation functions, the largest number to date. Moreover, the system features the largest active electrode array area to date (4.48×2.43 mm(2)) to accommodate 59,760 electrodes, while its power consumption, noise characteristics, and spatial resolution (13.5 mum electrode pitch) are comparable to the best state-of-the-art devices. The system includes: 2,048 action-potential (AP, bandwidth: 300 Hz to 10 kHz) recording units, 32 local-field-potential (LFP, bandwidth: 1 Hz to 300 Hz) recording units, 32 current recording units, 32 impedance measurement units, and 28 neurotransmitter detection units, in addition to the 16 dual-mode voltage-only or current/voltage-controlled stimulation units. The electrode array architecture is based on a switch matrix, which allows for connecting any measurement/stimulation unit to any electrode in the array and for performing different measurement/stimulation functions in parallel.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Biological cells are characterized by highly complex phenomena and processes that are, to a great extent, interdependent. To gain detailed insights, devices designed to study cellular phenomena need to enable tracking and manipulation of multiple cell parameters in parallel; they have to provide high signal quality and high spatiotemporal resolution. To this end, we have developed a CMOS-based microelectrode array system that integrates six measurement and stimulation functions, the largest number to date. Moreover, the system features the largest active electrode array area to date (4.48×2.43 mm(2)) to accommodate 59,760 electrodes, while its power consumption, noise characteristics, and spatial resolution (13.5 mum electrode pitch) are comparable to the best state-of-the-art devices. The system includes: 2,048 action-potential (AP, bandwidth: 300 Hz to 10 kHz) recording units, 32 local-field-potential (LFP, bandwidth: 1 Hz to 300 Hz) recording units, 32 current recording units, 32 impedance measurement units, and 28 neurotransmitter detection units, in addition to the 16 dual-mode voltage-only or current/voltage-controlled stimulation units. The electrode array architecture is based on a switch matrix, which allows for connecting any measurement/stimulation unit to any electrode in the array and for performing different measurement/stimulation functions in parallel. Close http://ieeexplore.ieee.org/document/7913669/ doi:10.1109/JSSC.2017.2686580 Close

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Publications

Publications

Selected Publications

High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels

Revealing Neuronal Function through Microelectrode Array Recordings

A 1024-Channel CMOS Microelectrode Array With 26,400 Electrodes for Recording and Stimulation of Electrogenic Cells In Vitro

Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites

Microelectronic System for High-Resolution Mapping of Extracellular Electric Fields Applied to Brain Slices

Modulation of Cardiomyocyte Electrical Properties Using Regulated Bone Morphogenetic Protein-2 Expression

All Publications

2020

2019

2018

2017