@article{Frey2016,
title = {Extracellularly Recorded Somatic and Neuritic Signal Shapes and Classification Algorithms for High-Density Microelectrode Array Electrophysiology},
author = {Kosmas Deligkaris and Torsten Bullmann and Urs Frey},
url = {https://www.frontiersin.org/article/10.3389/fnins.2016.00421},
doi = {10.3389/fnins.2016.00421},
issn = {1662-453X},
year = {2016},
date = {2016-09-14},
journal = {Frontiers in Neuroscience},
volume = {10},
pages = {421},
abstract = {High-density microelectrode arrays (HDMEA) have been recently introduced to study principles of neural function at high spatial resolution. However, the exact nature of the experimentally observed extracellular action potentials (EAPs) is still incompletely understood. The soma, axon and dendrites of a neuron can all exhibit regenerative action potentials that could be sensed with HDMEA electrodes. Here, we investigate the contribution of distinct neuronal sources of activity in HDMEA recordings from low-density neuronal cultures. We recorded EAPs with HDMEAs having 11,011 electrodes and then fixed and immunostained the cultures with beta3-tubulin for high-resolution fluorescence imaging. Immunofluorescence images overlaid with the activity maps showed EAPs both at neuronal somata and distal neurites. Neuritic EAPs had mostly narrow triphasic shapes, consisting of a positive, a pronounced negative peak and a second positive peak. EAPs near somata had wide monophasic or biphasic shapes with a main negative peak, and following optional positive peak. We show that about 86% of EAP recordings consist of somatic spikes, while the remaining 14% represent neuritic spikes. Furthermore, the adaptation of the waveform shape during bursts of these neuritic spikes suggested that they originate from axons, rather than from dendrites. Our study improves the understanding of HDMEA signals and can aid in the identification of the source of EAPs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Radivojevic2016,
title = {Electrical Identification and Selective Microstimulation of Neuronal Compartments Based on Features of Extracellular Action Potentials},
author = {Milos Radivojevic and David Jäckel and Michael Altermatt and Jan Müller and Vijay Viswam and Andreas Hierlemann and Douglas J Bakkum},
url = {http://www.nature.com/articles/srep31332},
doi = {10.1038/srep31332},
issn = {2045-2322},
year = {2016},
date = {2016-08-11},
journal = {Scientific Reports},
volume = {6},
number = {1},
pages = {1-20},
abstract = {A detailed, high-spatiotemporal-resolution characterization of neuronal responses to local electrical fields and the capability of precise extracellular microstimulation of selected neurons are pivotal for studying and manipulating neuronal activity and circuits in networks and for developing neural prosthetics. Here, we studied cultured neocortical neurons by using high-density microelectrode arrays and optical imaging, complemented by the patch-clamp technique, and with the aim to correlate morphological and electrical features of neuronal compartments with their responsiveness to extracellular stimulation. We developed strategies to electrically identify any neuron in the network, while subcellular spatial resolution recording of extracellular action potential (AP) traces enabled their assignment to the axon initial segment (AIS), axonal arbor and proximal somatodendritic compartments. Stimulation at the AIS required low voltages and provided immediate, selective and reliable neuronal activation, whereas stimulation at the soma required high voltages and produced delayed and unreliable responses. Subthreshold stimulation at the soma depolarized the somatic membrane potential without eliciting APs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Lewandowska2016,
title = {Cortical axons, isolated in channels, display activity-dependent signal modulation as a result of targeted stimulation},
author = {Marta K Lewandowska and Milos Radivojevic and David Jäckel and Jan Müller and Andreas Hierlemann},
url = {https://www.frontiersin.org/articles/10.3389/fnins.2016.00083/full},
doi = {10.3389/fnins.2016.00083},
issn = {1662453X},
year = {2016},
date = {2016-03-07},
journal = {Frontiers in Neuroscience},
volume = {10},
pages = {83},
abstract = {Mammalian cortical axons are extremely thin processes that are difficult to study as a result of their small diameter: they are too narrow to patch while intact, and super-resolution microscopy is needed to resolve single axons. We present a method for studying axonal physiology by pairing a high-density microelectrode array with a microfluidic axonal isolation device, and use it to study activity-dependent modulation of axonal signal propagation evoked by stimulation near the soma. Up to three axonal branches from a single neuron, isolated in different channels, were recorded from simultaneously using 10-20 electrodes per channel. The axonal channels amplified spikes such that propagations of individual signals along tens of electrodes could easily be discerned with high signal to noise. Stimulation from 10 up to 160 Hz demonstrated similar qualitative results from all of the cells studied: extracellular action potential characteristics changed drastically in response to stimulation. Spike height decreased, spike width increased, and latency increased, as a result of reduced propagation velocity, as the number of stimulations and the stimulation frequencies increased. Quantitatively, the strength of these changes manifested itself differently in cells at different frequencies of stimulation. Some cells' signal fidelity fell to 80% already at 10 Hz, while others maintained 80% signal fidelity at 80 Hz. Differences in modulation by axonal branches of the same cell were also seen for different stimulation frequencies, starting at 10 Hz. Potassium ion concentration changes altered the behavior of the cells causing propagation failures at lower concentrations and improving signal fidelity at higher concentrations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Franke2016,
title = {Structures of Neural Correlation and How They Favor Coding},
author = {Felix Franke and Michele Fiscella and Maksim Sevelev and Botond Roska and Andreas Hierlemann and Rava {Azeredo da Silveira}},
url = {http://www.sciencedirect.com/science/article/pii/S0896627315011393?via%3Dihub},
doi = {10.1016/j.neuron.2015.12.037},
issn = {10974199},
year = {2016},
date = {2016-01-20},
journal = {Neuron},
volume = {89},
number = {2},
pages = {409-422},
publisher = {Elsevier Inc.},
abstract = {The neural representation of information suffers from "noise"-the trial-to-trial variability in the response of neurons. The impact of correlated noise upon population coding has been debated, but a direct connection between theory and experiment remains tenuous. Here, we substantiate this connection and propose a refined theoretical picture. Using simultaneous recordings from a population of direction-selective retinal ganglion cells, we demonstrate that coding benefits from noise correlations. The effect is appreciable already in small populations, yet it is a collective phenomenon. Furthermore, the stimulus-dependent structure of correlation is key. We develop simple functional models that capture the stimulus-dependent statistics. We then use them to quantify the performance of population coding, which depends upon interplays of feature sensitivities and noise correlations in the population. Because favorable structures of correlation emerge robustly in circuits with noisy, nonlinear elements, they will arise and benefit coding beyond the confines of retina. Coding in the brain suffers from the variability of neural responses. Using experiment and theory, Franke et al. show that this "noise" comes with a particular structure, which emerges from circuit properties and which counteracts the harmful effect of variability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Muller2015,
title = {High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels},
author = {Jan Müller and Marco Ballini and Paolo Livi and Yihui Chen and Milos Radivojevic and Amir Shadmani and Vijay Viswam and Ian L Jones and Michele Fiscella and Roland Diggelmann and Alexander Stettler and Urs Frey and Douglas J Bakkum and Andreas Hierlemann},
url = {http://pubs.rsc.org/en/Content/ArticleLanding/2015/LC/C5LC00133A#!divAbstract},
doi = {10.1039/C5LC00133A},
issn = {1473-0197},
year = {2015},
date = {2015-07-07},
journal = {Lab Chip},
volume = {15},
number = {13},
pages = {2767-2780},
publisher = {Royal Society of Chemistry},
abstract = {Studies on information processing and learning properties of neuronal networks would benefit from simultaneous and parallel access to the activity of a large fraction of all neurons in such networks. Here, we present a CMOS-based device, capable of simultaneously recording the electrical activity of over a thousand cells in in vitro neuronal networks. The device provides sufficiently high spatiotemporal resolution to enable, at the same time, access to neuronal preparations on subcellular, cellular, and network level. The key feature is a rapidly reconfigurable array of 26 400 microelectrodes arranged at low pitch (17.5 um) within a large overall sensing area (3.85 × 2.10 mm2). An arbitrary subset of the electrodes can be simultaneously connected to 1024 low-noise readout channels as well as 32 stimulation units. Each electrode or electrode subset can be used to electrically stimulate or record the signals of virtually any neuron on the array. We demonstrate the applicability and potential of this device for various different experimental paradigms: large-scale recordings from whole networks of neurons as well as investigations of axonal properties of individual neurons.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Takahashi2015,
title = {Chronic Co-Variation of Neural Network Configuration and Activity in Mature Dissociated Cultures},
author = {Satoru Okawa and Takeshi Mita and Douglas J Bakkum and Urs Frey and Andreas Hierlemann and Ryohei Kanzaki and Hirokazu Takahashi},
url = {http://onlinelibrary.wiley.com/doi/10.1002/ecj.11736/abstract;jsessionid=791557FA80CF36B1F78DC538C1618924.f03t02},
doi = {10.1002/ecj.11736},
issn = {1942-9541},
year = {2015},
date = {2015-04-08},
journal = {Electronics and Communications in Japan},
volume = {98},
number = {5},
pages = {34-42},
abstract = {Spatiotemporal neural patterns depend on the physical structure of neural circuits. Neural plasticity can thus be associated with changes in the circuit structure. For example, newborn neurons migrate toward existing, already matured, neural networks in order to participate in neural computation. In the present study, we have conducted two experiments to investigate how neural migration is associated with the development of neural activity in primary dissociated cultures of neuronal cells. In Experiment 1, using a mature culture, a high-density CMOS microelectrode array was used to continuously monitor neural migration and activity for more than two weeks. Consequently, we found that even in mature neuronal cultures neurons moved 2.0 ± 1.0 mum a day and that the moving distance was negatively correlated with their firing rate, suggesting that neurons featuring low firing rates tend to migrate actively. In Experiment 2 using a co-culture of mature and immature neurons, we found that immature neurons moved more actively than matured neurons to achieve functional connections to other neurons. These findings suggest that neurons with low firing rates as well as newborn neurons actively migrate in order to establish their connections and function in a neuronal network.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Lewandowska2015,
title = {Recording large extracellular spikes in microchannels along many axonal sites from individual neurons},
author = {Marta K Lewandowska and Douglas J Bakkum and Santiago B Rompani and Andreas Hierlemann},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118514},
doi = {10.1371/journal.pone.0118514},
issn = {19326203},
year = {2015},
date = {2015-03-03},
journal = {PLoS ONE},
volume = {10},
number = {3},
pages = {1-24},
abstract = {The numerous connections between neuronal cell bodies, made by their dendrites and axons, are vital for information processing in the brain. While dendrites and synapses have been extensively studied, axons have remained elusive to a large extent. We present a novel platform to study axonal physiology and information processing based on combining an 11,011-electrode high-density complementary metal-oxide semiconductor microelectrode array with a poly(dimethylsiloxane) channel device, which isolates axons from somas and, importantly, significantly amplifies recorded axonal signals. The combination of the microelectrode array with recording and stimulation capability with the microfluidic isolation channels permitted us to study axonal signal behavior at great detail. The device, featuring two culture chambers with over 30 channels spanning in between, enabled long-term recording of single spikes from isolated axons with signal amplitudes of 100 uV up to 2 mV. Propagating signals along axons could be recorded with 10 to 50 electrodes per channel. We (i) describe the performance and capabilities of our device for axonal electrophysiology, and (ii) present novel data on axonal signals facilitated by the device. Spontaneous action potentials with characteristic shapes propagated from somas along axons between the two compartments, and these unique shapes could be used to identify individual axons within channels that contained many axonal branches. Stimulation through the electrode array facilitated the identification of somas and their respective axons, enabling interfacing with different compartments of a single cell. Complex spike shapes observed in channels were traced back to single cells, and we show that more complicated spike shapes originate from a linear superposition of multiple axonal signals rather than signal distortion by the channels.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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 = {},
pubstate = {published},
tppubtype = {article}
}

@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 = {},
pubstate = {published},
tppubtype = {article}
}

@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 = {},
pubstate = {published},
tppubtype = {article}
}

@article{Hierlemann2007,
title = {A CMOS-based microelectrode array for interaction with neuronal cultures},
author = {Sadik Hafizovic and Flavio Heer 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 = {},
pubstate = {published},
tppubtype = {article}
}

@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 = {},
pubstate = {published},
tppubtype = {article}
}

@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/ESSCIR.2005.1541628},
issn = {00189200},
year = {2006},
date = {2006-06-26},
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 = {},
pubstate = {published},
tppubtype = {article}
}