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Community-based benchmarking improves spike inference from two-photon calcium imaging data

View ORCID ProfilePhilipp Berens, Jeremy Freeman, View ORCID ProfileThomas Deneux, Nicolay Chenkov, View ORCID ProfileThomas McColgan, Artur Speiser, View ORCID ProfileJakob H. Macke, View ORCID ProfileSrinivas C. Turaga, View ORCID ProfilePatrick Mineault, Peter Rupprecht, View ORCID ProfileStephan Gerhard, View ORCID ProfileRainer W. Friedrich, View ORCID ProfileJohannes Friedrich, Liam Paninski, View ORCID ProfileMarius Pachitariu, View ORCID ProfileKenneth D. Harris, Ben Bolte, Timothy A. Machado, View ORCID ProfileDario Ringach, Jasmine Stone, Nicolas J. Sofroniew, Jacob Reimer, View ORCID ProfileEmmanoulis Froudarakis, View ORCID ProfileThomas Euler, Miroslav Román Rosón, Lucas Theis, View ORCID ProfileAndreas S. Tolias, Matthias Bethge
doi: https://doi.org/10.1101/177956
Philipp Berens
1Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
2Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
3Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany
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Jeremy Freeman
4Chan Zuckerberg Initiative, San Francisco, USA
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Thomas Deneux
5Unit de Neuroscience, Information et Complexit, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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Nicolay Chenkov
6Bernstein Center for Computational Neuroscience and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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Thomas McColgan
6Bernstein Center for Computational Neuroscience and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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Artur Speiser
7research center caesar, an associate of the Max Planck Society, Bonn, Germany
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Jakob H. Macke
7research center caesar, an associate of the Max Planck Society, Bonn, Germany
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Srinivas C. Turaga
8Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
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Patrick Mineault
9Independent Researcher
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Peter Rupprecht
10Friedrich Miescher Institute, Basel, Switzerland
11University of Basel, Basel, Switzerland
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Stephan Gerhard
10Friedrich Miescher Institute, Basel, Switzerland
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Rainer W. Friedrich
10Friedrich Miescher Institute, Basel, Switzerland
11University of Basel, Basel, Switzerland
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Johannes Friedrich
12Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, NY, USA
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Liam Paninski
12Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, NY, USA
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Marius Pachitariu
13University College, London, UK
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Kenneth D. Harris
13University College, London, UK
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Ben Bolte
14Emory University, Atlanta, USA
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Timothy A. Machado
12Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, NY, USA
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Dario Ringach
15University of California, Los Angeles, CA, USA
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Jasmine Stone
8Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
16Yale University, New Haven, CT, USA
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Nicolas J. Sofroniew
8Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
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Jacob Reimer
17Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
18Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
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Emmanoulis Froudarakis
17Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
18Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
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Thomas Euler
1Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
2Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
3Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany
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Miroslav Román Rosón
1Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
2Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
19Graduate School of Neural & Behavioural Sciences, International Max Planck Research School, University of Tübingen, Tübingen, Germany
20Division of Neurobiology, Department Biology II, LMU Munich, Munich, Germany
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Lucas Theis
21Twitter, London, UK
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Andreas S. Tolias
16Yale University, New Haven, CT, USA
17Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
22Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
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Matthias Bethge
2Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
3Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany
23Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany
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Abstract

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations1, 2. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators3. Different algorithms for estimating spike trains from noisy calcium measurements have been proposed in the past4‒8, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted August 19, 2017.
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Community-based benchmarking improves spike inference from two-photon calcium imaging data
Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H. Macke, Srinivas C. Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W. Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D. Harris, Ben Bolte, Timothy A. Machado, Dario Ringach, Jasmine Stone, Nicolas J. Sofroniew, Jacob Reimer, Emmanoulis Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S. Tolias, Matthias Bethge
bioRxiv 177956; doi: https://doi.org/10.1101/177956
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Community-based benchmarking improves spike inference from two-photon calcium imaging data
Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H. Macke, Srinivas C. Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W. Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D. Harris, Ben Bolte, Timothy A. Machado, Dario Ringach, Jasmine Stone, Nicolas J. Sofroniew, Jacob Reimer, Emmanoulis Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S. Tolias, Matthias Bethge
bioRxiv 177956; doi: https://doi.org/10.1101/177956

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