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

172 entries « ‹ 4 of 9 › »

61.	Duru Jens; Küchler, Joël; Ihle Stephan Forró Csaba; Bernardi Aeneas; Girardin Sophie; Hengsteler Julian; Wheeler Stephen; János; Ruff Tobias; J ; Vörös: Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays. In: 2022. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Duru2022, title = {Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays}, author = {Duru, Jens; Küchler, Joël; Ihle, Stephan J.;, Forró, Csaba; Bernardi, Aeneas; Girardin, Sophie; Hengsteler, Julian; Wheeler, Stephen; Vörös, János; Ruff, Tobias;}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.829884/full}, year = {2022}, date = {2022-02-21}, abstract = {In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.829884/full Close
62.	Xue, Xiaohan ; Buccino, Alessio Paolo ; Kumar, Sreedhar Saseendran ; Hierlemann, Andreas ; Bartram, Julian : Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking. In: bioRxiv, 2022. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Xue2022, title = {Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking}, author = {Xue, Xiaohan and Buccino, Alessio Paolo and Kumar, Sreedhar Saseendran and Hierlemann, Andreas and Bartram, Julian}, doi = {10.1101/2022.02.16.480643}, year = {2022}, date = {2022-02-16}, journal = {bioRxiv}, abstract = {Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community. Close doi:10.1101/2022.02.16.480643 Close
63.	McSweeney, Danny; Gabriel, Rafael; Jin, Kang; Pang, Zhiping P; Aronow, Bruce; Pak, ChangHui: Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons. In: BioRxiv, 2022. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{McSweeney2022, title = {Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons}, author = {Danny McSweeney and Rafael Gabriel and Kang Jin and Zhiping P. Pang and Bruce Aronow and ChangHui Pak}, url = {https://doi.org/10.1101/2022.02.14.480404}, doi = {10.1101/2022.02.14.480404}, year = {2022}, date = {2022-02-15}, journal = {BioRxiv}, abstract = {Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathogenesis of CASK-related disorders has been challenging due to limited human cellular models to study the dynamic roles of this molecule during neuronal and synapse development. Here, we generated CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and examined gene expression, morphometrics and synaptic function of induced neuronal cells during development. While young (immature) CASK KO neurons show robust neuronal outgrowth, mature CASK KO neurons displayed severe defects in synaptic transmission and synchronized burst activity without compromising neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathogenesis of CASK-related disorders has been challenging due to limited human cellular models to study the dynamic roles of this molecule during neuronal and synapse development. Here, we generated CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and examined gene expression, morphometrics and synaptic function of induced neuronal cells during development. While young (immature) CASK KO neurons show robust neuronal outgrowth, mature CASK KO neurons displayed severe defects in synaptic transmission and synchronized burst activity without compromising neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients. Close https://doi.org/10.1101/2022.02.14.480404 doi:10.1101/2022.02.14.480404 Close
64.	Paulsen, Bruna; Velasco, Silvia; Kedaigle, Amanda J; Pigoni, Martina; Quadrato, Giorgia; Deo, Anthony J; Adiconis, Xian; Uzquiano, Ana; Sartore, Rafaela; Yang, Sung Min; Simmons, Sean K; Symvoulidis, Panagiotis; Kim, Kwanho; Tsafou, Kalliopi; Podury, Archana; Abbate, Catherine; Tucewicz, Ashley; Smith, Samantha N; Albanese, Alexandre; Barrett, Lindy; Sanjana, Neville E; Shi, Xi; Chung, Kwanghun; Lage, Kasper; Boyden, Edward S; andJoshua Levin, Aviv Regev Z; Arlotta, Paola: Autism genes converge on asynchronous development of shared neuron classes. In: Nature, 602 , pp. 268–273, 2022. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Paulsen2022, title = {Autism genes converge on asynchronous development of shared neuron classes}, author = {Bruna Paulsen and Silvia Velasco and Amanda J. Kedaigle and Martina Pigoni and Giorgia Quadrato and Anthony J. Deo and Xian Adiconis and Ana Uzquiano and Rafaela Sartore and Sung Min Yang and Sean K. Simmons and Panagiotis Symvoulidis and Kwanho Kim and Kalliopi Tsafou and Archana Podury and Catherine Abbate and Ashley Tucewicz and Samantha N. Smith and Alexandre Albanese and Lindy Barrett and Neville E. Sanjana and Xi Shi and Kwanghun Chung and Kasper Lage and Edward S. Boyden and Aviv Regev andJoshua Z. Levin and Paola Arlotta }, url = {https://www.nature.com/articles/s41586-021-04358-6}, doi = {10.1038/s41586-021-04358-6}, year = {2022}, date = {2022-02-02}, journal = {Nature}, volume = {602}, pages = {268–273}, abstract = {Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1,2,3,4,5,6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes—SUV420H1 (also known as KMT5B), ARID1B and CHD8—in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages—γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons—but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1,2,3,4,5,6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes—SUV420H1 (also known as KMT5B), ARID1B and CHD8—in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages—γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons—but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology. Close https://www.nature.com/articles/s41586-021-04358-6 doi:10.1038/s41586-021-04358-6 Close
65.	Hruska-Plochan, Marian; Betz, Katharina M; Ronchi, Silvia; Wiersma, Vera I; Maniecka, Zuzanna; Hock, Eva-Maria; Laferriere, Florent; Sahadevan, Sonu; Hoop, Vanessa; Delvendahl, Igor; Panatta, Martina; van der Bourg, Alexander; Bohaciakova, Dasa; Frontzek, Karl; Aguzzi, Adriano; Lashley, Tammaryn; Robinson, Mark D; Karayannis, Theofanis; Mueller, Martin; Hierlemann, Andreas; Polymenidou, Magdalini: Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD. In: BioRxiv, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Hruska-Plochan2021, title = {Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD}, author = {Marian Hruska-Plochan and Katharina M. Betz and Silvia Ronchi and Vera I. Wiersma and Zuzanna Maniecka and Eva-Maria Hock and Florent Laferriere and Sonu Sahadevan and Vanessa Hoop and Igor Delvendahl and Martina Panatta and Alexander van der Bourg and Dasa Bohaciakova and Karl Frontzek and Adriano Aguzzi and Tammaryn Lashley and Mark D. Robinson and Theofanis Karayannis and Martin Mueller and Andreas Hierlemann and Magdalini Polymenidou}, url = {https://doi.org/10.1101/2021.12.08.471089}, doi = {10.1101/2021.12.08.471089}, year = {2021}, date = {2021-12-09}, journal = {BioRxiv}, abstract = {Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3–6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3–6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity. Close https://doi.org/10.1101/2021.12.08.471089 doi:10.1101/2021.12.08.471089 Close
66.	Kagan, Brett J; Kitchen, Andy C; Tran, Nhi T; Parker, Bradyn J; Bhat, Anjali; Rollo, Ben; Razi, Adeel; Friston, Karl J: In vitro neurons learn and exhibit sentience when embodied in a simulated game-world. In: BioRxiv, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Kagan2021, title = {In vitro neurons learn and exhibit sentience when embodied in a simulated game-world}, author = {Brett J. Kagan and Andy C. Kitchen and Nhi T. Tran and Bradyn J. Parker and Anjali Bhat and Ben Rollo and Adeel Razi and Karl J. Friston}, url = {https://www.biorxiv.org/content/10.1101/2021.12.02.471005v1 }, doi = {10.1101/2021.12.02.471005}, year = {2021}, date = {2021-12-03}, journal = {BioRxiv}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks. Close https://www.biorxiv.org/content/10.1101/2021.12.02.471005v1 doi:10.1101/2021.12.02.471005 Close
67.	Kubota, Tomoyuki; Takahashi, Hirokazu; and Nakajima, Kohei: Unifying framework for information processing in stochastically driven dynamical systems. In: Physical Review Research, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Kubota2023, title = {Unifying framework for information processing in stochastically driven dynamical systems}, author = {Tomoyuki Kubota and Hirokazu Takahashi and and Kohei Nakajima}, url = {https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.043135}, doi = {https://doi.org/10.1103/PhysRevResearch.3.043135}, year = {2021}, date = {2021-11-23}, journal = {Physical Review Research}, abstract = {A dynamical system is an information processing apparatus that encodes input streams from the external environment to its state and processes them through state transitions. The information processing capacity (IPC) is an excellent tool that comprehensively evaluates these processed inputs, providing details of unknown information processing in black box systems; however, this measure can be applied only to time-invariant systems. This paper extends the applicable range to time-variant systems and further reveals that the IPC is equivalent to coefficients of polynomial chaos (PC) expansion in more general dynamical systems. To achieve this objective, we tackle three issues. First, we establish a connection between the IPC for time-invariant systems and PC expansion, which is a type of polynomial expansion using orthogonal functions of input history as bases. We prove that the IPC corresponds to the squared norm of the coefficient vector of the basis in the PC expansion. Second, we show that an input following an arbitrary distribution can be used for the IPC, removing previous restrictions to specific input distributions. Third, we extend the conventional orthogonal bases to functions of both time and input history and propose the IPC for time-variant systems. To show the significance of our approach, we demonstrate that our measure can reveal information representations in not only machine learning networks but also a real, cultured neural network. Our generalized measure paves the way for unveiling the information processing capabilities of a wide variety of physical dynamics which have been left behind in nature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close A dynamical system is an information processing apparatus that encodes input streams from the external environment to its state and processes them through state transitions. The information processing capacity (IPC) is an excellent tool that comprehensively evaluates these processed inputs, providing details of unknown information processing in black box systems; however, this measure can be applied only to time-invariant systems. This paper extends the applicable range to time-variant systems and further reveals that the IPC is equivalent to coefficients of polynomial chaos (PC) expansion in more general dynamical systems. To achieve this objective, we tackle three issues. First, we establish a connection between the IPC for time-invariant systems and PC expansion, which is a type of polynomial expansion using orthogonal functions of input history as bases. We prove that the IPC corresponds to the squared norm of the coefficient vector of the basis in the PC expansion. Second, we show that an input following an arbitrary distribution can be used for the IPC, removing previous restrictions to specific input distributions. Third, we extend the conventional orthogonal bases to functions of both time and input history and propose the IPC for time-variant systems. To show the significance of our approach, we demonstrate that our measure can reveal information representations in not only machine learning networks but also a real, cultured neural network. Our generalized measure paves the way for unveiling the information processing capabilities of a wide variety of physical dynamics which have been left behind in nature. Close https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.043135 doi:https://doi.org/10.1103/PhysRevResearch.3.043135 Close
68.	Schenke, Maren; Prause, Hélène-Christine; Bergforth, Wiebke; Przykopanski, Adina: Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1. In: toxins, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Schenke2021, title = {Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1}, author = {Maren Schenke and Hélène-Christine Prause and Wiebke Bergforth and Adina Przykopanski}, url = {https://www.mdpi.com/2072-6651/13/8/585}, doi = {https://doi.org/10.3390/toxins13080585}, year = {2021}, date = {2021-08-22}, journal = {toxins}, abstract = {The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing. Close https://www.mdpi.com/2072-6651/13/8/585 doi:https://doi.org/10.3390/toxins13080585 Close
69.	Sundberg, Maria; Pinson, Hannah; Smith, Richard S; Winden, Kellen D; Venugopal, Pooja; Tai, Derek J C; Gusella, James F; Talkowski, Michael E; Walsh, Christopher A; Tegmark, Max; Sahin, Mustafa: 16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro. In: Nature Communications, 12 (2897 ), 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Sundberg2021, title = {16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro}, author = {Maria Sundberg and Hannah Pinson and Richard S. Smith and Kellen D. Winden and Pooja Venugopal and Derek J. C. Tai and James F. Gusella and Michael E. Talkowski and Christopher A. Walsh and Max Tegmark and Mustafa Sahin }, url = {https://www.nature.com/articles/s41467-021-23113-z}, doi = {10.1038/s41467-021-23113-z}, year = {2021}, date = {2021-05-18}, journal = {Nature Communications}, volume = {12}, number = {2897 }, abstract = {Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition. Close https://www.nature.com/articles/s41467-021-23113-z doi:10.1038/s41467-021-23113-z Close
70.	Kajiwara Motoki; Nomura, Ritsuki; Goetze Felix; Kawabata Masanori; Isomura Yoshikazu; Akutsu Tatsuya; Shimono Masanori; : Inhibitory neurons exhibit high controlling ability in the cortical microconnectome. In: PLOS Computational Biology, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Kajiwara2021, title = {Inhibitory neurons exhibit high controlling ability in the cortical microconnectome}, author = {Kajiwara, Motoki; Nomura, Ritsuki; Goetze, Felix; Kawabata, Masanori; Isomura, Yoshikazu; Akutsu, Tatsuya; Shimono, Masanori; }, url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008846}, year = {2021}, date = {2021-04-08}, journal = {PLOS Computational Biology}, abstract = {The brain is a network system in which excitatory and inhibitory neurons keep activity bal- anced in the highly non-random connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neu- rons in the cortex. So, in general, how inhibitory neurons can keep the balance with the sur- rounding excitatory neurons is an important question. There is much accumulated knowledge about this fundamental question. This study quantitatively evaluated the rela- tively higher functional contribution of inhibitory neurons in terms of not only properties of individual neurons, such as firing rate, but also in terms of topological mechanisms and con- trolling ability on other excitatory neurons. We combined simultaneous electrical recording (~2.5 hours) of ~1000 neurons in vitro, and quantitative evaluation of neuronal interactions including excitatory-inhibitory categorization. This study accurately defined recording brain anatomical targets, such as brain regions and cortical layers, by inter-referring MRI and immunostaining recordings. The interaction networks enabled us to quantify topological influence of individual neurons, in terms of controlling ability to other neurons. Especially, the result indicated that highly influential inhibitory neurons show higher controlling ability of other neurons than excitatory neurons, and are relatively often distributed in deeper layers of the cortex. Furthermore, the neurons having high controlling ability are more effectively limited in number than central nodes of k-cores, and these neurons also participate in more clustered motifs. In summary, this study suggested that the high controlling ability of inhibi- tory neurons is a key mechanism to keep balance with a large number of other excitatory neurons beyond simple higher firing rate. Application of the selection method of limited important neurons would be also applicable for the ability to effectively and selectively stimu- late E/I imbalanced disease states.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close The brain is a network system in which excitatory and inhibitory neurons keep activity bal- anced in the highly non-random connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neu- rons in the cortex. So, in general, how inhibitory neurons can keep the balance with the sur- rounding excitatory neurons is an important question. There is much accumulated knowledge about this fundamental question. This study quantitatively evaluated the rela- tively higher functional contribution of inhibitory neurons in terms of not only properties of individual neurons, such as firing rate, but also in terms of topological mechanisms and con- trolling ability on other excitatory neurons. We combined simultaneous electrical recording (~2.5 hours) of ~1000 neurons in vitro, and quantitative evaluation of neuronal interactions including excitatory-inhibitory categorization. This study accurately defined recording brain anatomical targets, such as brain regions and cortical layers, by inter-referring MRI and immunostaining recordings. The interaction networks enabled us to quantify topological influence of individual neurons, in terms of controlling ability to other neurons. Especially, the result indicated that highly influential inhibitory neurons show higher controlling ability of other neurons than excitatory neurons, and are relatively often distributed in deeper layers of the cortex. Furthermore, the neurons having high controlling ability are more effectively limited in number than central nodes of k-cores, and these neurons also participate in more clustered motifs. In summary, this study suggested that the high controlling ability of inhibi- tory neurons is a key mechanism to keep balance with a large number of other excitatory neurons beyond simple higher firing rate. Application of the selection method of limited important neurons would be also applicable for the ability to effectively and selectively stimu- late E/I imbalanced disease states. Close https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008846 Close
71.	Yuan, Xinyue; Hierlemann, Andreas; Frey, Urs: Extracellular Recording of Entire Neural Networks Using a Dual-Mode Microelectrode Array With 19,584 Electrodes and High SNR. In: IEEE, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Yuan2021, title = {Extracellular Recording of Entire Neural Networks Using a Dual-Mode Microelectrode Array With 19,584 Electrodes and High SNR}, author = {Xinyue Yuan and Andreas Hierlemann and Urs Frey}, url = {https://ieeexplore.ieee.org/document/9385387}, doi = {10.1109/JSSC.2021.3066043}, year = {2021}, date = {2021-03-24}, journal = {IEEE}, abstract = {Electrophysiological research on neural networks and their activity focuses on the recording and analysis of large data sets that include information of thousands of neurons. CMOS microelectrode arrays (MEAs) feature thousands of electrodes at a spatial resolution on the scale of single cells and are, therefore, ideal tools to support neural-network research. Moreover, they offer high spatio-temporal resolution and signal-to-noise ratio (SNR) to capture all features and subcellular-resolution details of neuronal signaling. Here, we present a dual-mode (DM) MEA, which enables simultaneous: 1) full-frame readout from all electrodes and 2) high-SNR readout from an arbitrarily selectable subset of electrodes. The DM-MEA includes 19,584 electrodes, 19,584 full-frame recording channels with noise levels of 10.4 μVrms in the action potential (AP) frequency band (300 Hz-5 kHz), 246 low-noise recording channels with noise levels of 3.0 μVrms in the AP band and eight stimulation units. The capacity to simultaneously perform full-frame and high-SNR recordings endows the presented DM-MEA with great flexibility for various applications in neuroscience and pharmacology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Electrophysiological research on neural networks and their activity focuses on the recording and analysis of large data sets that include information of thousands of neurons. CMOS microelectrode arrays (MEAs) feature thousands of electrodes at a spatial resolution on the scale of single cells and are, therefore, ideal tools to support neural-network research. Moreover, they offer high spatio-temporal resolution and signal-to-noise ratio (SNR) to capture all features and subcellular-resolution details of neuronal signaling. Here, we present a dual-mode (DM) MEA, which enables simultaneous: 1) full-frame readout from all electrodes and 2) high-SNR readout from an arbitrarily selectable subset of electrodes. The DM-MEA includes 19,584 electrodes, 19,584 full-frame recording channels with noise levels of 10.4 μVrms in the action potential (AP) frequency band (300 Hz-5 kHz), 246 low-noise recording channels with noise levels of 3.0 μVrms in the AP band and eight stimulation units. The capacity to simultaneously perform full-frame and high-SNR recordings endows the presented DM-MEA with great flexibility for various applications in neuroscience and pharmacology. Close https://ieeexplore.ieee.org/document/9385387 doi:10.1109/JSSC.2021.3066043 Close
72.	Ronchi, Silvia; Buccino, Alessio Paolo; Prack, Gustavo; Kumar, Sreedhar Saseendran; Schröter, Manuel; Fiscella, Michele; Hierlemann, Andreas: Microelectrode Arrays: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays. In: Advanced Biology, 5 (3), 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Ronchi2021, title = {Microelectrode Arrays: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Alessio Paolo Buccino and Gustavo Prack and Sreedhar Saseendran Kumar and Manuel Schröter and Michele Fiscella and Andreas Hierlemann}, url = {https://onlinelibrary.wiley.com/doi/10.1002/adbi.202000223}, doi = {10.1002/adbi.202000223}, year = {2021}, date = {2021-03-17}, journal = {Advanced Biology}, volume = {5}, number = {3}, abstract = {In article number 2000223, Silvia Ronchi, Michele Fiscella, and co-workers show neurons plated on a high-density microelectrode array. The small electrode size and the tight spacing between the 26 400 electrodes enable functional extracellular electrophysiological characterization of neurons across scales, from subcellular-resolution features, like axons and dendrites, through individual neuronal cells to entire networks.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close In article number 2000223, Silvia Ronchi, Michele Fiscella, and co-workers show neurons plated on a high-density microelectrode array. The small electrode size and the tight spacing between the 26 400 electrodes enable functional extracellular electrophysiological characterization of neurons across scales, from subcellular-resolution features, like axons and dendrites, through individual neuronal cells to entire networks. Close https://onlinelibrary.wiley.com/doi/10.1002/adbi.202000223 doi:10.1002/adbi.202000223 Close
73.	Sharf, Tal; van der Molen, Tjitse; Guzman, Elmer; Glasauer, Stella M K; Luna, Gabriel; Cheng, Zhouwei; Audouard, Morgane; Ranasinghe, Kamalini G; Kudo, Kiwamu; Nagarajan, Srikantan S; Tovar, Kenneth R; Petzold, Linda R; Hansma, Paul K; Kosik, Kenneth S: Intrinsic network activity in human brain organoids. In: BioRxiv, 2021. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Sharf2021, title = {Intrinsic network activity in human brain organoids}, author = {Tal Sharf and Tjitse van der Molen and Elmer Guzman and Stella M.K. Glasauer and Gabriel Luna and Zhouwei Cheng and Morgane Audouard and Kamalini G. Ranasinghe and Kiwamu Kudo and Srikantan S. Nagarajan and Kenneth R. Tovar and Linda R. Petzold and Paul K. Hansma and Kenneth S. Kosik}, url = {https://www.biorxiv.org/content/10.1101/2021.01.28.428643v1}, doi = {10.1101/2021.01.28.428643}, year = {2021}, date = {2021-01-28}, journal = {BioRxiv}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we probed broadband and three-dimensional spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single unit activity. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Increasing the intrinsic inhibitory tone with a benzodiazepine altered the functional network graph of the organoid by suppressing the network skeleton. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. An ensemble of spikes phase-locked to theta frequency oscillations were strongly interconnected as a sub-network within the larger network in which they were embedded. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we probed broadband and three-dimensional spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single unit activity. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Increasing the intrinsic inhibitory tone with a benzodiazepine altered the functional network graph of the organoid by suppressing the network skeleton. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. An ensemble of spikes phase-locked to theta frequency oscillations were strongly interconnected as a sub-network within the larger network in which they were embedded. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks. Close https://www.biorxiv.org/content/10.1101/2021.01.28.428643v1 doi:10.1101/2021.01.28.428643 Close
74.	Idrees, Saad; Münch, Thomas A: Different contrast encoding in ON and OFF visual pathways. In: BioRxiv, 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Idrees2020b, title = {Different contrast encoding in ON and OFF visual pathways}, author = {Saad Idrees and Thomas A. Münch }, url = {https://www.biorxiv.org/content/10.1101/2020.11.25.398230v1}, doi = {10.1101/2020.11.25.398230}, year = {2020}, date = {2020-11-26}, journal = {BioRxiv}, abstract = {Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli. Close https://www.biorxiv.org/content/10.1101/2020.11.25.398230v1 doi:10.1101/2020.11.25.398230 Close
75.	Battaglia, Chiara R; Cursano, Silvia; Calzia, Enrico; Catanese, Alberto; Boeckers, Tobias M: Corticotropin-releasing hormone (CRH) alters mitochondrial morphology and function by activating the NF-kB-DRP1 axis in hippocampal neurons. In: Cell Death & Disease, 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Battaglia2020, title = {Corticotropin-releasing hormone (CRH) alters mitochondrial morphology and function by activating the NF-kB-DRP1 axis in hippocampal neurons}, author = {Chiara R. Battaglia and Silvia Cursano and Enrico Calzia and Alberto Catanese and Tobias M. Boeckers }, url = {https://www.nature.com/articles/s41419-020-03204-3}, doi = {https://doi.org/10.1038/s41419-020-03204-3}, year = {2020}, date = {2020-11-23}, journal = {Cell Death & Disease}, abstract = {Neuronal stress-adaptation combines multiple molecular responses. We have previously reported that thorax trauma induces a transient loss of hippocampal excitatory synapses mediated by the local release of the stress-related hormone corticotropin-releasing hormone (CRH). Since a physiological synaptic activity relies also on mitochondrial functionality, we investigated the direct involvement of mitochondria in the (mal)-adaptive changes induced by the activation of neuronal CRH receptors 1 (CRHR1). We observed, in vivo and in vitro, a significant shift of mitochondrial dynamics towards fission, which correlated with increased swollen mitochondria and aberrant cristae. These morphological changes, which are associated with increased NF-kB activity and nitric oxide concentrations, correlated with a pronounced reduction of mitochondrial activity. However, ATP availability was unaltered, suggesting that neurons maintain a physiological energy metabolism to preserve them from apoptosis under CRH exposure. Our findings demonstrate that stress-induced CRHR1 activation leads to strong, but reversible, modifications of mitochondrial dynamics and morphology. These alterations are accompanied by bioenergetic defects and the reduction of neuronal activity, which are linked to increased intracellular oxidative stress, and to the activation of the NF-kB/c-Abl/DRP1 axis. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Neuronal stress-adaptation combines multiple molecular responses. We have previously reported that thorax trauma induces a transient loss of hippocampal excitatory synapses mediated by the local release of the stress-related hormone corticotropin-releasing hormone (CRH). Since a physiological synaptic activity relies also on mitochondrial functionality, we investigated the direct involvement of mitochondria in the (mal)-adaptive changes induced by the activation of neuronal CRH receptors 1 (CRHR1). We observed, in vivo and in vitro, a significant shift of mitochondrial dynamics towards fission, which correlated with increased swollen mitochondria and aberrant cristae. These morphological changes, which are associated with increased NF-kB activity and nitric oxide concentrations, correlated with a pronounced reduction of mitochondrial activity. However, ATP availability was unaltered, suggesting that neurons maintain a physiological energy metabolism to preserve them from apoptosis under CRH exposure. Our findings demonstrate that stress-induced CRHR1 activation leads to strong, but reversible, modifications of mitochondrial dynamics and morphology. These alterations are accompanied by bioenergetic defects and the reduction of neuronal activity, which are linked to increased intracellular oxidative stress, and to the activation of the NF-kB/c-Abl/DRP1 axis. Close https://www.nature.com/articles/s41419-020-03204-3 doi:https://doi.org/10.1038/s41419-020-03204-3 Close
76.	Ricci, Chiara; Frey, Urs; Obien, Marie Engelene J: MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro. In: IEEE, 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Ricci2020, title = {MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro}, author = {Chiara Ricci and Urs Frey and Marie Engelene J. Obien}, url = {https://ieeexplore.ieee.org/document/9175797/}, doi = {10.1109/EMBC44109.2020.9175797}, year = {2020}, date = {2020-10-08}, journal = {IEEE}, abstract = {We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds. Close https://ieeexplore.ieee.org/document/9175797/ doi:10.1109/EMBC44109.2020.9175797 Close
77.	Yuan, Xinyue; Schröter, Manuel; Obien, Marie Engelene J; Fiscella, Michele; Gong, Wei; Kikuchi, Tetsuhiro; Odawara, Aoi; Noji, Shuhei; Suzuki, Ikuro; Takahashi, Jun; Hierlemann, Andreas; Frey, Urs: Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level. In: Nature Communications, 11 (4854), 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Yuan2020, title = {Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level}, author = {Xinyue Yuan and Manuel Schröter and Marie Engelene J. Obien and Michele Fiscella and Wei Gong and Tetsuhiro Kikuchi and Aoi Odawara and Shuhei Noji and Ikuro Suzuki and Jun Takahashi and Andreas Hierlemann and Urs Frey}, url = {https://www.nature.com/articles/s41467-020-18620-4#citeas}, doi = {10.1038/s41467-020-18620-4}, year = {2020}, date = {2020-09-25}, journal = {Nature Communications}, volume = {11}, number = {4854}, abstract = {Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed. Close https://www.nature.com/articles/s41467-020-18620-4#citeas doi:10.1038/s41467-020-18620-4 Close
78.	Kim, Eunhee; Jeon, Sungwoong; An, Hyun-Kyu; Mehrnoosh Kianpour, Seong-Woon Yu ; Kim, Jin-young; Rah, Jong-Cheol; Choi, Hongsoo: A magnetically actuated microrobot for targeted neural cell delivery and selective connection of neural networks. In: Science Advances, 6 (39), 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Kim2020, title = {A magnetically actuated microrobot for targeted neural cell delivery and selective connection of neural networks}, author = {Eunhee Kim and Sungwoong Jeon and Hyun-Kyu An and Mehrnoosh Kianpour, Seong-Woon Yu and Jin-young Kim and Jong-Cheol Rah and Hongsoo Choi}, url = {https://advances.sciencemag.org/content/6/39/eabb5696}, doi = {10.1126/sciadv.abb5696}, year = {2020}, date = {2020-09-25}, journal = {Science Advances}, volume = {6}, number = {39}, abstract = {There has been a great deal of interest in the development of technologies for actively manipulating neural networks in vitro, providing natural but simplified environments in a highly reproducible manner in which to study brain function and related diseases. Platforms for these in vitro neural networks require precise and selective neural connections at the target location, with minimal external influences, and measurement of neural activity to determine how neurons communicate. Here, we report a neuron-loaded microrobot for selective connection of neural networks via precise delivery to a gap between two neural clusters by an external magnetic field. In addition, the extracellular action potential was propagated from one cluster to the other through the neurons on the microrobot. The proposed technique shows the potential for use in experiments to understand how neurons communicate in the neural network by actively connecting neural clusters.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close There has been a great deal of interest in the development of technologies for actively manipulating neural networks in vitro, providing natural but simplified environments in a highly reproducible manner in which to study brain function and related diseases. Platforms for these in vitro neural networks require precise and selective neural connections at the target location, with minimal external influences, and measurement of neural activity to determine how neurons communicate. Here, we report a neuron-loaded microrobot for selective connection of neural networks via precise delivery to a gap between two neural clusters by an external magnetic field. In addition, the extracellular action potential was propagated from one cluster to the other through the neurons on the microrobot. The proposed technique shows the potential for use in experiments to understand how neurons communicate in the neural network by actively connecting neural clusters. Close https://advances.sciencemag.org/content/6/39/eabb5696 doi:10.1126/sciadv.abb5696 Close
79.	Cowan, Cameron S; Renner, Magdalena; Gennaro, Martina De; Gross-Scherf, Brigitte; Goldblum, David; Hou, Yanyan; Munz, Martin; Rodrigues, Tiago M; Krol, Jacek; Szikra, Tamas; Cuttat, Rachel; Waldt, Annick; Papasaikas, Panagiotis; Diggelmann, Roland; Patino-Alvarez, Claudia P; Galliker, Patricia; Spirig, Stefan E; Pavlinic, Dinko; Gerber-Hollbach, Nadine; Schuierer, Sven; Srdanovic, Aldin; Balogh, Marton; Panero, Riccardo; Kusnyerik, Akos; Szabo, Arnold; Stadler, Michael B; Orgül, Selim; Picelli, Simone; Hasler, Pascal W; Hierlemann, Andreas; Scholl, Hendrik P N; Roma, Guglielmo; Nigsch, Florian; Roska, Botond: Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution. In: CellPress, 182 , pp. 1623–1640, 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Cowan2020, title = {Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution}, author = {Cameron S. Cowan and Magdalena Renner and Martina De Gennaro and Brigitte Gross-Scherf and David Goldblum and Yanyan Hou and Martin Munz and Tiago M. Rodrigues and Jacek Krol and Tamas Szikra and Rachel Cuttat and Annick Waldt and Panagiotis Papasaikas and Roland Diggelmann and Claudia P. Patino-Alvarez and Patricia Galliker and Stefan E. Spirig and Dinko Pavlinic and Nadine Gerber-Hollbach and Sven Schuierer and Aldin Srdanovic and Marton Balogh and Riccardo Panero and Akos Kusnyerik and Arnold Szabo and Michael B. Stadler and Selim Orgül and Simone Picelli and Pascal W. Hasler and Andreas Hierlemann and Hendrik P.N. Scholl and Guglielmo Roma and Florian Nigsch and Botond Roska}, url = {https://www.cell.com/cell/fulltext/S0092-8674(20)31004-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867420310047%3Fshowall%3Dtrue}, doi = {10.1016/j.cell.2020.08.013}, year = {2020}, date = {2020-09-17}, journal = {CellPress}, volume = {182}, pages = { 1623–1640}, abstract = {Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable “developed” state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable “developed” state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas. Close https://www.cell.com/cell/fulltext/S0092-8674(20)31004-7?_returnURL=https%3A%2F%[...] doi:10.1016/j.cell.2020.08.013 Close
80.	Ronchi, Silvia; Buccino, Alessio Paolo; Prack, Gustavo; Kumar, Sreedhar Saseendran; Schröter, Manuel; Fiscella, Michele; Hierlemann, Andreas: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays. In: BioRxiv, 2020. (Type: Journal Article \| Abstract \| Links \| BibTeX) @article{Ronchi2020, title = {Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Alessio Paolo Buccino and Gustavo Prack and Sreedhar Saseendran Kumar and Manuel Schröter and Michele Fiscella and Andreas Hierlemann }, url = {https://www.biorxiv.org/content/10.1101/2020.09.02.271403v1}, doi = {10.1101/2020.09.02.271403}, year = {2020}, date = {2020-09-02}, journal = {BioRxiv}, abstract = {Recent advances in the field of cellular reprogramming have opened a route to study the fundamental mechanisms underlying common neurological disorders. High-density microelectrode-arrays (HD-MEAs) provide unprecedented means to study neuronal physiology at different scales, ranging from network through single-neuron to subcellular features. In this work, we used HD-MEAs in vitro to characterize and compare human induced-pluripotent-stem-cell (iPSC)-derived dopaminergic and motor neurons, including isogenic neuronal lines modeling Parkinson’s disease and amyotrophic lateral sclerosis. We established reproducible electrophysiological network, single-cell and subcellular metrics, which were used for phenotype characterization and drug testing. Metrics such as burst shapes and axonal velocity enabled the distinction of healthy and diseased neurons. The HD-MEA metrics could also be used to detect the effects of dosing the drug retigabine to human motor neurons. Finally, we showed that the ability to detect drug effects and the observed culture-to-culture variability critically depend on the number of available recording electrodes}, keywords = {}, pubstate = {published}, tppubtype = {article} } Close Recent advances in the field of cellular reprogramming have opened a route to study the fundamental mechanisms underlying common neurological disorders. High-density microelectrode-arrays (HD-MEAs) provide unprecedented means to study neuronal physiology at different scales, ranging from network through single-neuron to subcellular features. In this work, we used HD-MEAs in vitro to characterize and compare human induced-pluripotent-stem-cell (iPSC)-derived dopaminergic and motor neurons, including isogenic neuronal lines modeling Parkinson’s disease and amyotrophic lateral sclerosis. We established reproducible electrophysiological network, single-cell and subcellular metrics, which were used for phenotype characterization and drug testing. Metrics such as burst shapes and axonal velocity enabled the distinction of healthy and diseased neurons. The HD-MEA metrics could also be used to detect the effects of dosing the drug retigabine to human motor neurons. Finally, we showed that the ability to detect drug effects and the observed culture-to-culture variability critically depend on the number of available recording electrodes Close https://www.biorxiv.org/content/10.1101/2020.09.02.271403v1 doi:10.1101/2020.09.02.271403 Close

172 entries « ‹ 4 of 9 › »

172 entries « ‹ 4 of 4 › »

2013
	Bakkum, Douglas J; Frey, Urs; Radivojevic, Milos; Russell, Thomas L; Müller, Jan; Fiscella, Michele; Takahashi, Hirokazu; Hierlemann, Andreas Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites Journal Article Nature Communications, 4 , pp. 1-12, 2013, ISSN: 2041-1723. Abstract \| Links \| BibTeX \| タグ: Data Analysis, ETH-CMOS-MEA, Neuronal Networks @article{Bakkum2013, title = {Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites}, author = {Douglas J Bakkum and Urs Frey and Milos Radivojevic and Thomas L Russell and Jan Müller and Michele Fiscella and Hirokazu Takahashi and Andreas Hierlemann}, url = {http://www.nature.com/doifinder/10.1038/ncomms3181}, doi = {10.1038/ncomms3181}, issn = {2041-1723}, year = {2013}, date = {2013-07-19}, journal = {Nature Communications}, volume = {4}, pages = {1-12}, abstract = {Axons are traditionally considered stable transmission cables, but evidence of the regulation of action potential propagation demonstrates that axons may have more important roles. However, their small diameters render intracellular recordings challenging, and low-magnitude extracellular signals are difficult to detect and assign. Better experimental access to axonal function would help to advance this field. Here we report methods to electrically visualize action potential propagation and network topology in cortical neurons grown over custom arrays, which contain 11,011 microelectrodes and are fabricated using complementary metal oxide semiconductor technology. Any neuron lying on the array can be recorded at high spatio-temporal resolution, and simultaneously precisely stimulated with little artifact. We find substantial velocity differences occurring locally within single axons, suggesting that the temporal control of a neuron's output may contribute to neuronal information processing.}, keywords = {Data Analysis, ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Axons are traditionally considered stable transmission cables, but evidence of the regulation of action potential propagation demonstrates that axons may have more important roles. However, their small diameters render intracellular recordings challenging, and low-magnitude extracellular signals are difficult to detect and assign. Better experimental access to axonal function would help to advance this field. Here we report methods to electrically visualize action potential propagation and network topology in cortical neurons grown over custom arrays, which contain 11,011 microelectrodes and are fabricated using complementary metal oxide semiconductor technology. Any neuron lying on the array can be recorded at high spatio-temporal resolution, and simultaneously precisely stimulated with little artifact. We find substantial velocity differences occurring locally within single axons, suggesting that the temporal control of a neuron's output may contribute to neuronal information processing. Close http://www.nature.com/doifinder/10.1038/ncomms3181 doi:10.1038/ncomms3181 Close
	Müller, Jan; Bakkum, Douglas J; Hierlemann, Andreas Sub-millisecond closed-loop feedback stimulation between arbitrary sets of individual neurons. Journal Article Frontiers in Neural Circuits, 6 , pp. 121, 2013, ISSN: 1662-5110. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation @article{Muller2012, title = {Sub-millisecond closed-loop feedback stimulation between arbitrary sets of individual neurons.}, author = {Jan Müller and Douglas J Bakkum and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fncir.2012.00121/full}, doi = {10.3389/fncir.2012.00121}, issn = {1662-5110}, year = {2013}, date = {2013-01-10}, journal = {Frontiers in Neural Circuits}, volume = {6}, pages = {121}, abstract = {We present a system to artificially correlate the spike timing between sets of arbitrary neurons that were interfaced to a complementary metal-oxide-semiconductor (CMOS) high-density microelectrode array (MEA). The system features a novel reprogrammable and flexible event engine unit to detect arbitrary spatio-temporal patterns of recorded action potentials and is capable of delivering sub-millisecond closed-loop feedback of electrical stimulation upon trigger events in real-time. The relative timing between action potentials of individual neurons as well as the temporal pattern among multiple neurons, or neuronal assemblies, is considered an important factor governing memory and learning in the brain. Artificially changing timings between arbitrary sets of spiking neurons with our system could provide a "knob" to tune information processing in the network.}, keywords = {ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation}, pubstate = {published}, tppubtype = {article} } Close We present a system to artificially correlate the spike timing between sets of arbitrary neurons that were interfaced to a complementary metal-oxide-semiconductor (CMOS) high-density microelectrode array (MEA). The system features a novel reprogrammable and flexible event engine unit to detect arbitrary spatio-temporal patterns of recorded action potentials and is capable of delivering sub-millisecond closed-loop feedback of electrical stimulation upon trigger events in real-time. The relative timing between action potentials of individual neurons as well as the temporal pattern among multiple neurons, or neuronal assemblies, is considered an important factor governing memory and learning in the brain. Artificially changing timings between arbitrary sets of spiking neurons with our system could provide a "knob" to tune information processing in the network. Close https://www.frontiersin.org/articles/10.3389/fncir.2012.00121/full doi:10.3389/fncir.2012.00121 Close
2012
	Franke, Felix; Jackel, David; Dragas, Jelena; Muller, Jan; Radivojevic, Milos; Bakkum, Douglas J; Hierlemann, Andreas High-density microelectrode array recordings and real-time spike sorting for closed-loop experiments: an emerging technology to study neural plasticity Journal Article Frontiers in Neural Circuits, 6 , pp. 105, 2012, ISSN: 1662-5110. Abstract \| Links \| BibTeX \| タグ: Neuronal Networks, Review, Spike Sorting @article{Hierlemann2012, title = {High-density microelectrode array recordings and real-time spike sorting for closed-loop experiments: an emerging technology to study neural plasticity}, author = {Felix Franke and David Jackel and Jelena Dragas and Jan Muller and Milos Radivojevic and Douglas J Bakkum and Andreas Hierlemann}, url = {https://www.frontiersin.org/article/10.3389/fncir.2012.00105}, doi = {10.3389/fncir.2012.00105}, issn = {1662-5110}, year = {2012}, date = {2012-12-20}, journal = {Frontiers in Neural Circuits}, volume = {6}, pages = {105}, abstract = {Understanding plasticity of neural networks is a key to comprehending their development and function. A powerful technique to study neural plasticity includes recording and control of pre- and postsynaptic neural activity, e.g., by using simultaneous intracellular recording and stimulation of several neurons. Intracellular recording is, however, a demanding technique and has its limitations in that only a small number of neurons can be stimulated and recorded from at the same time. Extracellular techniques offer the possibility to simultaneously record from larger numbers of neurons with relative ease, at the expenses of increased efforts to sort out single neuronal activities from the recorded mixture, which is a time consuming and error prone step, referred to as spike sorting. In this mini-review, we describe recent technological developments in two separate fields, namely CMOS-based high-density microelectrode arrays, which also allow for extracellular stimulation of neurons, and real-time spike sorting. We argue that these techniques, when combined, will provide a powerful tool to study plasticity in neural networks consisting of several thousand neurons in vitro.}, keywords = {Neuronal Networks, Review, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Understanding plasticity of neural networks is a key to comprehending their development and function. A powerful technique to study neural plasticity includes recording and control of pre- and postsynaptic neural activity, e.g., by using simultaneous intracellular recording and stimulation of several neurons. Intracellular recording is, however, a demanding technique and has its limitations in that only a small number of neurons can be stimulated and recorded from at the same time. Extracellular techniques offer the possibility to simultaneously record from larger numbers of neurons with relative ease, at the expenses of increased efforts to sort out single neuronal activities from the recorded mixture, which is a time consuming and error prone step, referred to as spike sorting. In this mini-review, we describe recent technological developments in two separate fields, namely CMOS-based high-density microelectrode arrays, which also allow for extracellular stimulation of neurons, and real-time spike sorting. We argue that these techniques, when combined, will provide a powerful tool to study plasticity in neural networks consisting of several thousand neurons in vitro. Close https://www.frontiersin.org/article/10.3389/fncir.2012.00105 doi:10.3389/fncir.2012.00105 Close
	Fiscella, Michele; Farrow, Karl; Jones, Ian L; Jäckel, David; Müller, Jan; Frey, Urs; Bakkum, Douglas J; Hantz, Péter; Roska, Botond; Hierlemann, Andreas Recording from defined populations of retinal ganglion cells using a high-density CMOS-integrated microelectrode array with real-time switchable electrode selection Journal Article Journal of Neuroscience Methods, 211 (1), pp. 103-113, 2012, ISSN: 01650270. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, Retina @article{Fiscella2012, title = {Recording from defined populations of retinal ganglion cells using a high-density CMOS-integrated microelectrode array with real-time switchable electrode selection}, author = {Michele Fiscella and Karl Farrow and Ian L Jones and David Jäckel and Jan Müller and Urs Frey and Douglas J Bakkum and Péter Hantz and Botond Roska and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S0165027012003287?via%3Dihub}, doi = {10.1016/j.jneumeth.2012.08.017}, issn = {01650270}, year = {2012}, date = {2012-08-16}, journal = {Journal of Neuroscience Methods}, volume = {211}, number = {1}, pages = {103-113}, publisher = {Elsevier B.V.}, abstract = {In order to understand how retinal circuits encode visual scenes, the neural activity of defined populations of retinal ganglion cells (RGCs) has to be investigated. Here we report on a method for stimulating, detecting, and subsequently targeting defined populations of RGCs. The possibility to select a distinct population of RGCs for extracellular recording enables the design of experiments that can increase our understanding of how these neurons extract precise spatio-temporal features from the visual scene, and how the brain interprets retinal signals. We used light stimulation to elicit a response from physiologically distinct types of RGCs and then utilized the dynamic-configurability capabilities of a microelectronics-based high-density microelectrode array (MEA) to record their synchronous action potentials. The layout characteristics of the MEA made it possible to stimulate and record from multiple, highly overlapping RGCs simultaneously without light-induced artifacts. The high-density of electrodes and the high signal-to-noise ratio of the MEA circuitry allowed for recording of the activity of each RGC on 14 ± 7 electrodes. The spatial features of the electrical activity of each RGC greatly facilitated spike sorting. We were thus able to localize, identify and record from defined RGCs within a region of mouse retina. In addition, we stimulated and recorded from genetically modified RGCs to demonstrate the applicability of optogenetic methods, which introduces an additional feature to target a defined cell type. The developed methodologies can likewise be applied to other neuronal preparations including brain slices or cultured neurons.}, keywords = {ETH-CMOS-MEA, Retina}, pubstate = {published}, tppubtype = {article} } Close In order to understand how retinal circuits encode visual scenes, the neural activity of defined populations of retinal ganglion cells (RGCs) has to be investigated. Here we report on a method for stimulating, detecting, and subsequently targeting defined populations of RGCs. The possibility to select a distinct population of RGCs for extracellular recording enables the design of experiments that can increase our understanding of how these neurons extract precise spatio-temporal features from the visual scene, and how the brain interprets retinal signals. We used light stimulation to elicit a response from physiologically distinct types of RGCs and then utilized the dynamic-configurability capabilities of a microelectronics-based high-density microelectrode array (MEA) to record their synchronous action potentials. The layout characteristics of the MEA made it possible to stimulate and record from multiple, highly overlapping RGCs simultaneously without light-induced artifacts. The high-density of electrodes and the high signal-to-noise ratio of the MEA circuitry allowed for recording of the activity of each RGC on 14 ± 7 electrodes. The spatial features of the electrical activity of each RGC greatly facilitated spike sorting. We were thus able to localize, identify and record from defined RGCs within a region of mouse retina. In addition, we stimulated and recorded from genetically modified RGCs to demonstrate the applicability of optogenetic methods, which introduces an additional feature to target a defined cell type. The developed methodologies can likewise be applied to other neuronal preparations including brain slices or cultured neurons. Close http://www.sciencedirect.com/science/article/pii/S0165027012003287?via%3Dihub doi:10.1016/j.jneumeth.2012.08.017 Close
	Jäckel, David; Frey, Urs; Fiscella, Michele; Franke, Felix; Hierlemann, Andreas Applicability of independent component analysis on high-density microelectrode array recordings Journal Article Journal of Neurophysiology, 108 (1), pp. 334-348, 2012, ISSN: 0022-3077. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, Spike Sorting @article{Jackel2012, title = {Applicability of independent component analysis on high-density microelectrode array recordings}, author = {David Jäckel and Urs Frey and Michele Fiscella and Felix Franke and Andreas Hierlemann}, url = {http://jn.physiology.org/cgi/doi/10.1152/jn.01106.2011}, doi = {10.1152/jn.01106.2011}, issn = {0022-3077}, year = {2012}, date = {2012-04-04}, journal = {Journal of Neurophysiology}, volume = {108}, number = {1}, pages = {334-348}, abstract = {Emerging complementary metal oxide semiconductor (CMOS)-based, high-density microelectrode array (HD-MEA) devices provide high spatial resolution at subcellular level and a large number of readout channels. These devices allow for simultaneous recording of extracellular activity of a large number of neurons with every neuron being detected by multiple electrodes. To analyze the recorded signals, spiking events have to be assigned to individual neurons, a process referred to as "spike sorting." For a set of observed signals, which constitute a linear mixture of a set of source signals, independent component (IC) analysis (ICA) can be used to demix blindly the data and extract the individual source signals. This technique offers great potential to alleviate the problem of spike sorting in HD-MEA recordings, as it represents an unsupervised method to separate the neuronal sources. The separated sources or ICs then constitute estimates of single-neuron signals, and threshold detection on the ICs yields the sorted spike times. However, it is unknown to what extent extracellular neuronal recordings meet the requirements of ICA. In this paper, we evaluate the applicability of ICA to spike sorting of HD-MEA recordings. The analysis of extracellular neuronal signals, recorded at high spatiotemporal resolution, reveals that the recorded data cannot be modeled as a purely linear mixture. As a consequence, ICA fails to separate completely the neuronal signals and cannot be used as a stand-alone method for spike sorting in HD-MEA recordings. We assessed the demixing performance of ICA using simulated data sets and found that the performance strongly depends on neuronal density and spike amplitude. Furthermore, we show how postprocessing techniques can be used to overcome the most severe limitations of ICA. In combination with these postprocessing techniques, ICA represents a viable method to facilitate rapid spike sorting of multidimensional neuronal recordings.}, keywords = {ETH-CMOS-MEA, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Emerging complementary metal oxide semiconductor (CMOS)-based, high-density microelectrode array (HD-MEA) devices provide high spatial resolution at subcellular level and a large number of readout channels. These devices allow for simultaneous recording of extracellular activity of a large number of neurons with every neuron being detected by multiple electrodes. To analyze the recorded signals, spiking events have to be assigned to individual neurons, a process referred to as "spike sorting." For a set of observed signals, which constitute a linear mixture of a set of source signals, independent component (IC) analysis (ICA) can be used to demix blindly the data and extract the individual source signals. This technique offers great potential to alleviate the problem of spike sorting in HD-MEA recordings, as it represents an unsupervised method to separate the neuronal sources. The separated sources or ICs then constitute estimates of single-neuron signals, and threshold detection on the ICs yields the sorted spike times. However, it is unknown to what extent extracellular neuronal recordings meet the requirements of ICA. In this paper, we evaluate the applicability of ICA to spike sorting of HD-MEA recordings. The analysis of extracellular neuronal signals, recorded at high spatiotemporal resolution, reveals that the recorded data cannot be modeled as a purely linear mixture. As a consequence, ICA fails to separate completely the neuronal signals and cannot be used as a stand-alone method for spike sorting in HD-MEA recordings. We assessed the demixing performance of ICA using simulated data sets and found that the performance strongly depends on neuronal density and spike amplitude. Furthermore, we show how postprocessing techniques can be used to overcome the most severe limitations of ICA. In combination with these postprocessing techniques, ICA represents a viable method to facilitate rapid spike sorting of multidimensional neuronal recordings. Close http://jn.physiology.org/cgi/doi/10.1152/jn.01106.2011 doi:10.1152/jn.01106.2011 Close
2011
	Jones, Ian L; Livi, Paolo; Lewandowska, Marta K; Fiscella, Michele; Roscic, Branka; Hierlemann, Andreas The potential of microelectrode arrays and microelectronics for biomedical research and diagnostics Journal Article Analytical and Bioanalytical Chemistry, 399 (7), pp. 2313-2329, 2011, ISSN: 1618-2650. Abstract \| Links \| BibTeX \| タグ: Review @article{Jones2011, title = {The potential of microelectrode arrays and microelectronics for biomedical research and diagnostics}, author = {Ian L Jones and Paolo Livi and Marta K Lewandowska and Michele Fiscella and Branka Roscic and Andreas Hierlemann}, url = {https://link.springer.com/article/10.1007%2Fs00216-010-3968-1}, doi = {10.1007/s00216-010-3968-1}, issn = {1618-2650}, year = {2011}, date = {2011-07-31}, journal = {Analytical and Bioanalytical Chemistry}, volume = {399}, number = {7}, pages = {2313-2329}, abstract = {Planar microelectrode arrays (MEAs) are devices that can be used in biomedical and basic in vitro research to provide extracellular electrophysiological information about biological systems at high spatial and temporal resolution. Complementary metal oxide semiconductor (CMOS) is a technology with which MEAs can be produced on a microscale featuring high spatial resolution and excellent signal-to-noise characteristics. CMOS MEAs are specialized for the analysis of complete electrogenic cellular networks at the cellular or subcellular level in dissociated cultures, organotypic cultures, and acute tissue slices; they can also function as biosensors to detect biochemical events. Models of disease or the response of cellular networks to pharmacological compounds can be studied in vitro, allowing one to investigate pathologies, such as cardiac arrhythmias, memory impairment due to Alzheimer's disease, or vision impairment caused by ganglion cell degeneration in the retina.}, keywords = {Review}, pubstate = {published}, tppubtype = {article} } Close Planar microelectrode arrays (MEAs) are devices that can be used in biomedical and basic in vitro research to provide extracellular electrophysiological information about biological systems at high spatial and temporal resolution. Complementary metal oxide semiconductor (CMOS) is a technology with which MEAs can be produced on a microscale featuring high spatial resolution and excellent signal-to-noise characteristics. CMOS MEAs are specialized for the analysis of complete electrogenic cellular networks at the cellular or subcellular level in dissociated cultures, organotypic cultures, and acute tissue slices; they can also function as biosensors to detect biochemical events. Models of disease or the response of cellular networks to pharmacological compounds can be studied in vitro, allowing one to investigate pathologies, such as cardiac arrhythmias, memory impairment due to Alzheimer's disease, or vision impairment caused by ganglion cell degeneration in the retina. Close https://link.springer.com/article/10.1007%2Fs00216-010-3968-1 doi:10.1007/s00216-010-3968-1 Close
	Hierlemann, Andreas; Frey, Urs; Hafizovic, Sadik; Heer, Flavio Growing cells atop microelectronic chips: Interfacing electrogenic cells in vitro with CMOS-based microelectrode arrays Journal Article Proceedings of the IEEE, 99 (2), pp. 252-284, 2011, ISSN: 00189219. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology, Review @article{Hierlemann2011, title = {Growing cells atop microelectronic chips: Interfacing electrogenic cells in vitro with CMOS-based microelectrode arrays}, author = {Andreas Hierlemann and Urs Frey and Sadik Hafizovic and Flavio Heer}, url = {http://ieeexplore.ieee.org/document/5594982/}, doi = {10.1109/JPROC.2010.2066532}, issn = {00189219}, year = {2011}, date = {2011-02-01}, journal = {Proceedings of the IEEE}, volume = {99}, number = {2}, pages = {252-284}, abstract = {Complementary semiconductor-metal-oxide (CMOS) technology is a very powerful technology that can be more or less directly interfaced to electrogenic cells, like heart or brain cells in vitro. To this end, the cells are cultured directly atop the CMOS chips, which usually undergo dedicated postprocessing to obtain a reliable bidirectional interface via noble-metal microelectrodes or high-k dielectrics. The big advantages of using CMOS integrated circuits (ICs) include connectivity, the possibility to address a large number of microelectrodes on a tiny chip, and signal quality, the possibility to condition small signals right at the spot of their generation. CMOS will be demonstrated to constitute an enabling technology that opens a route to high-spatio-temporal-resolution and low-noise electrophysiological recordings from a variety of biological preparations, such as brain slices, or cultured cardiac and brain cells. The recording technique is extracellular and noninvasive, and the CMOS chips do not leak out any toxic compounds, so that the cells remain viable for extended times. In turn, the CMOS chips have been demonstrated to survive several months of culturing while being fully immersed in saline solution and being exposed to cellular metabolic products. The latter requires dedicated passivation and packaging techniques as will be shown. Fully integrated, monolithic microelectrode systems, which feature large numbers of tightly spaced microelectrodes and the associated circuitry units for bidirectional interaction (stimulation and recording), will be in the focus of this review. The respective dense microelectrode arrays (MEAs) with small pixels enable subcellular-resolution investigation of regions of interest in, e.g., neurobiological preparations, and, at the same time, the large number of electrodes allows for studying the activity of entire neuronal networks . Application areas include neuroscience, as the devices enable fundamental neurophysiological insights at the cellular and circuit level, as well as medical diagnostics and pharmacology.}, keywords = {ETH-CMOS-MEA, MEA Technology, Review}, pubstate = {published}, tppubtype = {article} } Close Complementary semiconductor-metal-oxide (CMOS) technology is a very powerful technology that can be more or less directly interfaced to electrogenic cells, like heart or brain cells in vitro. To this end, the cells are cultured directly atop the CMOS chips, which usually undergo dedicated postprocessing to obtain a reliable bidirectional interface via noble-metal microelectrodes or high-k dielectrics. The big advantages of using CMOS integrated circuits (ICs) include connectivity, the possibility to address a large number of microelectrodes on a tiny chip, and signal quality, the possibility to condition small signals right at the spot of their generation. CMOS will be demonstrated to constitute an enabling technology that opens a route to high-spatio-temporal-resolution and low-noise electrophysiological recordings from a variety of biological preparations, such as brain slices, or cultured cardiac and brain cells. The recording technique is extracellular and noninvasive, and the CMOS chips do not leak out any toxic compounds, so that the cells remain viable for extended times. In turn, the CMOS chips have been demonstrated to survive several months of culturing while being fully immersed in saline solution and being exposed to cellular metabolic products. The latter requires dedicated passivation and packaging techniques as will be shown. Fully integrated, monolithic microelectrode systems, which feature large numbers of tightly spaced microelectrodes and the associated circuitry units for bidirectional interaction (stimulation and recording), will be in the focus of this review. The respective dense microelectrode arrays (MEAs) with small pixels enable subcellular-resolution investigation of regions of interest in, e.g., neurobiological preparations, and, at the same time, the large number of electrodes allows for studying the activity of entire neuronal networks . Application areas include neuroscience, as the devices enable fundamental neurophysiological insights at the cellular and circuit level, as well as medical diagnostics and pharmacology. Close http://ieeexplore.ieee.org/document/5594982/ doi:10.1109/JPROC.2010.2066532 Close
2010
	Livi, Paolo; Heer, Flavio; Frey, Urs; Bakkum, Douglas J; Hierlemann, Andreas Compact voltage and current stimulation buffer for high-density microelectrode arrays Journal Article IEEE Transactions on Biomedical Circuits and Systems, 4 (6), pp. 372-378, 2010, ISSN: 19324545. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology, Stimulation @article{Livi2010, title = {Compact voltage and current stimulation buffer for high-density microelectrode arrays}, author = {Paolo Livi and Flavio Heer and Urs Frey and Douglas J Bakkum and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/5617318/}, doi = {10.1109/TBCAS.2010.2080676}, issn = {19324545}, year = {2010}, date = {2010-11-01}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {4}, number = {6}, pages = {372-378}, abstract = {We report on a compact (0.02 mm2 ) buffer for both voltage and current stimulation of electrogenic cells on a complementary metal-oxide semiconductor microelectrode array. In voltage mode, the circuit is a high-current class-AB voltage follower, based on a local common-mode feedback (LCMFB) amplifier. In current mode, the circuit is a current conveyor of type II, using the same LCMFB amplifier with cascode stages to increase the gain. The circuit shows good linearity in the 0.5-3.5 V input range and has extensively been used for stimulation of neuronal cultures.}, keywords = {ETH-CMOS-MEA, MEA Technology, Stimulation}, pubstate = {published}, tppubtype = {article} } Close We report on a compact (0.02 mm2 ) buffer for both voltage and current stimulation of electrogenic cells on a complementary metal-oxide semiconductor microelectrode array. In voltage mode, the circuit is a high-current class-AB voltage follower, based on a local common-mode feedback (LCMFB) amplifier. In current mode, the circuit is a current conveyor of type II, using the same LCMFB amplifier with cascode stages to increase the gain. The circuit shows good linearity in the 0.5-3.5 V input range and has extensively been used for stimulation of neuronal cultures. Close http://ieeexplore.ieee.org/document/5617318/ doi:10.1109/TBCAS.2010.2080676 Close
	Frey, Urs; Sedivy, Jan; Heer, Flavio; Pedron, Rene; Ballini, Marco; Müller, Jan; Bakkum, Douglas J; Hafizovic, Sadik; Faraci, Francesca D; Greve, Frauke; Kirstein, Kay Uwe; Hierlemann, Andreas Switch-matrix-based high-density microelectrode array in CMOS technology Journal Article IEEE Journal of Solid-State Circuits, 45 (2), pp. 467-482, 2010, ISSN: 00189200. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology @article{Frey2010, title = {Switch-matrix-based high-density microelectrode array in CMOS technology}, author = {Urs Frey and Jan Sedivy and Flavio Heer and Rene Pedron and Marco Ballini and Jan Müller and Douglas J Bakkum and Sadik Hafizovic and Francesca D Faraci and Frauke Greve and Kay Uwe Kirstein and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/5405139/}, doi = {10.1109/JSSC.2009.2035196}, issn = {00189200}, year = {2010}, date = {2010-02-02}, journal = {IEEE Journal of Solid-State Circuits}, volume = {45}, number = {2}, pages = {467-482}, abstract = {We report on a CMOS-based microelectrode array (MEA) featuring 11, 011 metal electrodes and 126 channels, each of which comprises recording and stimulation electronics, for extracellular bidirectional communication with electrogenic cells, such as neurons or cardiomyocytes. The important features include: (i) high spatial resolution at (sub)cellular level with 3150 electrodes per mm2 (electrode diameter 7 um, electrode pitch 18 um); (ii) a reconflgurable routing of the recording sites to the 126 channels; and (iii) low noise levels.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close We report on a CMOS-based microelectrode array (MEA) featuring 11, 011 metal electrodes and 126 channels, each of which comprises recording and stimulation electronics, for extracellular bidirectional communication with electrogenic cells, such as neurons or cardiomyocytes. The important features include: (i) high spatial resolution at (sub)cellular level with 3150 electrodes per mm2 (electrode diameter 7 um, electrode pitch 18 um); (ii) a reconflgurable routing of the recording sites to the 126 channels; and (iii) low noise levels. Close http://ieeexplore.ieee.org/document/5405139/ doi:10.1109/JSSC.2009.2035196 Close
2009
	Frey, Urs; Egert, Ulrich; Heer, Flavio; Hafizovic, Sadik; Hierlemann, Andreas Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices Journal Article Biosensors and Bioelectronics, 24 (7), pp. 2191-2198, 2009, ISSN: 09565663. Abstract \| Links \| BibTeX \| タグ: Brain Slice, ETH-CMOS-MEA @article{Frey2009, title = {Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices}, author = {Urs Frey and Ulrich Egert and Flavio Heer and Sadik Hafizovic and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S095656630800643X?via%3Dihub}, doi = {10.1016/j.bios.2008.11.028}, issn = {09565663}, year = {2009}, date = {2009-03-15}, journal = {Biosensors and Bioelectronics}, volume = {24}, number = {7}, pages = {2191-2198}, abstract = {There is an enduring quest for technologies that provide - temporally and spatially - highly resolved information on electric neuronal or cardiac activity in functional tissues or cell cultures. Here, we present a planar high-density, low-noise microelectrode system realized in microelectronics technology that features 11,011 microelectrodes (3,150 electrodes per mm2), 126 of which can be arbitrarily selected and can, via a reconfigurable routing scheme, be connected to on-chip recording and stimulation circuits. This device enables long-term extracellular electrical-activity recordings at subcellular spatial resolution and microsecond temporal resolution to capture the entire dynamics of the cellular electrical signals. To illustrate the device performance, extracellular potentials of Purkinje cells (PCs) in acute slices of the cerebellum have been analyzed. A detailed and comprehensive picture of the distribution and dynamics of action potentials (APs) in the somatic and dendritic regions of a single cell was obtained from the recordings by applying spike sorting and spike-triggered averaging methods to the collected data. An analysis of the measured local current densities revealed a reproducible sink/source pattern within a single cell during an AP. The experimental data substantiated compartmental models and can be used to extend those models to better understand extracellular single-cell potential patterns and their contributions to the population activity. The presented devices can be conveniently applied to a broad variety of biological preparations, i.e., neural or cardiac tissues, slices, or cell cultures can be grown or placed directly atop of the chips for fundamental mechanistic or pharmacological studies.}, keywords = {Brain Slice, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close There is an enduring quest for technologies that provide - temporally and spatially - highly resolved information on electric neuronal or cardiac activity in functional tissues or cell cultures. Here, we present a planar high-density, low-noise microelectrode system realized in microelectronics technology that features 11,011 microelectrodes (3,150 electrodes per mm2), 126 of which can be arbitrarily selected and can, via a reconfigurable routing scheme, be connected to on-chip recording and stimulation circuits. This device enables long-term extracellular electrical-activity recordings at subcellular spatial resolution and microsecond temporal resolution to capture the entire dynamics of the cellular electrical signals. To illustrate the device performance, extracellular potentials of Purkinje cells (PCs) in acute slices of the cerebellum have been analyzed. A detailed and comprehensive picture of the distribution and dynamics of action potentials (APs) in the somatic and dendritic regions of a single cell was obtained from the recordings by applying spike sorting and spike-triggered averaging methods to the collected data. An analysis of the measured local current densities revealed a reproducible sink/source pattern within a single cell during an AP. The experimental data substantiated compartmental models and can be used to extend those models to better understand extracellular single-cell potential patterns and their contributions to the population activity. The presented devices can be conveniently applied to a broad variety of biological preparations, i.e., neural or cardiac tissues, slices, or cell cultures can be grown or placed directly atop of the chips for fundamental mechanistic or pharmacological studies. Close http://www.sciencedirect.com/science/article/pii/S095656630800643X?via%3Dihub doi:10.1016/j.bios.2008.11.028 Close
	Weber, Wilfried; Luzi, Stefan; Karlsson, Maria; Sanchez-Bustamante, Carlota Diaz; Frey, Urs; Hierlemann, Andreas; Fussenegger, Martin A synthetic mammalian electro-genetic transcription circuit Journal Article Nucleic Acids Research, 37 (4), pp. 1-8, 2009, ISSN: 03051048. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Weber2009, title = {A synthetic mammalian electro-genetic transcription circuit}, author = {Wilfried Weber and Stefan Luzi and Maria Karlsson and Carlota Diaz Sanchez-Bustamante and Urs Frey and Andreas Hierlemann and Martin Fussenegger}, url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp014}, doi = {10.1093/nar/gkp014}, issn = {03051048}, year = {2009}, date = {2009-02-03}, journal = {Nucleic Acids Research}, volume = {37}, number = {4}, pages = {1-8}, abstract = {Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electrogenetic implants assembled from electronic and genetic parts.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electrogenetic implants assembled from electronic and genetic parts. Close https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp014 doi:10.1093/nar/gkp014 Close
2008
	Sanchez-Bustamante, Carlota Diaz; Frey, Urs; Kelm, Jens M; Hierlemann, Andreas; Fussenegger, Martin Modulation of cardiomyocyte electrical properties using regulated bone morphogenetic protein-2 expression. Journal Article Tissue Engineering. Part A, 14 (12), pp. 1969-1988, 2008, ISSN: 1937-3341. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Sanchez-Bustamante2008, title = {Modulation of cardiomyocyte electrical properties using regulated bone morphogenetic protein-2 expression.}, author = {Carlota Diaz Sanchez-Bustamante and Urs Frey and Jens M Kelm and Andreas Hierlemann and Martin Fussenegger}, url = {http://online.liebertpub.com/doi/abs/10.1089/ten.tea.2007.0302?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed}, doi = {10.1089/ten.tea.2007.0302}, issn = {1937-3341}, year = {2008}, date = {2008-11-19}, journal = {Tissue Engineering. Part A}, volume = {14}, number = {12}, pages = {1969-1988}, abstract = {Because cardiomyocytes lose their ability to divide after birth, any subsequent cell loss or dysfunction results in pathologic cardiac rhythm initiation or impulse conduction. Strategies to restore and control the electrophysiological activity of the heart may, therefore, greatly affect the regeneration of cardiac tissue functionality. Using lentivirus-derived particles to regulate the bone morphogenetic protein-2 (BMP-2) gene expression in a pristinamycin- or gaseous acetaldehyde-inducible manner, we demonstrated the adjustment of cardiomyocyte electrophysiological characteristics. Complementary metal oxide semiconductor-based high-density microelectrode arrays (HD-MEAs) were used to monitor the electrophysiological activity of neonatal rat cardiomyocytes (NRCs) cultured as monolayers (NRCml) or as microtissues (NRCmt). NRCmt more closely resembled heart tissue physiology than did NRCml and could be conveniently monitored using HD-MEAs because of their ability to detect low-signal events and to sub-select the region of interest, namely, areas where the microtissues were placed. Cardiomyocyte-forming microtissues, transduced using lentiviral vectors encoding BMP-2, were capable of restoring myocardial microtissue electrical activity. We also engineered NRCmt to functionally couple within a cardiomyocyte monolayer, thus showing pacemaker-like activity upon local regulation of transgenic BMP-2 expression. The controlled expression of therapeutic transgenes represents a crucial advance for clinical interventions and gene-function analysis.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Because cardiomyocytes lose their ability to divide after birth, any subsequent cell loss or dysfunction results in pathologic cardiac rhythm initiation or impulse conduction. Strategies to restore and control the electrophysiological activity of the heart may, therefore, greatly affect the regeneration of cardiac tissue functionality. Using lentivirus-derived particles to regulate the bone morphogenetic protein-2 (BMP-2) gene expression in a pristinamycin- or gaseous acetaldehyde-inducible manner, we demonstrated the adjustment of cardiomyocyte electrophysiological characteristics. Complementary metal oxide semiconductor-based high-density microelectrode arrays (HD-MEAs) were used to monitor the electrophysiological activity of neonatal rat cardiomyocytes (NRCs) cultured as monolayers (NRCml) or as microtissues (NRCmt). NRCmt more closely resembled heart tissue physiology than did NRCml and could be conveniently monitored using HD-MEAs because of their ability to detect low-signal events and to sub-select the region of interest, namely, areas where the microtissues were placed. Cardiomyocyte-forming microtissues, transduced using lentiviral vectors encoding BMP-2, were capable of restoring myocardial microtissue electrical activity. We also engineered NRCmt to functionally couple within a cardiomyocyte monolayer, thus showing pacemaker-like activity upon local regulation of transgenic BMP-2 expression. The controlled expression of therapeutic transgenes represents a crucial advance for clinical interventions and gene-function analysis. Close http://online.liebertpub.com/doi/abs/10.1089/ten.tea.2007.0302?url_ver=Z39.88-20[...] doi:10.1089/ten.tea.2007.0302 Close
2007
	Heer, Flavio; Hafizovic, Sadik; Ugniwenko, T; Frey, Urs; Blau, Axel; Ziegler, Christiane; Hierlemann, Andreas A CMOS-based microelectrode array for interaction with neuronal cultures Journal Article Journal of Neuroscience Methods, 164 (1), pp. 93-106, 2007, ISSN: 0165-0270. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, Neuronal Networks @article{Hierlemann2007, title = {A CMOS-based microelectrode array for interaction with neuronal cultures}, author = {Flavio Heer and Sadik Hafizovic and T Ugniwenko and Urs Frey and Axel Blau and Christiane Ziegler and Andreas Hierlemann}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0165027007001781}, doi = {10.1016/j.jneumeth.2007.04.006}, issn = {0165-0270}, year = {2007}, date = {2007-04-19}, journal = {Journal of Neuroscience Methods}, volume = {164}, number = {1}, pages = {93-106}, abstract = {We report on the system integration of a CMOS chip that is capable of bidirectionally communicating (stimulation and recording) with electrogenic cells such as neurons or cardiomyocytes and that is targeted at investigating electrical signal propagation within cellular networks in vitro. The overall system consists of three major subunits: first, the core component is a 6.5 mm × 6.5 mm CMOS chip, on top of which the cells are cultured. It features 128 bidirectional electrodes, each equipped with dedicated analog filters and amplification stages and a stimulation buffer. The electrodes are sampled at 20 kHz with 8-bit resolution. The measured input-referred circuitry noise is 5.9 muV root mean square (10 Hz to 100 kHz), which allows to reliably detect the cell signals ranging from 1 mVpp down to 40 muVpp. Additionally, temperature sensors, a digital-to-analog converter for stimulation, and a digital interface for data transmission are integrated. Second, there is a reconfigurable logic device, which provides chip control, event detection, data buffering and an USB interface, capable of processing the 2.56 million samples per second. The third element includes software that is running on a standard PC performing data capturing, processing, and visualization. Experiments involving the stimulation of neurons with two different spatio-temporal patterns and the recording of the triggered spiking activity have been carried out. The response patterns have been successfully classified (83% correct) with respect to the different stimulation patterns. The advantages over current microelectrode arrays, as has been demonstrated in the experiments, include the capability to stimulate (voltage stimulation, 8 bit, 60 kHz) spatio-temporal patterns on arbitrary sets of electrodes and the fast stimulation reset mechanism that allows to record neuronal signals on a stimulating electrode 5 ms after stimulation (instantaneously on all other electrodes). Other advantages of the overall system include the small number of needed electrical connections due to the digital interface and the short latency time that allows to initiate a stimulation less than 2 ms after the detection of an action potential in closed-loop configurations.}, keywords = {ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close We report on the system integration of a CMOS chip that is capable of bidirectionally communicating (stimulation and recording) with electrogenic cells such as neurons or cardiomyocytes and that is targeted at investigating electrical signal propagation within cellular networks in vitro. The overall system consists of three major subunits: first, the core component is a 6.5 mm × 6.5 mm CMOS chip, on top of which the cells are cultured. It features 128 bidirectional electrodes, each equipped with dedicated analog filters and amplification stages and a stimulation buffer. The electrodes are sampled at 20 kHz with 8-bit resolution. The measured input-referred circuitry noise is 5.9 muV root mean square (10 Hz to 100 kHz), which allows to reliably detect the cell signals ranging from 1 mVpp down to 40 muVpp. Additionally, temperature sensors, a digital-to-analog converter for stimulation, and a digital interface for data transmission are integrated. Second, there is a reconfigurable logic device, which provides chip control, event detection, data buffering and an USB interface, capable of processing the 2.56 million samples per second. The third element includes software that is running on a standard PC performing data capturing, processing, and visualization. Experiments involving the stimulation of neurons with two different spatio-temporal patterns and the recording of the triggered spiking activity have been carried out. The response patterns have been successfully classified (83% correct) with respect to the different stimulation patterns. The advantages over current microelectrode arrays, as has been demonstrated in the experiments, include the capability to stimulate (voltage stimulation, 8 bit, 60 kHz) spatio-temporal patterns on arbitrary sets of electrodes and the fast stimulation reset mechanism that allows to record neuronal signals on a stimulating electrode 5 ms after stimulation (instantaneously on all other electrodes). Other advantages of the overall system include the small number of needed electrical connections due to the digital interface and the short latency time that allows to initiate a stimulation less than 2 ms after the detection of an action potential in closed-loop configurations. Close http://linkinghub.elsevier.com/retrieve/pii/S0165027007001781 doi:10.1016/j.jneumeth.2007.04.006 Close
	Greve, Frauke; Lichtenberg, Jan; Kirstein, Kay Uwe; Frey, Urs; Perriard, Jean Claude; Hierlemann, Andreas A perforated CMOS microchip platform for immobilization and activity monitoring of electrogenic cells Journal Article Journal of Micromechanics and Microengineering, 17 (3), pp. 462-471, 2007, ISSN: 0960-1317. Abstract \| Links \| BibTeX \| タグ: 2D Neuronal Culture, Cardiomyocytes, ETH-CMOS-MEA, MEA Technology @article{Greve2007, title = {A perforated CMOS microchip platform for immobilization and activity monitoring of electrogenic cells}, author = {Frauke Greve and Jan Lichtenberg and Kay Uwe Kirstein and Urs Frey and Jean Claude Perriard and Andreas Hierlemann}, url = {http://iopscience.iop.org/article/10.1088/0960-1317/17/3/007/}, doi = {10.1088/0960-1317/17/3/007}, issn = {0960-1317}, year = {2007}, date = {2007-01-30}, journal = {Journal of Micromechanics and Microengineering}, volume = {17}, number = {3}, pages = {462-471}, abstract = {CMOS-based microelectrode systems offer decisive advantages over conventional micro-electrode arrays, which include the possibility to perform on-chip signal conditioning or to efficiently use larger numbers of electrodes to obtain statistically relevant data, e.g., in pharmacological drug screening. A larger number of electrodes can only be realized with the help of on-chip multiplexing and readout schemes, which require integrated electronics. Another fundamental issue in performing high-fidelity recordings from electrogenic cells is a good electrical coupling between the cells and the microelectrodes, in particular, since the recorded extracellular signals are in the range of only 10–1000 µV. In this paper we present the first CMOS microelectrode system with integrated micromechanical cell-placement features fabricated in a commercial CMOS process with subsequent post-CMOS bulk micromachining. This new microdevice aims at enabling the precise placement of single cells in the center of the electrodes to ensure an efficient use of the available electrodes, even for low-density cell cultures. Small through-chip holes have been generated at the metal-electrode sites by using a combination of bulk micromachining and reactive-ion etching. These holes act as orifices so that cell immobilization can be achieved by means of pneumatic anchoring. The chip additionally hosts integrated circuitry, i.e., multiplexers to select the respective readout electrodes, an amplifier with selectable gain (2×, 10×, 100×), and a high-pass filter (100 Hz cut-off). In this paper we show that electrical signals from most of the electrodes can be recorded, even in low-density cultures of neonatal rat cardiomyocytes, by using perforated metal electrodes and by applying a small underpressure from the backside of the chip. The measurements evidenced that, in most cases, about 90% of the electrodes were covered with single cells, approximately 4% were covered with more than one cell due to clustering and approximately 6% were not covered with any cell, mostly as a consequence of orifice clogging. After 4 days of culturing, the cells were still in place on the electrodes so that the cell electrical activity could be measured using the on-chip circuitry. Measured signal amplitudes were in the range of 500–700 µV, while the input-referred noise of the readout was below 15 µVrms (100 Hz–4 kHz bandwidth). We report on the development and fabrication of this new cell-biological tool and present first results collected during the characterization and evaluation of the chip. The recordings of electrical potentials of neonatal rat cardiomyocytes after several days in vitro, which, on the one hand, were conventionally cultured (no pneumatic anchoring) and, on the other hand, were anchored and immobilized, will be detailed.}, keywords = {2D Neuronal Culture, Cardiomyocytes, ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close CMOS-based microelectrode systems offer decisive advantages over conventional micro-electrode arrays, which include the possibility to perform on-chip signal conditioning or to efficiently use larger numbers of electrodes to obtain statistically relevant data, e.g., in pharmacological drug screening. A larger number of electrodes can only be realized with the help of on-chip multiplexing and readout schemes, which require integrated electronics. Another fundamental issue in performing high-fidelity recordings from electrogenic cells is a good electrical coupling between the cells and the microelectrodes, in particular, since the recorded extracellular signals are in the range of only 10–1000 µV. In this paper we present the first CMOS microelectrode system with integrated micromechanical cell-placement features fabricated in a commercial CMOS process with subsequent post-CMOS bulk micromachining. This new microdevice aims at enabling the precise placement of single cells in the center of the electrodes to ensure an efficient use of the available electrodes, even for low-density cell cultures. Small through-chip holes have been generated at the metal-electrode sites by using a combination of bulk micromachining and reactive-ion etching. These holes act as orifices so that cell immobilization can be achieved by means of pneumatic anchoring. The chip additionally hosts integrated circuitry, i.e., multiplexers to select the respective readout electrodes, an amplifier with selectable gain (2×, 10×, 100×), and a high-pass filter (100 Hz cut-off). In this paper we show that electrical signals from most of the electrodes can be recorded, even in low-density cultures of neonatal rat cardiomyocytes, by using perforated metal electrodes and by applying a small underpressure from the backside of the chip. The measurements evidenced that, in most cases, about 90% of the electrodes were covered with single cells, approximately 4% were covered with more than one cell due to clustering and approximately 6% were not covered with any cell, mostly as a consequence of orifice clogging. After 4 days of culturing, the cells were still in place on the electrodes so that the cell electrical activity could be measured using the on-chip circuitry. Measured signal amplitudes were in the range of 500–700 µV, while the input-referred noise of the readout was below 15 µVrms (100 Hz–4 kHz bandwidth). We report on the development and fabrication of this new cell-biological tool and present first results collected during the characterization and evaluation of the chip. The recordings of electrical potentials of neonatal rat cardiomyocytes after several days in vitro, which, on the one hand, were conventionally cultured (no pneumatic anchoring) and, on the other hand, were anchored and immobilized, will be detailed. Close http://iopscience.iop.org/article/10.1088/0960-1317/17/3/007/ doi:10.1088/0960-1317/17/3/007 Close
2006
	Heer, Flavio; Hafizovic, Sadik; Ugniwenko, T; Frey, Urs; Franks, Wendy; Perriard, Evelyne; Perriard, Jean Claude; Blau, Axel; Ziegler, Christiane; Hierlemann, Andreas Single-chip microelectronic system to interface with living cells Journal Article Biosensors & Bioelectronics, 22 (11), pp. 2546-2553, 2006, ISSN: 0956-5663. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA, Neuronal Networks @article{Hierlemann2006, title = {Single-chip microelectronic system to interface with living cells}, author = {Flavio Heer and Sadik Hafizovic and T Ugniwenko and Urs Frey and Wendy Franks and Evelyne Perriard and Jean Claude Perriard and Axel Blau and Christiane Ziegler and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S0956566306004891?via%3Dihub}, doi = {10.1016/j.bios.2006.10.003}, issn = {0956-5663}, year = {2006}, date = {2006-11-13}, journal = {Biosensors & Bioelectronics}, volume = {22}, number = {11}, pages = {2546-2553}, abstract = {A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments. Close http://www.sciencedirect.com/science/article/pii/S0956566306004891?via%3Dihub doi:10.1016/j.bios.2006.10.003 Close
	Franks, Wendy; Tosatti, Samuele; Heer, Flavio; Seif, Philipp; Textor, Marcus; Hierlemann, Andreas Patterned cell adhesion by self-assembled structures for use with a CMOS cell-based biosensor Journal Article Biosensors & Bioelectronics, 22 (7), pp. 1426-1433, 2006, ISSN: 0956-5663. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Hierlemann2006b, title = {Patterned cell adhesion by self-assembled structures for use with a CMOS cell-based biosensor}, author = {Wendy Franks and Samuele Tosatti and Flavio Heer and Philipp Seif and Marcus Textor and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S095656630600282X?via%3Dihub}, doi = {10.1016/j.bios.2006.06.031}, issn = {0956-5663}, year = {2006}, date = {2006-10-19}, journal = {Biosensors & Bioelectronics}, volume = {22}, number = {7}, pages = {1426-1433}, abstract = {A strategy for patterned cell adhesion based on chemical surface modification is presented. To confine cell adhesion to specific locations, an engineered surface for high-contrast protein adsorption and, hence, cell attachment has been developed. Surface functionalization is based on selective molecular-assembly patterning (SMAP). An amine-terminated self-assembled monolayer is used to define areas of cell adhesion. A protein-repellent grafted copolymer, poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), is used to render the surrounding silicon dioxide resistant to protein adsorption. X-ray photoelectron spectroscopy, scanning ellipsometry and fluorescence microscopy techniques were used to monitor the individual steps of the patterning process. Successful guided growth using these layers is demonstrated with primary neonatal rat cardiomyocytes, up to 4 days in vitro, and with the HL-1 cardiomyocyte cell line, up to 7 days in vitro. The advantage of the presented method is that high-resolution engineered surfaces can be realized using a simple, cost-effective, dip-and-rinse process. The technique has been developed for application on a CMOS cell-based biosensor, which comprises an array of microelectrodes to extracellularly record electrical activity from cardiomyocytes.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close A strategy for patterned cell adhesion based on chemical surface modification is presented. To confine cell adhesion to specific locations, an engineered surface for high-contrast protein adsorption and, hence, cell attachment has been developed. Surface functionalization is based on selective molecular-assembly patterning (SMAP). An amine-terminated self-assembled monolayer is used to define areas of cell adhesion. A protein-repellent grafted copolymer, poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), is used to render the surrounding silicon dioxide resistant to protein adsorption. X-ray photoelectron spectroscopy, scanning ellipsometry and fluorescence microscopy techniques were used to monitor the individual steps of the patterning process. Successful guided growth using these layers is demonstrated with primary neonatal rat cardiomyocytes, up to 4 days in vitro, and with the HL-1 cardiomyocyte cell line, up to 7 days in vitro. The advantage of the presented method is that high-resolution engineered surfaces can be realized using a simple, cost-effective, dip-and-rinse process. The technique has been developed for application on a CMOS cell-based biosensor, which comprises an array of microelectrodes to extracellularly record electrical activity from cardiomyocytes. Close http://www.sciencedirect.com/science/article/pii/S095656630600282X?via%3Dihub doi:10.1016/j.bios.2006.06.031 Close
	Heer, Flavio; Hafizovic, Sadik; Franks, Wendy; Blau, Axel; Ziegler, Christiane; Hierlemann, Andreas CMOS microelectrode array for bidirectional interaction with neuronal networks Journal Article IEEE Journal of Solid-State Circuits, 41 (7), pp. 1620-1629, 2006, ISSN: 0018-9200. Abstract \| Links \| BibTeX \| タグ: 2D Neuronal Culture, ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation @article{Heer2006, title = {CMOS microelectrode array for bidirectional interaction with neuronal networks}, author = {Flavio Heer and Sadik Hafizovic and Wendy Franks and Axel Blau and Christiane Ziegler and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/1644873/}, doi = {10.1109/JSSC.2006.873677}, issn = {0018-9200}, year = {2006}, date = {2006-07-07}, journal = {IEEE Journal of Solid-State Circuits}, volume = {41}, number = {7}, pages = {1620-1629}, abstract = {A CMOS metal-electrode-based micro system for bidirectional communication (stimulation and recording) with neuronal cells in vitro is presented. The chip overcomes the interconnect challenge that limits today's bidirectional microelectrode arrays. The microsystem has been fabricated in an industrial CMOS technology with several post-CMOS processing steps to realize 128 biocompatible electrodes and to ensure chip stability in physiological saline. The system comprises all necessary control circuitry and on-chip A/D and D/A conversion. A modular design has been implemented, where individual stimulation- and signal-conditioning circuitry units are associated with each electrode. Stimulation signals with a resolution of 8 bits can be sent to any subset of electrodes at a rate of 60 kHz, while all electrodes of the chip are continuously sampled at a rate of 20 kHz. The circuitry at each electrode can be individually reset to its operating point in order to suppress artifacts evoked by the stimulation pulses. Biological measurements from cultured neuronal networks originating from dissociated cortical tissue of fertilized chicken eggs with amplitudes of up to 500 muVpp are presented.}, keywords = {2D Neuronal Culture, ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation}, pubstate = {published}, tppubtype = {article} } Close A CMOS metal-electrode-based micro system for bidirectional communication (stimulation and recording) with neuronal cells in vitro is presented. The chip overcomes the interconnect challenge that limits today's bidirectional microelectrode arrays. The microsystem has been fabricated in an industrial CMOS technology with several post-CMOS processing steps to realize 128 biocompatible electrodes and to ensure chip stability in physiological saline. The system comprises all necessary control circuitry and on-chip A/D and D/A conversion. A modular design has been implemented, where individual stimulation- and signal-conditioning circuitry units are associated with each electrode. Stimulation signals with a resolution of 8 bits can be sent to any subset of electrodes at a rate of 60 kHz, while all electrodes of the chip are continuously sampled at a rate of 20 kHz. The circuitry at each electrode can be individually reset to its operating point in order to suppress artifacts evoked by the stimulation pulses. Biological measurements from cultured neuronal networks originating from dissociated cortical tissue of fertilized chicken eggs with amplitudes of up to 500 muVpp are presented. Close http://ieeexplore.ieee.org/document/1644873/ doi:10.1109/JSSC.2006.873677 Close
	Linder, Vincent; Koster, Sander; Franks, Wendy; Kraus, Tobias; Verpoorte, Elisabeth; Heer, Flavio; Hierlemann, Andreas; de Rooij, Nico F Microfluidics/CMOS orthogonal capabilities for cell biology Journal Article Biomedical Microdevices, 8 (2), pp. 159-166, 2006, ISSN: 1572-8781. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Linder2006, title = {Microfluidics/CMOS orthogonal capabilities for cell biology}, author = {Vincent Linder and Sander Koster and Wendy Franks and Tobias Kraus and Elisabeth Verpoorte and Flavio Heer and Andreas Hierlemann and Nico F de Rooij}, url = {https://link.springer.com/article/10.1007%2Fs10544-006-7711-9}, doi = {10.1007/s10544-006-7711-9}, issn = {1572-8781}, year = {2006}, date = {2006-06-01}, journal = {Biomedical Microdevices}, volume = {8}, number = {2}, pages = {159-166}, abstract = {The study of individual cells and cellular networks can greatly benefit from the capabilities of microfabricated devices for the stimulation and the recording of electrical cellular events. In this contribution, we describe the development of a device, which combines capabilities for both electrical and pharmacological cell stimulation, and the subsequent recording of electrical cellular activity. The device combines the unique advantages of integrated circuitry (CMOS technology) for signal processing and microfluidics for drug delivery. Both techniques are ideally suited to study electrogenic mammalian cells, because feature sizes are of the same order as the cell diameter, ∼50 mum. Despite these attractive features, we observe a size mismatch between microfluidic devices, with bulky fluidic connections to the outside world, and highly miniaturized CMOS chips. To overcome this problem, we developed a microfluidic flow cell that accommodates a small CMOS chip. We simulated the performances of a flow cell based on a 3-D microfluidic system, and then fabricated the device to experimentally verify the nutrient delivery and localized drug delivery performance. The flow-cell has a constant nutrient flow, and six drug inlets that can individually deliver a drug to the cells. The experimental analysis of the nutrient and drug flow mass transfer properties in the flowcell are in good agreement with our simulations. For an experimental proof-of-principle, we successfully delivered, in a spatially resolved manner, a `drug' to a culture of HL-1 cardiac myocytes.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close The study of individual cells and cellular networks can greatly benefit from the capabilities of microfabricated devices for the stimulation and the recording of electrical cellular events. In this contribution, we describe the development of a device, which combines capabilities for both electrical and pharmacological cell stimulation, and the subsequent recording of electrical cellular activity. The device combines the unique advantages of integrated circuitry (CMOS technology) for signal processing and microfluidics for drug delivery. Both techniques are ideally suited to study electrogenic mammalian cells, because feature sizes are of the same order as the cell diameter, ∼50 mum. Despite these attractive features, we observe a size mismatch between microfluidic devices, with bulky fluidic connections to the outside world, and highly miniaturized CMOS chips. To overcome this problem, we developed a microfluidic flow cell that accommodates a small CMOS chip. We simulated the performances of a flow cell based on a 3-D microfluidic system, and then fabricated the device to experimentally verify the nutrient delivery and localized drug delivery performance. The flow-cell has a constant nutrient flow, and six drug inlets that can individually deliver a drug to the cells. The experimental analysis of the nutrient and drug flow mass transfer properties in the flowcell are in good agreement with our simulations. For an experimental proof-of-principle, we successfully delivered, in a spatially resolved manner, a `drug' to a culture of HL-1 cardiac myocytes. Close https://link.springer.com/article/10.1007%2Fs10544-006-7711-9 doi:10.1007/s10544-006-7711-9 Close
	Kraus, Tobias; Verpoorte, Elisabeth; Linder, Vincent; Franks, Wendy; Hierlemann, Andreas; Heer, Flavio; Hafizovic, Sadik; Fujii, Teruo; de Rooij, Nico F; Koster, Sander Characterization of a microfluidic dispensing system for localised stimulation of cellular networks Journal Article Lab Chip, 6 (2), pp. 218-229, 2006. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Koster2006, title = {Characterization of a microfluidic dispensing system for localised stimulation of cellular networks}, author = {Tobias Kraus and Elisabeth Verpoorte and Vincent Linder and Wendy Franks and Andreas Hierlemann and Flavio Heer and Sadik Hafizovic and Teruo Fujii and Nico F de Rooij and Sander Koster}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2006/LC/b511768b#!divAbstract}, doi = {10.1039/B511768B}, year = {2006}, date = {2006-01-04}, journal = {Lab Chip}, volume = {6}, number = {2}, pages = {218-229}, publisher = {The Royal Society of Chemistry}, abstract = {We present a 3-D microfluidic device designed for localized drug delivery to cellular networks. The device features a flow cell comprising a main channel for nutrient delivery as well as multiple channels for drug delivery. This device is one key component of a larger, fully integrated system now under development, based upon a microelectrode array (MEA) with on-chip CMOS circuitry for recording and stimulation of electrogenic cells (e.g. neurons, cardiomyocytes). As a critical system unit, the microfluidics must be carefully designed and characterized to ensure that candidate drugs are delivered to specific regions of the culture at known concentrations. Furthermore, microfluidic design and functionality is dictated by the size, geometry, and material/electrical characteristics of the CMOS MEA. Therefore, this paper reports on the design considerations and fabrication of the flow cell, including theoretical and experimental analysis of the mass transfer properties of the nutrient and drug flows, which are in good agreement with one another. To demonstrate proof of concept, the flow cell was mounted on a dummy CMOS chip, which had been plated with HL-1 cardiomyocytes. A test chemical compound was delivered to the cell culture in a spatially resolved manner. Envisioned applications of this stand-alone system include simultaneous toxicological testing of multiple compounds and chemical stimulation of natural neural networks for neuroscience investigations}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close We present a 3-D microfluidic device designed for localized drug delivery to cellular networks. The device features a flow cell comprising a main channel for nutrient delivery as well as multiple channels for drug delivery. This device is one key component of a larger, fully integrated system now under development, based upon a microelectrode array (MEA) with on-chip CMOS circuitry for recording and stimulation of electrogenic cells (e.g. neurons, cardiomyocytes). As a critical system unit, the microfluidics must be carefully designed and characterized to ensure that candidate drugs are delivered to specific regions of the culture at known concentrations. Furthermore, microfluidic design and functionality is dictated by the size, geometry, and material/electrical characteristics of the CMOS MEA. Therefore, this paper reports on the design considerations and fabrication of the flow cell, including theoretical and experimental analysis of the mass transfer properties of the nutrient and drug flows, which are in good agreement with one another. To demonstrate proof of concept, the flow cell was mounted on a dummy CMOS chip, which had been plated with HL-1 cardiomyocytes. A test chemical compound was delivered to the cell culture in a spatially resolved manner. Envisioned applications of this stand-alone system include simultaneous toxicological testing of multiple compounds and chemical stimulation of natural neural networks for neuroscience investigations Close http://pubs.rsc.org/en/Content/ArticleLanding/2006/LC/b511768b#!divAbstract doi:10.1039/B511768B Close
2005
	Franks, Wendy; Schenker, Iwan; Schmutz, Patrik; Hierlemann, Andreas Impedance characterization and modeling of electrodes for biomedical applications Journal Article IEEE Transactions on Biomedical Engineering, 52 (7), pp. 1295-1302, 2005, ISSN: 00189294. Abstract \| Links \| BibTeX \| タグ: MEA Technology @article{Franks2005, title = {Impedance characterization and modeling of electrodes for biomedical applications}, author = {Wendy Franks and Iwan Schenker and Patrik Schmutz and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/1440608/}, doi = {10.1109/TBME.2005.847523}, issn = {00189294}, year = {2005}, date = {2005-06-13}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {52}, number = {7}, pages = {1295-1302}, abstract = {A low electrode-electrolyte impedance interface is critical in the design of electrodes for biomedical applications. To design low-impedance interfaces a complete understanding of the physical processes contributing to the impedance is required. In this work a model describing these physical processes is validated and extended to quantify the effect of organic coatings and incubation time. Electrochemical impedance spectroscopy has been used to electrically characterize the interface for various electrode materials: platinum, platinum black, and titanium nitride; and varying electrode sizes: 1 cm2, and 900 mu m2. An equivalent circuit model comprising an interface capacitance, shunted by a charge transfer resistance, in series with the solution resistance has been fitted to the experimental results. Theoretical equations have been used to calculate the interface capacitance impedance and the solution resistance, yielding results that correspond well with the fitted parameter values, thereby confirming the validity of the equations. The effect of incubation time, and two organic cell-adhesion promoting coatings, poly-L-lysine and laminin, on the interface impedance has been quantified using the model. This demonstrates the benefits of using this model in developing better understanding of the physical processes occurring at the interface in more complex, biomedically relevant situations.}, keywords = {MEA Technology}, pubstate = {published}, tppubtype = {article} } Close A low electrode-electrolyte impedance interface is critical in the design of electrodes for biomedical applications. To design low-impedance interfaces a complete understanding of the physical processes contributing to the impedance is required. In this work a model describing these physical processes is validated and extended to quantify the effect of organic coatings and incubation time. Electrochemical impedance spectroscopy has been used to electrically characterize the interface for various electrode materials: platinum, platinum black, and titanium nitride; and varying electrode sizes: 1 cm2, and 900 mu m2. An equivalent circuit model comprising an interface capacitance, shunted by a charge transfer resistance, in series with the solution resistance has been fitted to the experimental results. Theoretical equations have been used to calculate the interface capacitance impedance and the solution resistance, yielding results that correspond well with the fitted parameter values, thereby confirming the validity of the equations. The effect of incubation time, and two organic cell-adhesion promoting coatings, poly-L-lysine and laminin, on the interface impedance has been quantified using the model. This demonstrates the benefits of using this model in developing better understanding of the physical processes occurring at the interface in more complex, biomedically relevant situations. Close http://ieeexplore.ieee.org/document/1440608/ doi:10.1109/TBME.2005.847523 Close
2004
	Jenkner, Martin; Tartagni, Marco; Hierlemann, Andreas; Thewes, Roland Cell-based CMOS sensor and actuator arrays Journal Article IEEE Journal of Solid-State Circuits, 39 (12), pp. 2431-2437, 2004, ISSN: 00189200. Abstract \| Links \| BibTeX \| タグ: MEA Technology, Review @article{Jenkner2004, title = {Cell-based CMOS sensor and actuator arrays}, author = {Martin Jenkner and Marco Tartagni and Andreas Hierlemann and Roland Thewes}, url = {http://ieeexplore.ieee.org/document/1362853/}, doi = {10.1109/JSSC.2004.837082}, issn = {00189200}, year = {2004}, date = {2004-11-30}, journal = {IEEE Journal of Solid-State Circuits}, volume = {39}, number = {12}, pages = {2431-2437}, abstract = {In recent years, increasing knowledge about in vitro cell handling and culturing has encouraged a variety of CMOS-based approaches to stimulate and detect electrical activity of biological cells. This paper outlines in a topical review the scope of cell-based biosensors and actuators for in vitro applications ranging from single-cell detection to multisite probing of complex neural tissue. Recent examples are selected to demonstrate how standard CMOS processes have been used to engineer arrays with different functionality.}, keywords = {MEA Technology, Review}, pubstate = {published}, tppubtype = {article} } Close In recent years, increasing knowledge about in vitro cell handling and culturing has encouraged a variety of CMOS-based approaches to stimulate and detect electrical activity of biological cells. This paper outlines in a topical review the scope of cell-based biosensors and actuators for in vitro applications ranging from single-cell detection to multisite probing of complex neural tissue. Recent examples are selected to demonstrate how standard CMOS processes have been used to engineer arrays with different functionality. Close http://ieeexplore.ieee.org/document/1362853/ doi:10.1109/JSSC.2004.837082 Close
	Heer, Flavio; Franks, Wendy; Blau, Axel; Taschini, S; Ziegler, Christiane; Hierlemann, Andreas; Baltes, Henry CMOS microelectrode array for the monitoring of electrogenic cells Journal Article Biosensors & Bioelectronics, 20 (2), pp. 358-366, 2004, ISSN: 0956-5663. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology @article{Baltes2004, title = {CMOS microelectrode array for the monitoring of electrogenic cells}, author = {Flavio Heer and Wendy Franks and Axel Blau and S Taschini and Christiane Ziegler and Andreas Hierlemann and Henry Baltes}, url = {http://www.sciencedirect.com/science/article/pii/S0956566304000806?via%3Dihub}, doi = {10.1016/j.bios.2004.02.006}, issn = {0956-5663}, year = {2004}, date = {2004-03-19}, journal = {Biosensors & Bioelectronics}, volume = {20}, number = {2}, pages = {358-366}, abstract = {Signal degradation and an array size dictated by the number of available interconnects are the two main limitations inherent to standalone microelectrode arrays (MEAs). A new biochip consisting of an array of microelectrodes with fully-integrated analog and digital circuitry realized in an industrial CMOS process addresses these issues. The device is capable of on-chip signal filtering for improved signal-to-noise ratio (SNR), on-chip analog and digital conversion, and multiplexing, thereby facilitating simultaneous stimulation and recording of electrogenic cell activity. The designed electrode pitch of 250 mu m significantly limits the space available for circuitry: a repeated unit of circuitry associated with each electrode comprises a stimulation buffer and a bandpass filter for readout. The bandpass filter has corner frequencies of 100 Hz and 50 kHz, and a gain of 1000. Stimulation voltages are generated from an 8-bit digital signal and converted to an analog signal at a frequency of 120 kHz. Functionality of the read-out circuitry is demonstrated by the measurement of cardiomyocyte activity. The microelectrode is realized in a shifted design for flexibility and biocompatibility. Several microelectrode materials (platinum, platinum black and titanium nitride) have been electrically characterized. An equivalent circuit model, where each parameter represents a macroscopic physical quantity contributing to the interface impedance, has been successfully fitted to experimental results.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Signal degradation and an array size dictated by the number of available interconnects are the two main limitations inherent to standalone microelectrode arrays (MEAs). A new biochip consisting of an array of microelectrodes with fully-integrated analog and digital circuitry realized in an industrial CMOS process addresses these issues. The device is capable of on-chip signal filtering for improved signal-to-noise ratio (SNR), on-chip analog and digital conversion, and multiplexing, thereby facilitating simultaneous stimulation and recording of electrogenic cell activity. The designed electrode pitch of 250 mu m significantly limits the space available for circuitry: a repeated unit of circuitry associated with each electrode comprises a stimulation buffer and a bandpass filter for readout. The bandpass filter has corner frequencies of 100 Hz and 50 kHz, and a gain of 1000. Stimulation voltages are generated from an 8-bit digital signal and converted to an analog signal at a frequency of 120 kHz. Functionality of the read-out circuitry is demonstrated by the measurement of cardiomyocyte activity. The microelectrode is realized in a shifted design for flexibility and biocompatibility. Several microelectrode materials (platinum, platinum black and titanium nitride) have been electrically characterized. An equivalent circuit model, where each parameter represents a macroscopic physical quantity contributing to the interface impedance, has been successfully fitted to experimental results. Close http://www.sciencedirect.com/science/article/pii/S0956566304000806?via%3Dihub doi:10.1016/j.bios.2004.02.006 Close

172 entries « ‹ 4 of 4 › »

2013
	Bakkum, Douglas J; Frey, Urs; Radivojevic, Milos; Russell, Thomas L; Müller, Jan; Fiscella, Michele; Takahashi, Hirokazu; Hierlemann, Andreas Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites Journal Article Nature Communications, 4 , pp. 1-12, 2013, ISSN: 2041-1723. Abstract \| Links \| BibTeX \| タグ: Data Analysis, ETH-CMOS-MEA, Neuronal Networks @article{Bakkum2013, title = {Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites}, author = {Douglas J Bakkum and Urs Frey and Milos Radivojevic and Thomas L Russell and Jan Müller and Michele Fiscella and Hirokazu Takahashi and Andreas Hierlemann}, url = {http://www.nature.com/doifinder/10.1038/ncomms3181}, doi = {10.1038/ncomms3181}, issn = {2041-1723}, year = {2013}, date = {2013-07-19}, journal = {Nature Communications}, volume = {4}, pages = {1-12}, abstract = {Axons are traditionally considered stable transmission cables, but evidence of the regulation of action potential propagation demonstrates that axons may have more important roles. However, their small diameters render intracellular recordings challenging, and low-magnitude extracellular signals are difficult to detect and assign. Better experimental access to axonal function would help to advance this field. Here we report methods to electrically visualize action potential propagation and network topology in cortical neurons grown over custom arrays, which contain 11,011 microelectrodes and are fabricated using complementary metal oxide semiconductor technology. Any neuron lying on the array can be recorded at high spatio-temporal resolution, and simultaneously precisely stimulated with little artifact. We find substantial velocity differences occurring locally within single axons, suggesting that the temporal control of a neuron's output may contribute to neuronal information processing.}, keywords = {Data Analysis, ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Axons are traditionally considered stable transmission cables, but evidence of the regulation of action potential propagation demonstrates that axons may have more important roles. However, their small diameters render intracellular recordings challenging, and low-magnitude extracellular signals are difficult to detect and assign. Better experimental access to axonal function would help to advance this field. Here we report methods to electrically visualize action potential propagation and network topology in cortical neurons grown over custom arrays, which contain 11,011 microelectrodes and are fabricated using complementary metal oxide semiconductor technology. Any neuron lying on the array can be recorded at high spatio-temporal resolution, and simultaneously precisely stimulated with little artifact. We find substantial velocity differences occurring locally within single axons, suggesting that the temporal control of a neuron's output may contribute to neuronal information processing. Close http://www.nature.com/doifinder/10.1038/ncomms3181 doi:10.1038/ncomms3181 Close
	Müller, Jan; Bakkum, Douglas J; Hierlemann, Andreas Sub-millisecond closed-loop feedback stimulation between arbitrary sets of individual neurons. Journal Article Frontiers in Neural Circuits, 6 , pp. 121, 2013, ISSN: 1662-5110. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation @article{Muller2012, title = {Sub-millisecond closed-loop feedback stimulation between arbitrary sets of individual neurons.}, author = {Jan Müller and Douglas J Bakkum and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fncir.2012.00121/full}, doi = {10.3389/fncir.2012.00121}, issn = {1662-5110}, year = {2013}, date = {2013-01-10}, journal = {Frontiers in Neural Circuits}, volume = {6}, pages = {121}, abstract = {We present a system to artificially correlate the spike timing between sets of arbitrary neurons that were interfaced to a complementary metal-oxide-semiconductor (CMOS) high-density microelectrode array (MEA). The system features a novel reprogrammable and flexible event engine unit to detect arbitrary spatio-temporal patterns of recorded action potentials and is capable of delivering sub-millisecond closed-loop feedback of electrical stimulation upon trigger events in real-time. The relative timing between action potentials of individual neurons as well as the temporal pattern among multiple neurons, or neuronal assemblies, is considered an important factor governing memory and learning in the brain. Artificially changing timings between arbitrary sets of spiking neurons with our system could provide a "knob" to tune information processing in the network.}, keywords = {ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation}, pubstate = {published}, tppubtype = {article} } Close We present a system to artificially correlate the spike timing between sets of arbitrary neurons that were interfaced to a complementary metal-oxide-semiconductor (CMOS) high-density microelectrode array (MEA). The system features a novel reprogrammable and flexible event engine unit to detect arbitrary spatio-temporal patterns of recorded action potentials and is capable of delivering sub-millisecond closed-loop feedback of electrical stimulation upon trigger events in real-time. The relative timing between action potentials of individual neurons as well as the temporal pattern among multiple neurons, or neuronal assemblies, is considered an important factor governing memory and learning in the brain. Artificially changing timings between arbitrary sets of spiking neurons with our system could provide a "knob" to tune information processing in the network. Close https://www.frontiersin.org/articles/10.3389/fncir.2012.00121/full doi:10.3389/fncir.2012.00121 Close
2012
	Franke, Felix; Jackel, David; Dragas, Jelena; Muller, Jan; Radivojevic, Milos; Bakkum, Douglas J; Hierlemann, Andreas High-density microelectrode array recordings and real-time spike sorting for closed-loop experiments: an emerging technology to study neural plasticity Journal Article Frontiers in Neural Circuits, 6 , pp. 105, 2012, ISSN: 1662-5110. Abstract \| Links \| BibTeX \| タグ: Neuronal Networks, Review, Spike Sorting @article{Hierlemann2012, title = {High-density microelectrode array recordings and real-time spike sorting for closed-loop experiments: an emerging technology to study neural plasticity}, author = {Felix Franke and David Jackel and Jelena Dragas and Jan Muller and Milos Radivojevic and Douglas J Bakkum and Andreas Hierlemann}, url = {https://www.frontiersin.org/article/10.3389/fncir.2012.00105}, doi = {10.3389/fncir.2012.00105}, issn = {1662-5110}, year = {2012}, date = {2012-12-20}, journal = {Frontiers in Neural Circuits}, volume = {6}, pages = {105}, abstract = {Understanding plasticity of neural networks is a key to comprehending their development and function. A powerful technique to study neural plasticity includes recording and control of pre- and postsynaptic neural activity, e.g., by using simultaneous intracellular recording and stimulation of several neurons. Intracellular recording is, however, a demanding technique and has its limitations in that only a small number of neurons can be stimulated and recorded from at the same time. Extracellular techniques offer the possibility to simultaneously record from larger numbers of neurons with relative ease, at the expenses of increased efforts to sort out single neuronal activities from the recorded mixture, which is a time consuming and error prone step, referred to as spike sorting. In this mini-review, we describe recent technological developments in two separate fields, namely CMOS-based high-density microelectrode arrays, which also allow for extracellular stimulation of neurons, and real-time spike sorting. We argue that these techniques, when combined, will provide a powerful tool to study plasticity in neural networks consisting of several thousand neurons in vitro.}, keywords = {Neuronal Networks, Review, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Understanding plasticity of neural networks is a key to comprehending their development and function. A powerful technique to study neural plasticity includes recording and control of pre- and postsynaptic neural activity, e.g., by using simultaneous intracellular recording and stimulation of several neurons. Intracellular recording is, however, a demanding technique and has its limitations in that only a small number of neurons can be stimulated and recorded from at the same time. Extracellular techniques offer the possibility to simultaneously record from larger numbers of neurons with relative ease, at the expenses of increased efforts to sort out single neuronal activities from the recorded mixture, which is a time consuming and error prone step, referred to as spike sorting. In this mini-review, we describe recent technological developments in two separate fields, namely CMOS-based high-density microelectrode arrays, which also allow for extracellular stimulation of neurons, and real-time spike sorting. We argue that these techniques, when combined, will provide a powerful tool to study plasticity in neural networks consisting of several thousand neurons in vitro. Close https://www.frontiersin.org/article/10.3389/fncir.2012.00105 doi:10.3389/fncir.2012.00105 Close
	Fiscella, Michele; Farrow, Karl; Jones, Ian L; Jäckel, David; Müller, Jan; Frey, Urs; Bakkum, Douglas J; Hantz, Péter; Roska, Botond; Hierlemann, Andreas Recording from defined populations of retinal ganglion cells using a high-density CMOS-integrated microelectrode array with real-time switchable electrode selection Journal Article Journal of Neuroscience Methods, 211 (1), pp. 103-113, 2012, ISSN: 01650270. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, Retina @article{Fiscella2012, title = {Recording from defined populations of retinal ganglion cells using a high-density CMOS-integrated microelectrode array with real-time switchable electrode selection}, author = {Michele Fiscella and Karl Farrow and Ian L Jones and David Jäckel and Jan Müller and Urs Frey and Douglas J Bakkum and Péter Hantz and Botond Roska and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S0165027012003287?via%3Dihub}, doi = {10.1016/j.jneumeth.2012.08.017}, issn = {01650270}, year = {2012}, date = {2012-08-16}, journal = {Journal of Neuroscience Methods}, volume = {211}, number = {1}, pages = {103-113}, publisher = {Elsevier B.V.}, abstract = {In order to understand how retinal circuits encode visual scenes, the neural activity of defined populations of retinal ganglion cells (RGCs) has to be investigated. Here we report on a method for stimulating, detecting, and subsequently targeting defined populations of RGCs. The possibility to select a distinct population of RGCs for extracellular recording enables the design of experiments that can increase our understanding of how these neurons extract precise spatio-temporal features from the visual scene, and how the brain interprets retinal signals. We used light stimulation to elicit a response from physiologically distinct types of RGCs and then utilized the dynamic-configurability capabilities of a microelectronics-based high-density microelectrode array (MEA) to record their synchronous action potentials. The layout characteristics of the MEA made it possible to stimulate and record from multiple, highly overlapping RGCs simultaneously without light-induced artifacts. The high-density of electrodes and the high signal-to-noise ratio of the MEA circuitry allowed for recording of the activity of each RGC on 14 ± 7 electrodes. The spatial features of the electrical activity of each RGC greatly facilitated spike sorting. We were thus able to localize, identify and record from defined RGCs within a region of mouse retina. In addition, we stimulated and recorded from genetically modified RGCs to demonstrate the applicability of optogenetic methods, which introduces an additional feature to target a defined cell type. The developed methodologies can likewise be applied to other neuronal preparations including brain slices or cultured neurons.}, keywords = {ETH-CMOS-MEA, Retina}, pubstate = {published}, tppubtype = {article} } Close In order to understand how retinal circuits encode visual scenes, the neural activity of defined populations of retinal ganglion cells (RGCs) has to be investigated. Here we report on a method for stimulating, detecting, and subsequently targeting defined populations of RGCs. The possibility to select a distinct population of RGCs for extracellular recording enables the design of experiments that can increase our understanding of how these neurons extract precise spatio-temporal features from the visual scene, and how the brain interprets retinal signals. We used light stimulation to elicit a response from physiologically distinct types of RGCs and then utilized the dynamic-configurability capabilities of a microelectronics-based high-density microelectrode array (MEA) to record their synchronous action potentials. The layout characteristics of the MEA made it possible to stimulate and record from multiple, highly overlapping RGCs simultaneously without light-induced artifacts. The high-density of electrodes and the high signal-to-noise ratio of the MEA circuitry allowed for recording of the activity of each RGC on 14 ± 7 electrodes. The spatial features of the electrical activity of each RGC greatly facilitated spike sorting. We were thus able to localize, identify and record from defined RGCs within a region of mouse retina. In addition, we stimulated and recorded from genetically modified RGCs to demonstrate the applicability of optogenetic methods, which introduces an additional feature to target a defined cell type. The developed methodologies can likewise be applied to other neuronal preparations including brain slices or cultured neurons. Close http://www.sciencedirect.com/science/article/pii/S0165027012003287?via%3Dihub doi:10.1016/j.jneumeth.2012.08.017 Close
	Jäckel, David; Frey, Urs; Fiscella, Michele; Franke, Felix; Hierlemann, Andreas Applicability of independent component analysis on high-density microelectrode array recordings Journal Article Journal of Neurophysiology, 108 (1), pp. 334-348, 2012, ISSN: 0022-3077. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, Spike Sorting @article{Jackel2012, title = {Applicability of independent component analysis on high-density microelectrode array recordings}, author = {David Jäckel and Urs Frey and Michele Fiscella and Felix Franke and Andreas Hierlemann}, url = {http://jn.physiology.org/cgi/doi/10.1152/jn.01106.2011}, doi = {10.1152/jn.01106.2011}, issn = {0022-3077}, year = {2012}, date = {2012-04-04}, journal = {Journal of Neurophysiology}, volume = {108}, number = {1}, pages = {334-348}, abstract = {Emerging complementary metal oxide semiconductor (CMOS)-based, high-density microelectrode array (HD-MEA) devices provide high spatial resolution at subcellular level and a large number of readout channels. These devices allow for simultaneous recording of extracellular activity of a large number of neurons with every neuron being detected by multiple electrodes. To analyze the recorded signals, spiking events have to be assigned to individual neurons, a process referred to as "spike sorting." For a set of observed signals, which constitute a linear mixture of a set of source signals, independent component (IC) analysis (ICA) can be used to demix blindly the data and extract the individual source signals. This technique offers great potential to alleviate the problem of spike sorting in HD-MEA recordings, as it represents an unsupervised method to separate the neuronal sources. The separated sources or ICs then constitute estimates of single-neuron signals, and threshold detection on the ICs yields the sorted spike times. However, it is unknown to what extent extracellular neuronal recordings meet the requirements of ICA. In this paper, we evaluate the applicability of ICA to spike sorting of HD-MEA recordings. The analysis of extracellular neuronal signals, recorded at high spatiotemporal resolution, reveals that the recorded data cannot be modeled as a purely linear mixture. As a consequence, ICA fails to separate completely the neuronal signals and cannot be used as a stand-alone method for spike sorting in HD-MEA recordings. We assessed the demixing performance of ICA using simulated data sets and found that the performance strongly depends on neuronal density and spike amplitude. Furthermore, we show how postprocessing techniques can be used to overcome the most severe limitations of ICA. In combination with these postprocessing techniques, ICA represents a viable method to facilitate rapid spike sorting of multidimensional neuronal recordings.}, keywords = {ETH-CMOS-MEA, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Emerging complementary metal oxide semiconductor (CMOS)-based, high-density microelectrode array (HD-MEA) devices provide high spatial resolution at subcellular level and a large number of readout channels. These devices allow for simultaneous recording of extracellular activity of a large number of neurons with every neuron being detected by multiple electrodes. To analyze the recorded signals, spiking events have to be assigned to individual neurons, a process referred to as "spike sorting." For a set of observed signals, which constitute a linear mixture of a set of source signals, independent component (IC) analysis (ICA) can be used to demix blindly the data and extract the individual source signals. This technique offers great potential to alleviate the problem of spike sorting in HD-MEA recordings, as it represents an unsupervised method to separate the neuronal sources. The separated sources or ICs then constitute estimates of single-neuron signals, and threshold detection on the ICs yields the sorted spike times. However, it is unknown to what extent extracellular neuronal recordings meet the requirements of ICA. In this paper, we evaluate the applicability of ICA to spike sorting of HD-MEA recordings. The analysis of extracellular neuronal signals, recorded at high spatiotemporal resolution, reveals that the recorded data cannot be modeled as a purely linear mixture. As a consequence, ICA fails to separate completely the neuronal signals and cannot be used as a stand-alone method for spike sorting in HD-MEA recordings. We assessed the demixing performance of ICA using simulated data sets and found that the performance strongly depends on neuronal density and spike amplitude. Furthermore, we show how postprocessing techniques can be used to overcome the most severe limitations of ICA. In combination with these postprocessing techniques, ICA represents a viable method to facilitate rapid spike sorting of multidimensional neuronal recordings. Close http://jn.physiology.org/cgi/doi/10.1152/jn.01106.2011 doi:10.1152/jn.01106.2011 Close
2011
	Jones, Ian L; Livi, Paolo; Lewandowska, Marta K; Fiscella, Michele; Roscic, Branka; Hierlemann, Andreas The potential of microelectrode arrays and microelectronics for biomedical research and diagnostics Journal Article Analytical and Bioanalytical Chemistry, 399 (7), pp. 2313-2329, 2011, ISSN: 1618-2650. Abstract \| Links \| BibTeX \| タグ: Review @article{Jones2011, title = {The potential of microelectrode arrays and microelectronics for biomedical research and diagnostics}, author = {Ian L Jones and Paolo Livi and Marta K Lewandowska and Michele Fiscella and Branka Roscic and Andreas Hierlemann}, url = {https://link.springer.com/article/10.1007%2Fs00216-010-3968-1}, doi = {10.1007/s00216-010-3968-1}, issn = {1618-2650}, year = {2011}, date = {2011-07-31}, journal = {Analytical and Bioanalytical Chemistry}, volume = {399}, number = {7}, pages = {2313-2329}, abstract = {Planar microelectrode arrays (MEAs) are devices that can be used in biomedical and basic in vitro research to provide extracellular electrophysiological information about biological systems at high spatial and temporal resolution. Complementary metal oxide semiconductor (CMOS) is a technology with which MEAs can be produced on a microscale featuring high spatial resolution and excellent signal-to-noise characteristics. CMOS MEAs are specialized for the analysis of complete electrogenic cellular networks at the cellular or subcellular level in dissociated cultures, organotypic cultures, and acute tissue slices; they can also function as biosensors to detect biochemical events. Models of disease or the response of cellular networks to pharmacological compounds can be studied in vitro, allowing one to investigate pathologies, such as cardiac arrhythmias, memory impairment due to Alzheimer's disease, or vision impairment caused by ganglion cell degeneration in the retina.}, keywords = {Review}, pubstate = {published}, tppubtype = {article} } Close Planar microelectrode arrays (MEAs) are devices that can be used in biomedical and basic in vitro research to provide extracellular electrophysiological information about biological systems at high spatial and temporal resolution. Complementary metal oxide semiconductor (CMOS) is a technology with which MEAs can be produced on a microscale featuring high spatial resolution and excellent signal-to-noise characteristics. CMOS MEAs are specialized for the analysis of complete electrogenic cellular networks at the cellular or subcellular level in dissociated cultures, organotypic cultures, and acute tissue slices; they can also function as biosensors to detect biochemical events. Models of disease or the response of cellular networks to pharmacological compounds can be studied in vitro, allowing one to investigate pathologies, such as cardiac arrhythmias, memory impairment due to Alzheimer's disease, or vision impairment caused by ganglion cell degeneration in the retina. Close https://link.springer.com/article/10.1007%2Fs00216-010-3968-1 doi:10.1007/s00216-010-3968-1 Close
	Hierlemann, Andreas; Frey, Urs; Hafizovic, Sadik; Heer, Flavio Growing cells atop microelectronic chips: Interfacing electrogenic cells in vitro with CMOS-based microelectrode arrays Journal Article Proceedings of the IEEE, 99 (2), pp. 252-284, 2011, ISSN: 00189219. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology, Review @article{Hierlemann2011, title = {Growing cells atop microelectronic chips: Interfacing electrogenic cells in vitro with CMOS-based microelectrode arrays}, author = {Andreas Hierlemann and Urs Frey and Sadik Hafizovic and Flavio Heer}, url = {http://ieeexplore.ieee.org/document/5594982/}, doi = {10.1109/JPROC.2010.2066532}, issn = {00189219}, year = {2011}, date = {2011-02-01}, journal = {Proceedings of the IEEE}, volume = {99}, number = {2}, pages = {252-284}, abstract = {Complementary semiconductor-metal-oxide (CMOS) technology is a very powerful technology that can be more or less directly interfaced to electrogenic cells, like heart or brain cells in vitro. To this end, the cells are cultured directly atop the CMOS chips, which usually undergo dedicated postprocessing to obtain a reliable bidirectional interface via noble-metal microelectrodes or high-k dielectrics. The big advantages of using CMOS integrated circuits (ICs) include connectivity, the possibility to address a large number of microelectrodes on a tiny chip, and signal quality, the possibility to condition small signals right at the spot of their generation. CMOS will be demonstrated to constitute an enabling technology that opens a route to high-spatio-temporal-resolution and low-noise electrophysiological recordings from a variety of biological preparations, such as brain slices, or cultured cardiac and brain cells. The recording technique is extracellular and noninvasive, and the CMOS chips do not leak out any toxic compounds, so that the cells remain viable for extended times. In turn, the CMOS chips have been demonstrated to survive several months of culturing while being fully immersed in saline solution and being exposed to cellular metabolic products. The latter requires dedicated passivation and packaging techniques as will be shown. Fully integrated, monolithic microelectrode systems, which feature large numbers of tightly spaced microelectrodes and the associated circuitry units for bidirectional interaction (stimulation and recording), will be in the focus of this review. The respective dense microelectrode arrays (MEAs) with small pixels enable subcellular-resolution investigation of regions of interest in, e.g., neurobiological preparations, and, at the same time, the large number of electrodes allows for studying the activity of entire neuronal networks . Application areas include neuroscience, as the devices enable fundamental neurophysiological insights at the cellular and circuit level, as well as medical diagnostics and pharmacology.}, keywords = {ETH-CMOS-MEA, MEA Technology, Review}, pubstate = {published}, tppubtype = {article} } Close Complementary semiconductor-metal-oxide (CMOS) technology is a very powerful technology that can be more or less directly interfaced to electrogenic cells, like heart or brain cells in vitro. To this end, the cells are cultured directly atop the CMOS chips, which usually undergo dedicated postprocessing to obtain a reliable bidirectional interface via noble-metal microelectrodes or high-k dielectrics. The big advantages of using CMOS integrated circuits (ICs) include connectivity, the possibility to address a large number of microelectrodes on a tiny chip, and signal quality, the possibility to condition small signals right at the spot of their generation. CMOS will be demonstrated to constitute an enabling technology that opens a route to high-spatio-temporal-resolution and low-noise electrophysiological recordings from a variety of biological preparations, such as brain slices, or cultured cardiac and brain cells. The recording technique is extracellular and noninvasive, and the CMOS chips do not leak out any toxic compounds, so that the cells remain viable for extended times. In turn, the CMOS chips have been demonstrated to survive several months of culturing while being fully immersed in saline solution and being exposed to cellular metabolic products. The latter requires dedicated passivation and packaging techniques as will be shown. Fully integrated, monolithic microelectrode systems, which feature large numbers of tightly spaced microelectrodes and the associated circuitry units for bidirectional interaction (stimulation and recording), will be in the focus of this review. The respective dense microelectrode arrays (MEAs) with small pixels enable subcellular-resolution investigation of regions of interest in, e.g., neurobiological preparations, and, at the same time, the large number of electrodes allows for studying the activity of entire neuronal networks . Application areas include neuroscience, as the devices enable fundamental neurophysiological insights at the cellular and circuit level, as well as medical diagnostics and pharmacology. Close http://ieeexplore.ieee.org/document/5594982/ doi:10.1109/JPROC.2010.2066532 Close
2010
	Livi, Paolo; Heer, Flavio; Frey, Urs; Bakkum, Douglas J; Hierlemann, Andreas Compact voltage and current stimulation buffer for high-density microelectrode arrays Journal Article IEEE Transactions on Biomedical Circuits and Systems, 4 (6), pp. 372-378, 2010, ISSN: 19324545. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology, Stimulation @article{Livi2010, title = {Compact voltage and current stimulation buffer for high-density microelectrode arrays}, author = {Paolo Livi and Flavio Heer and Urs Frey and Douglas J Bakkum and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/5617318/}, doi = {10.1109/TBCAS.2010.2080676}, issn = {19324545}, year = {2010}, date = {2010-11-01}, journal = {IEEE Transactions on Biomedical Circuits and Systems}, volume = {4}, number = {6}, pages = {372-378}, abstract = {We report on a compact (0.02 mm2 ) buffer for both voltage and current stimulation of electrogenic cells on a complementary metal-oxide semiconductor microelectrode array. In voltage mode, the circuit is a high-current class-AB voltage follower, based on a local common-mode feedback (LCMFB) amplifier. In current mode, the circuit is a current conveyor of type II, using the same LCMFB amplifier with cascode stages to increase the gain. The circuit shows good linearity in the 0.5-3.5 V input range and has extensively been used for stimulation of neuronal cultures.}, keywords = {ETH-CMOS-MEA, MEA Technology, Stimulation}, pubstate = {published}, tppubtype = {article} } Close We report on a compact (0.02 mm2 ) buffer for both voltage and current stimulation of electrogenic cells on a complementary metal-oxide semiconductor microelectrode array. In voltage mode, the circuit is a high-current class-AB voltage follower, based on a local common-mode feedback (LCMFB) amplifier. In current mode, the circuit is a current conveyor of type II, using the same LCMFB amplifier with cascode stages to increase the gain. The circuit shows good linearity in the 0.5-3.5 V input range and has extensively been used for stimulation of neuronal cultures. Close http://ieeexplore.ieee.org/document/5617318/ doi:10.1109/TBCAS.2010.2080676 Close
	Frey, Urs; Sedivy, Jan; Heer, Flavio; Pedron, Rene; Ballini, Marco; Müller, Jan; Bakkum, Douglas J; Hafizovic, Sadik; Faraci, Francesca D; Greve, Frauke; Kirstein, Kay Uwe; Hierlemann, Andreas Switch-matrix-based high-density microelectrode array in CMOS technology Journal Article IEEE Journal of Solid-State Circuits, 45 (2), pp. 467-482, 2010, ISSN: 00189200. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology @article{Frey2010, title = {Switch-matrix-based high-density microelectrode array in CMOS technology}, author = {Urs Frey and Jan Sedivy and Flavio Heer and Rene Pedron and Marco Ballini and Jan Müller and Douglas J Bakkum and Sadik Hafizovic and Francesca D Faraci and Frauke Greve and Kay Uwe Kirstein and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/5405139/}, doi = {10.1109/JSSC.2009.2035196}, issn = {00189200}, year = {2010}, date = {2010-02-02}, journal = {IEEE Journal of Solid-State Circuits}, volume = {45}, number = {2}, pages = {467-482}, abstract = {We report on a CMOS-based microelectrode array (MEA) featuring 11, 011 metal electrodes and 126 channels, each of which comprises recording and stimulation electronics, for extracellular bidirectional communication with electrogenic cells, such as neurons or cardiomyocytes. The important features include: (i) high spatial resolution at (sub)cellular level with 3150 electrodes per mm2 (electrode diameter 7 um, electrode pitch 18 um); (ii) a reconflgurable routing of the recording sites to the 126 channels; and (iii) low noise levels.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close We report on a CMOS-based microelectrode array (MEA) featuring 11, 011 metal electrodes and 126 channels, each of which comprises recording and stimulation electronics, for extracellular bidirectional communication with electrogenic cells, such as neurons or cardiomyocytes. The important features include: (i) high spatial resolution at (sub)cellular level with 3150 electrodes per mm2 (electrode diameter 7 um, electrode pitch 18 um); (ii) a reconflgurable routing of the recording sites to the 126 channels; and (iii) low noise levels. Close http://ieeexplore.ieee.org/document/5405139/ doi:10.1109/JSSC.2009.2035196 Close
2009
	Frey, Urs; Egert, Ulrich; Heer, Flavio; Hafizovic, Sadik; Hierlemann, Andreas Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices Journal Article Biosensors and Bioelectronics, 24 (7), pp. 2191-2198, 2009, ISSN: 09565663. Abstract \| Links \| BibTeX \| タグ: Brain Slice, ETH-CMOS-MEA @article{Frey2009, title = {Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices}, author = {Urs Frey and Ulrich Egert and Flavio Heer and Sadik Hafizovic and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S095656630800643X?via%3Dihub}, doi = {10.1016/j.bios.2008.11.028}, issn = {09565663}, year = {2009}, date = {2009-03-15}, journal = {Biosensors and Bioelectronics}, volume = {24}, number = {7}, pages = {2191-2198}, abstract = {There is an enduring quest for technologies that provide - temporally and spatially - highly resolved information on electric neuronal or cardiac activity in functional tissues or cell cultures. Here, we present a planar high-density, low-noise microelectrode system realized in microelectronics technology that features 11,011 microelectrodes (3,150 electrodes per mm2), 126 of which can be arbitrarily selected and can, via a reconfigurable routing scheme, be connected to on-chip recording and stimulation circuits. This device enables long-term extracellular electrical-activity recordings at subcellular spatial resolution and microsecond temporal resolution to capture the entire dynamics of the cellular electrical signals. To illustrate the device performance, extracellular potentials of Purkinje cells (PCs) in acute slices of the cerebellum have been analyzed. A detailed and comprehensive picture of the distribution and dynamics of action potentials (APs) in the somatic and dendritic regions of a single cell was obtained from the recordings by applying spike sorting and spike-triggered averaging methods to the collected data. An analysis of the measured local current densities revealed a reproducible sink/source pattern within a single cell during an AP. The experimental data substantiated compartmental models and can be used to extend those models to better understand extracellular single-cell potential patterns and their contributions to the population activity. The presented devices can be conveniently applied to a broad variety of biological preparations, i.e., neural or cardiac tissues, slices, or cell cultures can be grown or placed directly atop of the chips for fundamental mechanistic or pharmacological studies.}, keywords = {Brain Slice, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close There is an enduring quest for technologies that provide - temporally and spatially - highly resolved information on electric neuronal or cardiac activity in functional tissues or cell cultures. Here, we present a planar high-density, low-noise microelectrode system realized in microelectronics technology that features 11,011 microelectrodes (3,150 electrodes per mm2), 126 of which can be arbitrarily selected and can, via a reconfigurable routing scheme, be connected to on-chip recording and stimulation circuits. This device enables long-term extracellular electrical-activity recordings at subcellular spatial resolution and microsecond temporal resolution to capture the entire dynamics of the cellular electrical signals. To illustrate the device performance, extracellular potentials of Purkinje cells (PCs) in acute slices of the cerebellum have been analyzed. A detailed and comprehensive picture of the distribution and dynamics of action potentials (APs) in the somatic and dendritic regions of a single cell was obtained from the recordings by applying spike sorting and spike-triggered averaging methods to the collected data. An analysis of the measured local current densities revealed a reproducible sink/source pattern within a single cell during an AP. The experimental data substantiated compartmental models and can be used to extend those models to better understand extracellular single-cell potential patterns and their contributions to the population activity. The presented devices can be conveniently applied to a broad variety of biological preparations, i.e., neural or cardiac tissues, slices, or cell cultures can be grown or placed directly atop of the chips for fundamental mechanistic or pharmacological studies. Close http://www.sciencedirect.com/science/article/pii/S095656630800643X?via%3Dihub doi:10.1016/j.bios.2008.11.028 Close
	Weber, Wilfried; Luzi, Stefan; Karlsson, Maria; Sanchez-Bustamante, Carlota Diaz; Frey, Urs; Hierlemann, Andreas; Fussenegger, Martin A synthetic mammalian electro-genetic transcription circuit Journal Article Nucleic Acids Research, 37 (4), pp. 1-8, 2009, ISSN: 03051048. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Weber2009, title = {A synthetic mammalian electro-genetic transcription circuit}, author = {Wilfried Weber and Stefan Luzi and Maria Karlsson and Carlota Diaz Sanchez-Bustamante and Urs Frey and Andreas Hierlemann and Martin Fussenegger}, url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp014}, doi = {10.1093/nar/gkp014}, issn = {03051048}, year = {2009}, date = {2009-02-03}, journal = {Nucleic Acids Research}, volume = {37}, number = {4}, pages = {1-8}, abstract = {Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electrogenetic implants assembled from electronic and genetic parts.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Electric signal processing has evolved to manage rapid information transfer in neuronal networks and muscular contraction in multicellular organisms and controls the most sophisticated man-built devices. Using a synthetic biology approach to assemble electronic parts with genetic control units engineered into mammalian cells, we designed an electric power-adjustable transcription control circuit able to integrate the intensity of a direct current over time, to translate the amplitude or frequency of an alternating current into an adjustable genetic readout or to modulate the beating frequency of primary heart cells. Successful miniaturization of the electro-genetic devices may pave the way for the design of novel hybrid electrogenetic implants assembled from electronic and genetic parts. Close https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp014 doi:10.1093/nar/gkp014 Close
2008
	Sanchez-Bustamante, Carlota Diaz; Frey, Urs; Kelm, Jens M; Hierlemann, Andreas; Fussenegger, Martin Modulation of cardiomyocyte electrical properties using regulated bone morphogenetic protein-2 expression. Journal Article Tissue Engineering. Part A, 14 (12), pp. 1969-1988, 2008, ISSN: 1937-3341. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Sanchez-Bustamante2008, title = {Modulation of cardiomyocyte electrical properties using regulated bone morphogenetic protein-2 expression.}, author = {Carlota Diaz Sanchez-Bustamante and Urs Frey and Jens M Kelm and Andreas Hierlemann and Martin Fussenegger}, url = {http://online.liebertpub.com/doi/abs/10.1089/ten.tea.2007.0302?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed}, doi = {10.1089/ten.tea.2007.0302}, issn = {1937-3341}, year = {2008}, date = {2008-11-19}, journal = {Tissue Engineering. Part A}, volume = {14}, number = {12}, pages = {1969-1988}, abstract = {Because cardiomyocytes lose their ability to divide after birth, any subsequent cell loss or dysfunction results in pathologic cardiac rhythm initiation or impulse conduction. Strategies to restore and control the electrophysiological activity of the heart may, therefore, greatly affect the regeneration of cardiac tissue functionality. Using lentivirus-derived particles to regulate the bone morphogenetic protein-2 (BMP-2) gene expression in a pristinamycin- or gaseous acetaldehyde-inducible manner, we demonstrated the adjustment of cardiomyocyte electrophysiological characteristics. Complementary metal oxide semiconductor-based high-density microelectrode arrays (HD-MEAs) were used to monitor the electrophysiological activity of neonatal rat cardiomyocytes (NRCs) cultured as monolayers (NRCml) or as microtissues (NRCmt). NRCmt more closely resembled heart tissue physiology than did NRCml and could be conveniently monitored using HD-MEAs because of their ability to detect low-signal events and to sub-select the region of interest, namely, areas where the microtissues were placed. Cardiomyocyte-forming microtissues, transduced using lentiviral vectors encoding BMP-2, were capable of restoring myocardial microtissue electrical activity. We also engineered NRCmt to functionally couple within a cardiomyocyte monolayer, thus showing pacemaker-like activity upon local regulation of transgenic BMP-2 expression. The controlled expression of therapeutic transgenes represents a crucial advance for clinical interventions and gene-function analysis.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Because cardiomyocytes lose their ability to divide after birth, any subsequent cell loss or dysfunction results in pathologic cardiac rhythm initiation or impulse conduction. Strategies to restore and control the electrophysiological activity of the heart may, therefore, greatly affect the regeneration of cardiac tissue functionality. Using lentivirus-derived particles to regulate the bone morphogenetic protein-2 (BMP-2) gene expression in a pristinamycin- or gaseous acetaldehyde-inducible manner, we demonstrated the adjustment of cardiomyocyte electrophysiological characteristics. Complementary metal oxide semiconductor-based high-density microelectrode arrays (HD-MEAs) were used to monitor the electrophysiological activity of neonatal rat cardiomyocytes (NRCs) cultured as monolayers (NRCml) or as microtissues (NRCmt). NRCmt more closely resembled heart tissue physiology than did NRCml and could be conveniently monitored using HD-MEAs because of their ability to detect low-signal events and to sub-select the region of interest, namely, areas where the microtissues were placed. Cardiomyocyte-forming microtissues, transduced using lentiviral vectors encoding BMP-2, were capable of restoring myocardial microtissue electrical activity. We also engineered NRCmt to functionally couple within a cardiomyocyte monolayer, thus showing pacemaker-like activity upon local regulation of transgenic BMP-2 expression. The controlled expression of therapeutic transgenes represents a crucial advance for clinical interventions and gene-function analysis. Close http://online.liebertpub.com/doi/abs/10.1089/ten.tea.2007.0302?url_ver=Z39.88-20[...] doi:10.1089/ten.tea.2007.0302 Close
2007
	Heer, Flavio; Hafizovic, Sadik; Ugniwenko, T; Frey, Urs; Blau, Axel; Ziegler, Christiane; Hierlemann, Andreas A CMOS-based microelectrode array for interaction with neuronal cultures Journal Article Journal of Neuroscience Methods, 164 (1), pp. 93-106, 2007, ISSN: 0165-0270. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, Neuronal Networks @article{Hierlemann2007, title = {A CMOS-based microelectrode array for interaction with neuronal cultures}, author = {Flavio Heer and Sadik Hafizovic and T Ugniwenko and Urs Frey and Axel Blau and Christiane Ziegler and Andreas Hierlemann}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0165027007001781}, doi = {10.1016/j.jneumeth.2007.04.006}, issn = {0165-0270}, year = {2007}, date = {2007-04-19}, journal = {Journal of Neuroscience Methods}, volume = {164}, number = {1}, pages = {93-106}, abstract = {We report on the system integration of a CMOS chip that is capable of bidirectionally communicating (stimulation and recording) with electrogenic cells such as neurons or cardiomyocytes and that is targeted at investigating electrical signal propagation within cellular networks in vitro. The overall system consists of three major subunits: first, the core component is a 6.5 mm × 6.5 mm CMOS chip, on top of which the cells are cultured. It features 128 bidirectional electrodes, each equipped with dedicated analog filters and amplification stages and a stimulation buffer. The electrodes are sampled at 20 kHz with 8-bit resolution. The measured input-referred circuitry noise is 5.9 muV root mean square (10 Hz to 100 kHz), which allows to reliably detect the cell signals ranging from 1 mVpp down to 40 muVpp. Additionally, temperature sensors, a digital-to-analog converter for stimulation, and a digital interface for data transmission are integrated. Second, there is a reconfigurable logic device, which provides chip control, event detection, data buffering and an USB interface, capable of processing the 2.56 million samples per second. The third element includes software that is running on a standard PC performing data capturing, processing, and visualization. Experiments involving the stimulation of neurons with two different spatio-temporal patterns and the recording of the triggered spiking activity have been carried out. The response patterns have been successfully classified (83% correct) with respect to the different stimulation patterns. The advantages over current microelectrode arrays, as has been demonstrated in the experiments, include the capability to stimulate (voltage stimulation, 8 bit, 60 kHz) spatio-temporal patterns on arbitrary sets of electrodes and the fast stimulation reset mechanism that allows to record neuronal signals on a stimulating electrode 5 ms after stimulation (instantaneously on all other electrodes). Other advantages of the overall system include the small number of needed electrical connections due to the digital interface and the short latency time that allows to initiate a stimulation less than 2 ms after the detection of an action potential in closed-loop configurations.}, keywords = {ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close We report on the system integration of a CMOS chip that is capable of bidirectionally communicating (stimulation and recording) with electrogenic cells such as neurons or cardiomyocytes and that is targeted at investigating electrical signal propagation within cellular networks in vitro. The overall system consists of three major subunits: first, the core component is a 6.5 mm × 6.5 mm CMOS chip, on top of which the cells are cultured. It features 128 bidirectional electrodes, each equipped with dedicated analog filters and amplification stages and a stimulation buffer. The electrodes are sampled at 20 kHz with 8-bit resolution. The measured input-referred circuitry noise is 5.9 muV root mean square (10 Hz to 100 kHz), which allows to reliably detect the cell signals ranging from 1 mVpp down to 40 muVpp. Additionally, temperature sensors, a digital-to-analog converter for stimulation, and a digital interface for data transmission are integrated. Second, there is a reconfigurable logic device, which provides chip control, event detection, data buffering and an USB interface, capable of processing the 2.56 million samples per second. The third element includes software that is running on a standard PC performing data capturing, processing, and visualization. Experiments involving the stimulation of neurons with two different spatio-temporal patterns and the recording of the triggered spiking activity have been carried out. The response patterns have been successfully classified (83% correct) with respect to the different stimulation patterns. The advantages over current microelectrode arrays, as has been demonstrated in the experiments, include the capability to stimulate (voltage stimulation, 8 bit, 60 kHz) spatio-temporal patterns on arbitrary sets of electrodes and the fast stimulation reset mechanism that allows to record neuronal signals on a stimulating electrode 5 ms after stimulation (instantaneously on all other electrodes). Other advantages of the overall system include the small number of needed electrical connections due to the digital interface and the short latency time that allows to initiate a stimulation less than 2 ms after the detection of an action potential in closed-loop configurations. Close http://linkinghub.elsevier.com/retrieve/pii/S0165027007001781 doi:10.1016/j.jneumeth.2007.04.006 Close
	Greve, Frauke; Lichtenberg, Jan; Kirstein, Kay Uwe; Frey, Urs; Perriard, Jean Claude; Hierlemann, Andreas A perforated CMOS microchip platform for immobilization and activity monitoring of electrogenic cells Journal Article Journal of Micromechanics and Microengineering, 17 (3), pp. 462-471, 2007, ISSN: 0960-1317. Abstract \| Links \| BibTeX \| タグ: 2D Neuronal Culture, Cardiomyocytes, ETH-CMOS-MEA, MEA Technology @article{Greve2007, title = {A perforated CMOS microchip platform for immobilization and activity monitoring of electrogenic cells}, author = {Frauke Greve and Jan Lichtenberg and Kay Uwe Kirstein and Urs Frey and Jean Claude Perriard and Andreas Hierlemann}, url = {http://iopscience.iop.org/article/10.1088/0960-1317/17/3/007/}, doi = {10.1088/0960-1317/17/3/007}, issn = {0960-1317}, year = {2007}, date = {2007-01-30}, journal = {Journal of Micromechanics and Microengineering}, volume = {17}, number = {3}, pages = {462-471}, abstract = {CMOS-based microelectrode systems offer decisive advantages over conventional micro-electrode arrays, which include the possibility to perform on-chip signal conditioning or to efficiently use larger numbers of electrodes to obtain statistically relevant data, e.g., in pharmacological drug screening. A larger number of electrodes can only be realized with the help of on-chip multiplexing and readout schemes, which require integrated electronics. Another fundamental issue in performing high-fidelity recordings from electrogenic cells is a good electrical coupling between the cells and the microelectrodes, in particular, since the recorded extracellular signals are in the range of only 10–1000 µV. In this paper we present the first CMOS microelectrode system with integrated micromechanical cell-placement features fabricated in a commercial CMOS process with subsequent post-CMOS bulk micromachining. This new microdevice aims at enabling the precise placement of single cells in the center of the electrodes to ensure an efficient use of the available electrodes, even for low-density cell cultures. Small through-chip holes have been generated at the metal-electrode sites by using a combination of bulk micromachining and reactive-ion etching. These holes act as orifices so that cell immobilization can be achieved by means of pneumatic anchoring. The chip additionally hosts integrated circuitry, i.e., multiplexers to select the respective readout electrodes, an amplifier with selectable gain (2×, 10×, 100×), and a high-pass filter (100 Hz cut-off). In this paper we show that electrical signals from most of the electrodes can be recorded, even in low-density cultures of neonatal rat cardiomyocytes, by using perforated metal electrodes and by applying a small underpressure from the backside of the chip. The measurements evidenced that, in most cases, about 90% of the electrodes were covered with single cells, approximately 4% were covered with more than one cell due to clustering and approximately 6% were not covered with any cell, mostly as a consequence of orifice clogging. After 4 days of culturing, the cells were still in place on the electrodes so that the cell electrical activity could be measured using the on-chip circuitry. Measured signal amplitudes were in the range of 500–700 µV, while the input-referred noise of the readout was below 15 µVrms (100 Hz–4 kHz bandwidth). We report on the development and fabrication of this new cell-biological tool and present first results collected during the characterization and evaluation of the chip. The recordings of electrical potentials of neonatal rat cardiomyocytes after several days in vitro, which, on the one hand, were conventionally cultured (no pneumatic anchoring) and, on the other hand, were anchored and immobilized, will be detailed.}, keywords = {2D Neuronal Culture, Cardiomyocytes, ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close CMOS-based microelectrode systems offer decisive advantages over conventional micro-electrode arrays, which include the possibility to perform on-chip signal conditioning or to efficiently use larger numbers of electrodes to obtain statistically relevant data, e.g., in pharmacological drug screening. A larger number of electrodes can only be realized with the help of on-chip multiplexing and readout schemes, which require integrated electronics. Another fundamental issue in performing high-fidelity recordings from electrogenic cells is a good electrical coupling between the cells and the microelectrodes, in particular, since the recorded extracellular signals are in the range of only 10–1000 µV. In this paper we present the first CMOS microelectrode system with integrated micromechanical cell-placement features fabricated in a commercial CMOS process with subsequent post-CMOS bulk micromachining. This new microdevice aims at enabling the precise placement of single cells in the center of the electrodes to ensure an efficient use of the available electrodes, even for low-density cell cultures. Small through-chip holes have been generated at the metal-electrode sites by using a combination of bulk micromachining and reactive-ion etching. These holes act as orifices so that cell immobilization can be achieved by means of pneumatic anchoring. The chip additionally hosts integrated circuitry, i.e., multiplexers to select the respective readout electrodes, an amplifier with selectable gain (2×, 10×, 100×), and a high-pass filter (100 Hz cut-off). In this paper we show that electrical signals from most of the electrodes can be recorded, even in low-density cultures of neonatal rat cardiomyocytes, by using perforated metal electrodes and by applying a small underpressure from the backside of the chip. The measurements evidenced that, in most cases, about 90% of the electrodes were covered with single cells, approximately 4% were covered with more than one cell due to clustering and approximately 6% were not covered with any cell, mostly as a consequence of orifice clogging. After 4 days of culturing, the cells were still in place on the electrodes so that the cell electrical activity could be measured using the on-chip circuitry. Measured signal amplitudes were in the range of 500–700 µV, while the input-referred noise of the readout was below 15 µVrms (100 Hz–4 kHz bandwidth). We report on the development and fabrication of this new cell-biological tool and present first results collected during the characterization and evaluation of the chip. The recordings of electrical potentials of neonatal rat cardiomyocytes after several days in vitro, which, on the one hand, were conventionally cultured (no pneumatic anchoring) and, on the other hand, were anchored and immobilized, will be detailed. Close http://iopscience.iop.org/article/10.1088/0960-1317/17/3/007/ doi:10.1088/0960-1317/17/3/007 Close
2006
	Heer, Flavio; Hafizovic, Sadik; Ugniwenko, T; Frey, Urs; Franks, Wendy; Perriard, Evelyne; Perriard, Jean Claude; Blau, Axel; Ziegler, Christiane; Hierlemann, Andreas Single-chip microelectronic system to interface with living cells Journal Article Biosensors & Bioelectronics, 22 (11), pp. 2546-2553, 2006, ISSN: 0956-5663. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA, Neuronal Networks @article{Hierlemann2006, title = {Single-chip microelectronic system to interface with living cells}, author = {Flavio Heer and Sadik Hafizovic and T Ugniwenko and Urs Frey and Wendy Franks and Evelyne Perriard and Jean Claude Perriard and Axel Blau and Christiane Ziegler and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S0956566306004891?via%3Dihub}, doi = {10.1016/j.bios.2006.10.003}, issn = {0956-5663}, year = {2006}, date = {2006-11-13}, journal = {Biosensors & Bioelectronics}, volume = {22}, number = {11}, pages = {2546-2553}, abstract = {A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments. Close http://www.sciencedirect.com/science/article/pii/S0956566306004891?via%3Dihub doi:10.1016/j.bios.2006.10.003 Close
	Franks, Wendy; Tosatti, Samuele; Heer, Flavio; Seif, Philipp; Textor, Marcus; Hierlemann, Andreas Patterned cell adhesion by self-assembled structures for use with a CMOS cell-based biosensor Journal Article Biosensors & Bioelectronics, 22 (7), pp. 1426-1433, 2006, ISSN: 0956-5663. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Hierlemann2006b, title = {Patterned cell adhesion by self-assembled structures for use with a CMOS cell-based biosensor}, author = {Wendy Franks and Samuele Tosatti and Flavio Heer and Philipp Seif and Marcus Textor and Andreas Hierlemann}, url = {http://www.sciencedirect.com/science/article/pii/S095656630600282X?via%3Dihub}, doi = {10.1016/j.bios.2006.06.031}, issn = {0956-5663}, year = {2006}, date = {2006-10-19}, journal = {Biosensors & Bioelectronics}, volume = {22}, number = {7}, pages = {1426-1433}, abstract = {A strategy for patterned cell adhesion based on chemical surface modification is presented. To confine cell adhesion to specific locations, an engineered surface for high-contrast protein adsorption and, hence, cell attachment has been developed. Surface functionalization is based on selective molecular-assembly patterning (SMAP). An amine-terminated self-assembled monolayer is used to define areas of cell adhesion. A protein-repellent grafted copolymer, poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), is used to render the surrounding silicon dioxide resistant to protein adsorption. X-ray photoelectron spectroscopy, scanning ellipsometry and fluorescence microscopy techniques were used to monitor the individual steps of the patterning process. Successful guided growth using these layers is demonstrated with primary neonatal rat cardiomyocytes, up to 4 days in vitro, and with the HL-1 cardiomyocyte cell line, up to 7 days in vitro. The advantage of the presented method is that high-resolution engineered surfaces can be realized using a simple, cost-effective, dip-and-rinse process. The technique has been developed for application on a CMOS cell-based biosensor, which comprises an array of microelectrodes to extracellularly record electrical activity from cardiomyocytes.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close A strategy for patterned cell adhesion based on chemical surface modification is presented. To confine cell adhesion to specific locations, an engineered surface for high-contrast protein adsorption and, hence, cell attachment has been developed. Surface functionalization is based on selective molecular-assembly patterning (SMAP). An amine-terminated self-assembled monolayer is used to define areas of cell adhesion. A protein-repellent grafted copolymer, poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), is used to render the surrounding silicon dioxide resistant to protein adsorption. X-ray photoelectron spectroscopy, scanning ellipsometry and fluorescence microscopy techniques were used to monitor the individual steps of the patterning process. Successful guided growth using these layers is demonstrated with primary neonatal rat cardiomyocytes, up to 4 days in vitro, and with the HL-1 cardiomyocyte cell line, up to 7 days in vitro. The advantage of the presented method is that high-resolution engineered surfaces can be realized using a simple, cost-effective, dip-and-rinse process. The technique has been developed for application on a CMOS cell-based biosensor, which comprises an array of microelectrodes to extracellularly record electrical activity from cardiomyocytes. Close http://www.sciencedirect.com/science/article/pii/S095656630600282X?via%3Dihub doi:10.1016/j.bios.2006.06.031 Close
	Heer, Flavio; Hafizovic, Sadik; Franks, Wendy; Blau, Axel; Ziegler, Christiane; Hierlemann, Andreas CMOS microelectrode array for bidirectional interaction with neuronal networks Journal Article IEEE Journal of Solid-State Circuits, 41 (7), pp. 1620-1629, 2006, ISSN: 0018-9200. Abstract \| Links \| BibTeX \| タグ: 2D Neuronal Culture, ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation @article{Heer2006, title = {CMOS microelectrode array for bidirectional interaction with neuronal networks}, author = {Flavio Heer and Sadik Hafizovic and Wendy Franks and Axel Blau and Christiane Ziegler and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/1644873/}, doi = {10.1109/JSSC.2006.873677}, issn = {0018-9200}, year = {2006}, date = {2006-07-07}, journal = {IEEE Journal of Solid-State Circuits}, volume = {41}, number = {7}, pages = {1620-1629}, abstract = {A CMOS metal-electrode-based micro system for bidirectional communication (stimulation and recording) with neuronal cells in vitro is presented. The chip overcomes the interconnect challenge that limits today's bidirectional microelectrode arrays. The microsystem has been fabricated in an industrial CMOS technology with several post-CMOS processing steps to realize 128 biocompatible electrodes and to ensure chip stability in physiological saline. The system comprises all necessary control circuitry and on-chip A/D and D/A conversion. A modular design has been implemented, where individual stimulation- and signal-conditioning circuitry units are associated with each electrode. Stimulation signals with a resolution of 8 bits can be sent to any subset of electrodes at a rate of 60 kHz, while all electrodes of the chip are continuously sampled at a rate of 20 kHz. The circuitry at each electrode can be individually reset to its operating point in order to suppress artifacts evoked by the stimulation pulses. Biological measurements from cultured neuronal networks originating from dissociated cortical tissue of fertilized chicken eggs with amplitudes of up to 500 muVpp are presented.}, keywords = {2D Neuronal Culture, ETH-CMOS-MEA, MEA Technology, Neuronal Networks, Stimulation}, pubstate = {published}, tppubtype = {article} } Close A CMOS metal-electrode-based micro system for bidirectional communication (stimulation and recording) with neuronal cells in vitro is presented. The chip overcomes the interconnect challenge that limits today's bidirectional microelectrode arrays. The microsystem has been fabricated in an industrial CMOS technology with several post-CMOS processing steps to realize 128 biocompatible electrodes and to ensure chip stability in physiological saline. The system comprises all necessary control circuitry and on-chip A/D and D/A conversion. A modular design has been implemented, where individual stimulation- and signal-conditioning circuitry units are associated with each electrode. Stimulation signals with a resolution of 8 bits can be sent to any subset of electrodes at a rate of 60 kHz, while all electrodes of the chip are continuously sampled at a rate of 20 kHz. The circuitry at each electrode can be individually reset to its operating point in order to suppress artifacts evoked by the stimulation pulses. Biological measurements from cultured neuronal networks originating from dissociated cortical tissue of fertilized chicken eggs with amplitudes of up to 500 muVpp are presented. Close http://ieeexplore.ieee.org/document/1644873/ doi:10.1109/JSSC.2006.873677 Close
	Linder, Vincent; Koster, Sander; Franks, Wendy; Kraus, Tobias; Verpoorte, Elisabeth; Heer, Flavio; Hierlemann, Andreas; de Rooij, Nico F Microfluidics/CMOS orthogonal capabilities for cell biology Journal Article Biomedical Microdevices, 8 (2), pp. 159-166, 2006, ISSN: 1572-8781. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Linder2006, title = {Microfluidics/CMOS orthogonal capabilities for cell biology}, author = {Vincent Linder and Sander Koster and Wendy Franks and Tobias Kraus and Elisabeth Verpoorte and Flavio Heer and Andreas Hierlemann and Nico F de Rooij}, url = {https://link.springer.com/article/10.1007%2Fs10544-006-7711-9}, doi = {10.1007/s10544-006-7711-9}, issn = {1572-8781}, year = {2006}, date = {2006-06-01}, journal = {Biomedical Microdevices}, volume = {8}, number = {2}, pages = {159-166}, abstract = {The study of individual cells and cellular networks can greatly benefit from the capabilities of microfabricated devices for the stimulation and the recording of electrical cellular events. In this contribution, we describe the development of a device, which combines capabilities for both electrical and pharmacological cell stimulation, and the subsequent recording of electrical cellular activity. The device combines the unique advantages of integrated circuitry (CMOS technology) for signal processing and microfluidics for drug delivery. Both techniques are ideally suited to study electrogenic mammalian cells, because feature sizes are of the same order as the cell diameter, ∼50 mum. Despite these attractive features, we observe a size mismatch between microfluidic devices, with bulky fluidic connections to the outside world, and highly miniaturized CMOS chips. To overcome this problem, we developed a microfluidic flow cell that accommodates a small CMOS chip. We simulated the performances of a flow cell based on a 3-D microfluidic system, and then fabricated the device to experimentally verify the nutrient delivery and localized drug delivery performance. The flow-cell has a constant nutrient flow, and six drug inlets that can individually deliver a drug to the cells. The experimental analysis of the nutrient and drug flow mass transfer properties in the flowcell are in good agreement with our simulations. For an experimental proof-of-principle, we successfully delivered, in a spatially resolved manner, a `drug' to a culture of HL-1 cardiac myocytes.}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close The study of individual cells and cellular networks can greatly benefit from the capabilities of microfabricated devices for the stimulation and the recording of electrical cellular events. In this contribution, we describe the development of a device, which combines capabilities for both electrical and pharmacological cell stimulation, and the subsequent recording of electrical cellular activity. The device combines the unique advantages of integrated circuitry (CMOS technology) for signal processing and microfluidics for drug delivery. Both techniques are ideally suited to study electrogenic mammalian cells, because feature sizes are of the same order as the cell diameter, ∼50 mum. Despite these attractive features, we observe a size mismatch between microfluidic devices, with bulky fluidic connections to the outside world, and highly miniaturized CMOS chips. To overcome this problem, we developed a microfluidic flow cell that accommodates a small CMOS chip. We simulated the performances of a flow cell based on a 3-D microfluidic system, and then fabricated the device to experimentally verify the nutrient delivery and localized drug delivery performance. The flow-cell has a constant nutrient flow, and six drug inlets that can individually deliver a drug to the cells. The experimental analysis of the nutrient and drug flow mass transfer properties in the flowcell are in good agreement with our simulations. For an experimental proof-of-principle, we successfully delivered, in a spatially resolved manner, a `drug' to a culture of HL-1 cardiac myocytes. Close https://link.springer.com/article/10.1007%2Fs10544-006-7711-9 doi:10.1007/s10544-006-7711-9 Close
	Kraus, Tobias; Verpoorte, Elisabeth; Linder, Vincent; Franks, Wendy; Hierlemann, Andreas; Heer, Flavio; Hafizovic, Sadik; Fujii, Teruo; de Rooij, Nico F; Koster, Sander Characterization of a microfluidic dispensing system for localised stimulation of cellular networks Journal Article Lab Chip, 6 (2), pp. 218-229, 2006. Abstract \| Links \| BibTeX \| タグ: Cardiomyocytes, ETH-CMOS-MEA @article{Koster2006, title = {Characterization of a microfluidic dispensing system for localised stimulation of cellular networks}, author = {Tobias Kraus and Elisabeth Verpoorte and Vincent Linder and Wendy Franks and Andreas Hierlemann and Flavio Heer and Sadik Hafizovic and Teruo Fujii and Nico F de Rooij and Sander Koster}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2006/LC/b511768b#!divAbstract}, doi = {10.1039/B511768B}, year = {2006}, date = {2006-01-04}, journal = {Lab Chip}, volume = {6}, number = {2}, pages = {218-229}, publisher = {The Royal Society of Chemistry}, abstract = {We present a 3-D microfluidic device designed for localized drug delivery to cellular networks. The device features a flow cell comprising a main channel for nutrient delivery as well as multiple channels for drug delivery. This device is one key component of a larger, fully integrated system now under development, based upon a microelectrode array (MEA) with on-chip CMOS circuitry for recording and stimulation of electrogenic cells (e.g. neurons, cardiomyocytes). As a critical system unit, the microfluidics must be carefully designed and characterized to ensure that candidate drugs are delivered to specific regions of the culture at known concentrations. Furthermore, microfluidic design and functionality is dictated by the size, geometry, and material/electrical characteristics of the CMOS MEA. Therefore, this paper reports on the design considerations and fabrication of the flow cell, including theoretical and experimental analysis of the mass transfer properties of the nutrient and drug flows, which are in good agreement with one another. To demonstrate proof of concept, the flow cell was mounted on a dummy CMOS chip, which had been plated with HL-1 cardiomyocytes. A test chemical compound was delivered to the cell culture in a spatially resolved manner. Envisioned applications of this stand-alone system include simultaneous toxicological testing of multiple compounds and chemical stimulation of natural neural networks for neuroscience investigations}, keywords = {Cardiomyocytes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close We present a 3-D microfluidic device designed for localized drug delivery to cellular networks. The device features a flow cell comprising a main channel for nutrient delivery as well as multiple channels for drug delivery. This device is one key component of a larger, fully integrated system now under development, based upon a microelectrode array (MEA) with on-chip CMOS circuitry for recording and stimulation of electrogenic cells (e.g. neurons, cardiomyocytes). As a critical system unit, the microfluidics must be carefully designed and characterized to ensure that candidate drugs are delivered to specific regions of the culture at known concentrations. Furthermore, microfluidic design and functionality is dictated by the size, geometry, and material/electrical characteristics of the CMOS MEA. Therefore, this paper reports on the design considerations and fabrication of the flow cell, including theoretical and experimental analysis of the mass transfer properties of the nutrient and drug flows, which are in good agreement with one another. To demonstrate proof of concept, the flow cell was mounted on a dummy CMOS chip, which had been plated with HL-1 cardiomyocytes. A test chemical compound was delivered to the cell culture in a spatially resolved manner. Envisioned applications of this stand-alone system include simultaneous toxicological testing of multiple compounds and chemical stimulation of natural neural networks for neuroscience investigations Close http://pubs.rsc.org/en/Content/ArticleLanding/2006/LC/b511768b#!divAbstract doi:10.1039/B511768B Close
2005
	Franks, Wendy; Schenker, Iwan; Schmutz, Patrik; Hierlemann, Andreas Impedance characterization and modeling of electrodes for biomedical applications Journal Article IEEE Transactions on Biomedical Engineering, 52 (7), pp. 1295-1302, 2005, ISSN: 00189294. Abstract \| Links \| BibTeX \| タグ: MEA Technology @article{Franks2005, title = {Impedance characterization and modeling of electrodes for biomedical applications}, author = {Wendy Franks and Iwan Schenker and Patrik Schmutz and Andreas Hierlemann}, url = {http://ieeexplore.ieee.org/document/1440608/}, doi = {10.1109/TBME.2005.847523}, issn = {00189294}, year = {2005}, date = {2005-06-13}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {52}, number = {7}, pages = {1295-1302}, abstract = {A low electrode-electrolyte impedance interface is critical in the design of electrodes for biomedical applications. To design low-impedance interfaces a complete understanding of the physical processes contributing to the impedance is required. In this work a model describing these physical processes is validated and extended to quantify the effect of organic coatings and incubation time. Electrochemical impedance spectroscopy has been used to electrically characterize the interface for various electrode materials: platinum, platinum black, and titanium nitride; and varying electrode sizes: 1 cm2, and 900 mu m2. An equivalent circuit model comprising an interface capacitance, shunted by a charge transfer resistance, in series with the solution resistance has been fitted to the experimental results. Theoretical equations have been used to calculate the interface capacitance impedance and the solution resistance, yielding results that correspond well with the fitted parameter values, thereby confirming the validity of the equations. The effect of incubation time, and two organic cell-adhesion promoting coatings, poly-L-lysine and laminin, on the interface impedance has been quantified using the model. This demonstrates the benefits of using this model in developing better understanding of the physical processes occurring at the interface in more complex, biomedically relevant situations.}, keywords = {MEA Technology}, pubstate = {published}, tppubtype = {article} } Close A low electrode-electrolyte impedance interface is critical in the design of electrodes for biomedical applications. To design low-impedance interfaces a complete understanding of the physical processes contributing to the impedance is required. In this work a model describing these physical processes is validated and extended to quantify the effect of organic coatings and incubation time. Electrochemical impedance spectroscopy has been used to electrically characterize the interface for various electrode materials: platinum, platinum black, and titanium nitride; and varying electrode sizes: 1 cm2, and 900 mu m2. An equivalent circuit model comprising an interface capacitance, shunted by a charge transfer resistance, in series with the solution resistance has been fitted to the experimental results. Theoretical equations have been used to calculate the interface capacitance impedance and the solution resistance, yielding results that correspond well with the fitted parameter values, thereby confirming the validity of the equations. The effect of incubation time, and two organic cell-adhesion promoting coatings, poly-L-lysine and laminin, on the interface impedance has been quantified using the model. This demonstrates the benefits of using this model in developing better understanding of the physical processes occurring at the interface in more complex, biomedically relevant situations. Close http://ieeexplore.ieee.org/document/1440608/ doi:10.1109/TBME.2005.847523 Close
2004
	Jenkner, Martin; Tartagni, Marco; Hierlemann, Andreas; Thewes, Roland Cell-based CMOS sensor and actuator arrays Journal Article IEEE Journal of Solid-State Circuits, 39 (12), pp. 2431-2437, 2004, ISSN: 00189200. Abstract \| Links \| BibTeX \| タグ: MEA Technology, Review @article{Jenkner2004, title = {Cell-based CMOS sensor and actuator arrays}, author = {Martin Jenkner and Marco Tartagni and Andreas Hierlemann and Roland Thewes}, url = {http://ieeexplore.ieee.org/document/1362853/}, doi = {10.1109/JSSC.2004.837082}, issn = {00189200}, year = {2004}, date = {2004-11-30}, journal = {IEEE Journal of Solid-State Circuits}, volume = {39}, number = {12}, pages = {2431-2437}, abstract = {In recent years, increasing knowledge about in vitro cell handling and culturing has encouraged a variety of CMOS-based approaches to stimulate and detect electrical activity of biological cells. This paper outlines in a topical review the scope of cell-based biosensors and actuators for in vitro applications ranging from single-cell detection to multisite probing of complex neural tissue. Recent examples are selected to demonstrate how standard CMOS processes have been used to engineer arrays with different functionality.}, keywords = {MEA Technology, Review}, pubstate = {published}, tppubtype = {article} } Close In recent years, increasing knowledge about in vitro cell handling and culturing has encouraged a variety of CMOS-based approaches to stimulate and detect electrical activity of biological cells. This paper outlines in a topical review the scope of cell-based biosensors and actuators for in vitro applications ranging from single-cell detection to multisite probing of complex neural tissue. Recent examples are selected to demonstrate how standard CMOS processes have been used to engineer arrays with different functionality. Close http://ieeexplore.ieee.org/document/1362853/ doi:10.1109/JSSC.2004.837082 Close
	Heer, Flavio; Franks, Wendy; Blau, Axel; Taschini, S; Ziegler, Christiane; Hierlemann, Andreas; Baltes, Henry CMOS microelectrode array for the monitoring of electrogenic cells Journal Article Biosensors & Bioelectronics, 20 (2), pp. 358-366, 2004, ISSN: 0956-5663. Abstract \| Links \| BibTeX \| タグ: ETH-CMOS-MEA, MEA Technology @article{Baltes2004, title = {CMOS microelectrode array for the monitoring of electrogenic cells}, author = {Flavio Heer and Wendy Franks and Axel Blau and S Taschini and Christiane Ziegler and Andreas Hierlemann and Henry Baltes}, url = {http://www.sciencedirect.com/science/article/pii/S0956566304000806?via%3Dihub}, doi = {10.1016/j.bios.2004.02.006}, issn = {0956-5663}, year = {2004}, date = {2004-03-19}, journal = {Biosensors & Bioelectronics}, volume = {20}, number = {2}, pages = {358-366}, abstract = {Signal degradation and an array size dictated by the number of available interconnects are the two main limitations inherent to standalone microelectrode arrays (MEAs). A new biochip consisting of an array of microelectrodes with fully-integrated analog and digital circuitry realized in an industrial CMOS process addresses these issues. The device is capable of on-chip signal filtering for improved signal-to-noise ratio (SNR), on-chip analog and digital conversion, and multiplexing, thereby facilitating simultaneous stimulation and recording of electrogenic cell activity. The designed electrode pitch of 250 mu m significantly limits the space available for circuitry: a repeated unit of circuitry associated with each electrode comprises a stimulation buffer and a bandpass filter for readout. The bandpass filter has corner frequencies of 100 Hz and 50 kHz, and a gain of 1000. Stimulation voltages are generated from an 8-bit digital signal and converted to an analog signal at a frequency of 120 kHz. Functionality of the read-out circuitry is demonstrated by the measurement of cardiomyocyte activity. The microelectrode is realized in a shifted design for flexibility and biocompatibility. Several microelectrode materials (platinum, platinum black and titanium nitride) have been electrically characterized. An equivalent circuit model, where each parameter represents a macroscopic physical quantity contributing to the interface impedance, has been successfully fitted to experimental results.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Signal degradation and an array size dictated by the number of available interconnects are the two main limitations inherent to standalone microelectrode arrays (MEAs). A new biochip consisting of an array of microelectrodes with fully-integrated analog and digital circuitry realized in an industrial CMOS process addresses these issues. The device is capable of on-chip signal filtering for improved signal-to-noise ratio (SNR), on-chip analog and digital conversion, and multiplexing, thereby facilitating simultaneous stimulation and recording of electrogenic cell activity. The designed electrode pitch of 250 mu m significantly limits the space available for circuitry: a repeated unit of circuitry associated with each electrode comprises a stimulation buffer and a bandpass filter for readout. The bandpass filter has corner frequencies of 100 Hz and 50 kHz, and a gain of 1000. Stimulation voltages are generated from an 8-bit digital signal and converted to an analog signal at a frequency of 120 kHz. Functionality of the read-out circuitry is demonstrated by the measurement of cardiomyocyte activity. The microelectrode is realized in a shifted design for flexibility and biocompatibility. Several microelectrode materials (platinum, platinum black and titanium nitride) have been electrically characterized. An equivalent circuit model, where each parameter represents a macroscopic physical quantity contributing to the interface impedance, has been successfully fitted to experimental results. Close http://www.sciencedirect.com/science/article/pii/S0956566304000806?via%3Dihub doi:10.1016/j.bios.2004.02.006 Close

論文

Publications

Selected Publications

<img decoding="async" class="floatLeft aligncenter" src="https://www.mxwbio.com/wp-content/uploads/2016/06/Mueller2015.jpg" alt="Mueller2015" width="200" /> High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels

<img decoding="async" class="floatLeft aligncenter" src="https://www.mxwbio.com/wp-content/uploads/2016/06/Obien2014frontiersrev.jpg" alt="Obien2014" width="200" /> 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

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

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

Revealing Neuronal Function through Microelectrode Array Recordings