title: Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays.
abstract: We present a method for automated spike sorting for recordings with high-density, large-scale multielectrode arrays. Exploiting the dense sampling of single neurons by multiple electrodes, an efficient, low-dimensional representation of detected spikes consisting of estimated spatial spike locations and dominant spike shape features is exploited for fast and reliable clustering into single units. Millions of events can be sorted in minutes, and the method is parallelized and scales better than quadratically with the number of detected spikes. Performance is demonstrated using recordings with a 4,096-channel array and validated using anatomical imaging, optogenetic stimulation, and model-based quality control. A comparison with semi-automated, shape-based spike sorting exposes significant limitations of conventional methods. Our approach demonstrates that it is feasible to reliably isolate the activity of up to thousands of neurons and that dense, multi-channel probes substantially aid reliable spike sorting.
authors.affiliation: Institute of Neuroscience, Newcastle University, Newcastle NE2 4HH, UK.
authors.forename: Gerrit
authors.initials: G
authors.lastname: Hilgen
authors.affiliation: Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK; Department of Computational Biology, School of Computer Science and Communication, Royal Institute of Technology, Stockholm 100 44, Sweden.
authors.forename: Martino
authors.initials: M
authors.lastname: Sorbaro
authors.affiliation: Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
authors.forename: Sahar
authors.initials: S
authors.lastname: Pirmoradian
authors.affiliation: Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK; Manipal University, Manipal 576104, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.
authors.forename: Jens-Oliver
authors.initials: JO
authors.lastname: Muthmann
authors.affiliation: Nanophysics (NAPH), Istituto Italiano di Tecnologia, Genova 16163, Italy; Faculty of Science, Engineering and Computing, Kingston University, Kingston KT1 2EE, UK.
authors.forename: Ibolya Edit
authors.initials: IE
authors.lastname: Kepiro
authors.affiliation: Pattern Analysis and Computer Vision (PAVIS), Istituto Italiano di Tecnologia, Genova 16163, Italy.
authors.forename: Simona
authors.initials: S
authors.lastname: Ullo
authors.affiliation: Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
authors.forename: Cesar Juarez
authors.initials: CJ
authors.lastname: Ramirez
authors.affiliation: Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
authors.forename: Albert
authors.initials: A
authors.lastname: Puente Encinas
authors.affiliation: Neuroscience and Brain Technologies (NBT), Istituto Italiano di Tecnologia, Genova 16163, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Maccione
authors.affiliation: Neuroscience and Brain Technologies (NBT), Istituto Italiano di Tecnologia, Genova 16163, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Berdondini
authors.affiliation: Pattern Analysis and Computer Vision (PAVIS), Istituto Italiano di Tecnologia, Genova 16163, Italy.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Murino
authors.affiliation: Pattern Analysis and Computer Vision (PAVIS), Istituto Italiano di Tecnologia, Genova 16163, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Sona
authors.affiliation: Nanophysics (NAPH), Istituto Italiano di Tecnologia, Genova 16163, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Cella Zanacchi
authors.affiliation: Institute of Neuroscience, Newcastle University, Newcastle NE2 4HH, UK.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Sernagor
authors.affiliation: Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK. Electronic address: m.hennig@ed.ac.uk.
authors.forename: Matthias Helge
authors.initials: MH
authors.lastname: Hennig
mesh_terms: D000200:Action Potentials / Q000502:physiology*; D000818:Animals; D004566:Electrodes; D004594:Electrophysiology / Q000295:instrumentation*; D021621:Imaging, Three-Dimensional; D008810:Mice, Inbred C57BL; D008959:Models, Neurological; D062308:Optogenetics; D015203:Reproducibility of Results; D012165:Retinal Ganglion Cells / Q000502:physiology
keywords: electrophysiology; high-density multielectrode array; neural cultures; retina; spike sorting