Project

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Image processing by mosaics of retinal cells

English title Image processing by mosaics of retinal cells
Applicant Hierlemann Andreas
Number 141801
Funding scheme Sinergia
Research institution Computational Systems Biology Department of Biosystems, D-BSSE ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Neurophysiology and Brain Research
Start/End 01.07.2013 - 31.12.2016
Approved amount 1'200'000.00
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All Disciplines (3)

Discipline
Neurophysiology and Brain Research
Microelectronics. Optoelectronics
Mathematics

Keywords (5)

Genetics; Retina; Electrophysiology; Information processing; Microelectronics

Lay Summary (English)

Lead
Lay summary

The present project aims at understanding how a certain population of neurons, which share genetic, morphological, or physiological traits, processes sensory information. The elucidation of this question is essential to understanding the brain. The central task is to examine the way, in which populations of same-type and different-type neuronal cells, or in the retina the respective types of retinal ganglion cells, process visual information. To this end, we will need to genetically label and manipulate ganglion cells, to carry out high-throughput recordings of their electrical or spiking activity, and to analyze the resulting data with mathematical and computational methods. This project will focus on the retina but we expect that the scientific questions and the experimental and computational approaches of this project will be transferable to cortical and other areas.

Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Automatic spike sorting for high-density microelectrode arrays
Diggelmann Roland, Fiscella Michele, Hierlemann Andreas, Franke Felix (2018), Automatic spike sorting for high-density microelectrode arrays, in Journal of Neurophysiology, 120(6), 3155-3171.
How Diverse Retinal Functions Arise from Feedback at the First Visual Synapse
Drinnenberg Antonia, Franke Felix, Morikawa Rei K., Jüttner Josephine, Hillier Daniel, Hantz Peter, Hierlemann Andreas, Azeredo da Silveira Rava, Roska Botond (2018), How Diverse Retinal Functions Arise from Feedback at the First Visual Synapse, in Neuron, 99(1), 117-134.e11.
Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex
Hillier Daniel, Fiscella Michele, Drinnenberg Antonia, Trenholm Stuart, Rompani Santiago B, Raics Zoltan, Katona Gergely, Juettner Josephine, Hierlemann Andreas, Rozsa Balazs, Roska Botond (2017), Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex, in Nature Neuroscience, 20(7), 960-968.
Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction Selectivity.
Yonehara Keisuke, Fiscella Michele, Drinnenberg Antonia, Esposti Federico, Trenholm Stuart, Krol Jacek, Franke Felix, Scherf Brigitte Gross, Kusnyerik Akos, Müller Jan, Szabo Arnold, Jüttner Josephine, Cordoba Francisco, Reddy Ashrithpal Police, Németh János, Nagy Zoltán Zsolt, Munier Francis, Hierlemann Andreas, Roska Botond (2016), Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction Selectivity., in Neuron, 89(1), 177-93.
Screening Transgenic Mouse Models of Human Eye Diseases with CMOS High-Density Microelectrode Arrays
Michele Fiscella, Keisuke Yonehara, Antonia Drinnenberg, Felix Franke, Jan Muller, Botond Roska, Andreas Hierlemann (2016), Screening Transgenic Mouse Models of Human Eye Diseases with CMOS High-Density Microelectrode Arrays, in Frontiers in Neuroscience, 10, 1.
Structures of Neural Correlation and How They Favor Coding.
Franke Felix, Fiscella Michele, Sevelev Maksim, Roska Botond, Hierlemann Andreas, da Silveira Rava Azeredo (2016), Structures of Neural Correlation and How They Favor Coding., in Neuron, 89(2), 409-22.
Using High-Density MEAs For High-Throughput Retinal Ganglion Cell Type Classification
Roland Diggelmann, Michele Fiscella, Antonia Drinnenberg, Felix Franke, Botond Roska, Andreas Hierlemann (2016), Using High-Density MEAs For High-Throughput Retinal Ganglion Cell Type Classification, in Frontiers in Neuroscience, 10, 1.
A Method for Electrophysiological Characterization of Hamster Retinal Ganglion Cells Using a High-Density CMOS Microelectrode Array
IL Jones, TL Russell, K Farrow, M Fiscella, F Franke, D Jäckel, A Hierlemann (2015), A Method for Electrophysiological Characterization of Hamster Retinal Ganglion Cells Using a High-Density CMOS Microelectrode Array, in Frontiers in Neuroscience, 9, 360.
A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture.
Krol Jacek, Krol Ilona, Alvarez Claudia Patricia Patino, Fiscella Michele, Hierlemann Andreas, Roska Botond, Filipowicz Witold (2015), A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture., in Nature communications, 6, 7305-7305.
Highly integrated CMOS microsystems to interface with neurons at subcellular resolution
Hierlemann Andreas, Muller Jan, Bakkum Douglas, Franke Felix (2015), Highly integrated CMOS microsystems to interface with neurons at subcellular resolution, in 2015 IEEE International Electron Devices Meeting (IEDM), Washington, DC, USAIEEE, Piscataway.
PRESYNAPTIC NETWORKS. Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules.
Wertz Adrian, Trenholm Stuart, Yonehara Keisuke, Hillier Daniel, Raics Zoltan, Leinweber Marcus, Szalay Gergely, Ghanem Alexander, Keller Georg, Rózsa Balázs, Conzelmann Karl-Klaus, Roska Botond (2015), PRESYNAPTIC NETWORKS. Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules., in Science (New York, N.Y.), 349(6243), 70-4.
Visual Coding with a Population of Direction-Selective Neurons
Fiscella Michele, Franke Felix, Farrow Karl, Müller Jan, Roska Botond, Azeredo da Silveira Rava, Hierlemann Andreas (2015), Visual Coding with a Population of Direction-Selective Neurons, in Journal of Neurophysiology, 1.
Complexity Optimization and High-Throughput Low-Latency Hardware Implementation of a Multi-Electrode Spike-Sorting Algorithm
Dragas Jelena, Jäckel David, Hierlemann Andreas, Franke Felix (2014), Complexity Optimization and High-Throughput Low-Latency Hardware Implementation of a Multi-Electrode Spike-Sorting Algorithm, in IEEE Transactions on Neural Systems and Rehabilitation Engineering, 23(2), 149-158.
Noninvasive optical inhibition with a red-shifted microbial rhodopsin.
Chuong Amy S, Miri Mitra L, Busskamp Volker, Matthews Gillian A C, Acker Leah C, Sørensen Andreas T, Young Andrew, Klapoetke Nathan C, Henninger Mike A, Kodandaramaiah Suhasa B, Ogawa Masaaki, Ramanlal Shreshtha B, Bandler Rachel C, Allen Brian D, Forest Craig R, Chow Brian Y, Han Xue, Lin Yingxi, Tye Kay M, Roska Botond, Cardin Jessica A, Boyden Edward S (2014), Noninvasive optical inhibition with a red-shifted microbial rhodopsin., in Nature neuroscience, 17(8), 1123-9.
Rods in daylight act as relay cells for cone-driven horizontal cell-mediated surround inhibition.
Szikra Tamas, Trenholm Stuart, Drinnenberg Antonia, Jüttner Josephine, Raics Zoltan, Farrow Karl, Biel Martin, Awatramani Gautam, Clark Damon A, Sahel José-Alain, da Silveira Rava Azeredo, Roska Botond (2014), Rods in daylight act as relay cells for cone-driven horizontal cell-mediated surround inhibition., in Nature neuroscience, 17(12), 1728-35.
The first stage of cardinal direction selectivity is localized to the dendrites of retinal ganglion cells.
Yonehara Keisuke, Farrow Karl, Ghanem Alexander, Hillier Daniel, Balint Kamill, Teixeira Miguel, Jüttner Josephine, Noda Masaharu, Neve Rachael L, Conzelmann Karl-Klaus, Roska Botond (2013), The first stage of cardinal direction selectivity is localized to the dendrites of retinal ganglion cells., in Neuron, 79(6), 1078-85.
miRNAs 182 and 183 Are Necessary to Maintain Adult Cone Photoreceptor Outer Segments and Visual Function.
Busskamp Volker, Krol Jacek, Nelidova Dasha, Daum Janine, Szikra Tamas, Tsuda Ben, Jüttner Josephine, Farrow Karl, Scherf Brigitte Gross, Alvarez Claudia Patricia Patino, Genoud Christel, Sothilingam Vithiyanjali, Tanimoto Naoyuki, Stadler Michael, Seeliger Mathias, Stoffel Markus, Filipowicz Witold, Roska Botond, miRNAs 182 and 183 Are Necessary to Maintain Adult Cone Photoreceptor Outer Segments and Visual Function., in Neuron, on.

Collaboration

Group / person Country
Types of collaboration
HHMI Janielia Campus United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Berry Lab/Princeton University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
BI conference Talk given at a conference Modeling retinal disease 18.01.2017 Vienna, Austria Roska Botond;
EPFL Neuronal Circuit symposium Talk given at a conference Retina to cortex 12.12.2016 Lausanne, EPFL, Switzerland Roska Botond;
MDC Berlin invited talk Individual talk First steps in vision 25.11.2016 Berlin, Germany Roska Botond;
Rutgers University invited talk Individual talk Coding with Correlated Neurons 07.11.2016 New Brunswick, United States of America da Silveira Rava Azeredo;
HiFo Symposium Talk given at a conference First steps in vision 03.11.2016 Zurich, Switzerland Roska Botond;
University of Pennsylvania invited talk Individual talk Coding with Correlated Neurons 01.11.2016 Philadelphia, United States of America da Silveira Rava Azeredo;
Bressler Symposium Talk given at a conference Optogenetic vision restoration 29.10.2016 New York, United States of America Roska Botond;
EMBL Rome invited talk Individual talk First steps in vision 21.10.2016 Rome, Italy Roska Botond;
Rita Montalcini conference Talk given at a conference First steps in vision 17.10.2016 Rome, Italy Roska Botond;
EPFL invited talk Individual talk First steps of vision 30.09.2016 Lausanne, EPFL, Switzerland Roska Botond;
ETH Zurich invited talk Individual talk Coding with Correlated Neurons 30.09.2016 Zurich, Switzerland da Silveira Rava Azeredo;
Inscopix summit Talk given at a conference Cell type targeted therapies 28.09.2016 Stanford, United States of America Roska Botond;
Biophysics Talk given at a conference Ontogenetic therapy 11.09.2016 Ascona, Switzerland Roska Botond;
University of Trondheim invited talk Individual talk First steps in vision 08.09.2016 Trondheim, Norway Roska Botond;
AREADNE Conference Poster Interpretation of correlated variability from models of spiking neural networks 24.06.2016 Santorini, Greece Pernice Volker;
Weizmann institute invited talk Individual talk First steps in vision 13.06.2016 Rehovot, Weizmann institute, Israel Roska Botond;
Restoring vision Talk given at a conference Ontogenetic vision restoration 06.06.2016 College de France, France Roska Botond;
Universitaet zu Koeln invited talk Individual talk Where does all the noise come from? Poisson processes as model for activity in mouse auditory cortex 01.06.2016 Koeln, Germany Pernice Volker;
9th Bernstein Sparks Workshop: Recent advances in recurrent network theory Poster Estimating effects of neural circuit architecture on information through the analysis of correlated variability 26.05.2016 Goettingen, Germany Pernice Volker;
Keystone Neuronal Circuit Meeting Talk given at a conference First steps of vision 22.05.2016 Alpbach, Austria Roska Botond;
McGill University invited talk Individual talk First steps of vision 06.05.2016 Montreal, McGill University , Canada Roska Botond;
ARVO 2016 Talk given at a conference First steps of vision 01.05.2016 Seattle, United States of America Roska Botond;
University of Victoria invited talk Individual talk First steps of vision 28.04.2016 University of Victoria, Canada Roska Botond;
CSHL Neuronal Circuit meeting Talk given at a conference First steps of vision 06.04.2016 New York, Cold Spring Harbor Laboratories, United States of America Roska Botond;
College de France invited talk Individual talk Optogenetics 30.03.2016 Paris, College de France, France Roska Botond;
Ecole Normale Superieure invited talk Individual talk First steps in vision 14.03.2016 Paris, Ecole Normale Superieure, France Roska Botond;
College de France invited talk Individual talk Visual system 17.02.2016 Paris, College de France , France Roska Botond;
Bernstein Center Retreat Talk given at a conference Where does all the noise come from? Poisson processes as model for activity in mouse auditory cortex 07.09.2015 Freiburg, Germany Pernice Volker;
Cold Spring Harbor Labs Vision Course Talk given at a conference Retina-thalamus-cortex 07.07.2015 New York, United States of America Roska Botond;
Ecole Normale Superieure invited talk Individual talk Tuning circuits for correlations which facilitate stimulus discrimination 02.07.2015 Paris, France Pernice Volker;
Group for Neural Theory - Theoretical Neuroscience Seminar Individual talk Tuning circuits for correlations which facilitate stimulus discrimination 02.07.2015 Paris, France Pernice Volker;
McKnight Foundation meeting Talk given at a conference Retinal repair 12.06.2015 Aspen, United States of America Roska Botond;
KNAW Biophyiscs Meeting Talk given at a conference The Orchestral Brain 26.05.2015 Amsterdam, Netherlands da Silveira Rava Azeredo;
ARVO meeting Talk given at a conference Optogenetic vision restoration 02.05.2015 Denver, United States of America Roska Botond;
Insect vision meeting Talk given at a conference Retina-thalamus-cortex 20.04.2015 Janelia Farm, Washington, United States of America Roska Botond;
Neuronal Circuit Meeting Talk given at a conference Retina-thalamus-cortex 30.03.2015 Florida Max Planck Institute, United States of America Roska Botond;
Neuronal Circuit Meeting Talk given at a conference Visual processin in cortex 09.03.2015 Les Treilles, France Roska Botond;
Special Evening Session ES2 "Brain Machine Interfaces", Digest of Technical Papers of the International Solid-State Circuits Conference (ISSCC) Talk given at a conference "CMOS Technology to Interface with Single Neurons and Axons" 22.02.2015 San Francisco, United States of America Hierlemann Andreas;
Challenges in the Frontiers of Brain and Cognition Research Talk given at a conference Sensory Coding with Correlated Neurons 09.02.2015 Rehovot, Israel da Silveira Rava Azeredo;
Pasteur Institute invited talk Individual talk Retina-thalamus-cortex 05.02.2015 Paris, France Roska Botond;
Life Sciences Switzerland meeting Talk given at a conference Optogenetic vision restoration 29.01.2015 Zurich, Switzerland Roska Botond;
Neuronal Circuit Meeting Talk given at a conference Retina-thalamus-cortex 21.01.2015 Vienna, Austria Roska Botond;
Biophysics Meeting Talk given at a conference Retina-thalamus-cortex 15.01.2015 Klosters, Switzerland Roska Botond;
Semmelweis Medical School invited talk Individual talk Retina-thalamus-cortex 11.12.2014 Budapest, Hungary Roska Botond;
ICTP Winter School on Systems Neuroscience Talk given at a conference Retina-LGN-cortex 05.12.2014 Trieste, Italy Roska Botond;
Workshop on stochastic neural computation Poster Effect of connectivity on noise correlations and coding accuracy in coupled neural populations 27.11.2014 Paris, France Pernice Volker;
HBP workshop on stochastic neural computation Poster Effect of connectivity on noise correlations and coding accuracy in coupled neural populations 27.11.2014 Paris, France Pernice Volker;
Society for Neuroscience conference Talk given at a conference From retina to cortex, Presidential talk 16.11.2014 Washington, United States of America Roska Botond;
University of Helsinki invited talk Individual talk Retina-thalamus-cortex 03.11.2014 Helsinki, Finland Roska Botond;
European Society for Gene and Cell Therapy meeting, Hague Talk given at a conference Optogenetics 24.10.2014 Hague, Netherlands Roska Botond;
Vision Institute of Paris retreat Talk given at a conference Retina-LGN-cortex 22.10.2014 Amboise, France Roska Botond;
University of Alicante invited talk Individual talk Retina-thalamus-cortex 03.10.2014 Alicante, Spain Roska Botond;
University of Leuven invited lecture Individual talk Retina-thalamus-cortex 26.09.2014 Leuven, Belgium Roska Botond;
Bernstein Conference 2014 Talk given at a conference The interplay of noise correlations with heterogeneity of tuning function properties 15.09.2014 Heidelberg, Germany Franke Felix;
Bernstein Conference 2014 Talk given at a conference Dynamical Adaptation, Outer Retina, and Simple Models 15.09.2014 Heidelberg, Germany da Silveira Rava Azeredo;
Characterizing Natural Scenes: Retinal Coding and Statistical Theory Talk given at a conference Computation and adaptation in the retina 02.09.2014 Goettingen, Germany da Silveira Rava Azeredo;
9th International Meeting on Substrate-Integrated Microelectrode Arrays Poster Decoding of Motion Directions by Direction-Selective Retina Cells 01.07.2014 Reutlingen, Germany Hierlemann Andreas; Fiscella Michele; Franke Felix;
9th International Meeting on Substrate-Integrated Micro Electrode Arrays, 2014, Reutlingen, Germany, Poster "Characterization of Mammalian Retinal Ganglion Cell Response to Voltage Stimulus" 01.07.2014 Reutlingen, Germany Hierlemann Andreas; Fiscella Michele; Roska Botond;
AREADNE Research in Encoding and Decoding of Neural Ensembles Poster High-Resolution Coding with Correlated Neurons: Theory and Application to Direction-Selective Retinal Ganglion Cells 25.06.2014 Firá, Santorini, Greece Hierlemann Andreas; da Silveira Rava Azeredo; Fiscella Michele; Franke Felix; Roska Botond;
Neural Networks in the Arctic Talk given at a conference Visual computation in retina and cortex 05.06.2014 Longyearbyen, Norway Roska Botond;
OCCAM Osnabrück Computational Cognition Alliance Meeting Poster The Interplay of Noise Correlations and Tuning Properties: High-Resolution Coding in Retinal Direction-Selective Ganglion Cells 07.05.2014 Osnabrück, Germany Franke Felix; Roska Botond; Hierlemann Andreas; da Silveira Rava Azeredo; Fiscella Michele;
Ecole Normale Superieure invited talk Individual talk Correlations and connectivity in networks of simple neuron models 29.04.2014 Paris, France Pernice Volker;
Massachusetts Institute of Technology invited talk Individual talk Coding with Correlated Neurons 30.10.2013 Cambridge, United States of America da Silveira Rava Azeredo;


Self-organised

Title Date Place
Dowling-Werblin symposium 06.10.2016 California, United States of America
FENS forum 2014 06.07.2014 Milan, Italy
FENS Forum of Neuroscience 05.07.2014 Milan, Italy
Controlling Neurons, Circuits and Behavior 20.04.2014 Rungstedgaard, Rungsted, Denmark, Denmark

Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
College de France lecture Talk 30.03.2016 Paris, Switzerland Roska Botond;
Talk to organization for blind about vision restoration Talk 18.04.2015 Fribourg, Switzerland Roska Botond;
Les machines penseront-elles pour nous demain ? Talk 06.06.2014 Paris, France da Silveira Rava Azeredo;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Defect in retinal computation linked to congenital nystagmus International 2016
Media relations: print media, online media Smart viruses enlighten vision in the brain International 2015
Talks/events/exhibitions BSSE Open house German-speaking Switzerland 2014
Media relations: print media, online media Inducing visual function International 2014
Talks/events/exhibitions Les machines penseront-elles pour nous demain ? International 2014
Media relations: print media, online media New function for rods in daylight International 2014

Awards

Title Year
ERC Advanced Grant 2016
Swiss OphthAward 2016
Cogan award of the American Association for Research in Vision and Ophthalmology 2015
ERC Consolidator Grant 2015
Alfred Vogt Preis 2013

Associated projects

Number Title Start Funding scheme
173728 Visual processing in foveated retinæ in the presence of self-motion 01.01.2018 Sinergia
157092 Microtechnology and microelectronics to study mammalian axons 01.09.2015 Project funding (Div. I-III)
173728 Visual processing in foveated retinæ in the presence of self-motion 01.01.2018 Sinergia

Abstract

The present project aims at understanding how a given population of neurons, which share genetic, morphological, or physiological traits, processes sensory information. This question has never been tackled before, and its elucidation is essential to understanding the brain. In order to approach it, advanced electrophysiological and genetic tools, as well as recently developed computational methods, will be combined.Two recent lines of investigation have attempted to understand, first, how single cells carry out sophisticated computations and, second, how a neural population as a whole represents information. These investigations have gone particularly far in the retina, in which the visual world is parsed into ~20 channels; each of these corresponds to a mosaic of ganglion cells of given type, which tiles the retina and conveys to the brain selective information on spatio-temporal patterns in the stimulus. As yet, effort investigations have concerned computations, carried out by a ganglion cell of a given type, and representations of information by local populations of ganglion cells, irrespective of their types. Both lines of work are valuable and ongoing. However, they represent an incomplete approach to sensory processing. While the visual pathway is organized retinotopically and, hence, it is natural to study the interaction of visual cells at a given point in space, the visual pathway is also organized functionally, so that one would like to understand, how visual cells interact in the functional space. For this, it is essential to examine the way, in which populations of same-type and different-type ganglion cells process visual information. Hitherto, this has not been pursued.To embark on this new direction of investigations, we shall need to genetically label and manipulate ganglion cells; to carry out high-throughput recordings of their spiking activity; and to analyze the resulting data with involved mathematical and computational methods.This project will focus on the retina for good reasons. First, we shall gather the necessary genetic and anatomical knowledge (as a product of Subproject A). Second, we shall have access to voluminous electrophysiological data sets (as a product of Subproject B). Third, the organization of the retina and the control, which one has over the visual input, make it computationally tractable (see Subproject C). We emphasize, nonetheless, that while the present project focuses on the retina, we expect that the questions that it will raise and the experimental and computational approaches that it will propose will be transferable to cortical and other areas. As such, this projet may be viewed as the initial step in a much broader research program.Keywords: High-density multielectrode arrays, electrophysiology, genetic identification of cells, neural code, computational neuroscience, retina, visual coding.
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