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Suite2p: beyond 10,000 neurons with standard two-photon microscopy

Marius Pachitariu, Carsen Stringer, Sylvia Schröder, Mario Dipoppa, L. Federico Rossi, Matteo Carandini, Kenneth D. Harris
doi: https://doi.org/10.1101/061507
Marius Pachitariu
1UCL Institute of Neurology, London WC1E 6DE, United Kingdom
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6DE, United Kingdom
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  • For correspondence: marius.pachitariu.10@ucl.ac.uk
Carsen Stringer
3Gatsby Computational Neuroscience Unit, London W1T 4JG, United Kingdom
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Sylvia Schröder
4UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom
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Mario Dipoppa
1UCL Institute of Neurology, London WC1E 6DE, United Kingdom
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6DE, United Kingdom
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L. Federico Rossi
4UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom
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Matteo Carandini
4UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom
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Kenneth D. Harris
1UCL Institute of Neurology, London WC1E 6DE, United Kingdom
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6DE, United Kingdom
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Abstract

The combination of two-photon microscopy recordings and powerful calcium-dependent fluorescent sensors enables simultaneous recording of unprecedentedly large populations of neurons. While these sensors have matured over several generations of development, computational methods to process their fluorescence remain inefficient and the results hard to interpret. Here, we introduce a set of practical methods based on novel clustering algorithms, and provide a complete pipeline from raw image data to neuronal calcium traces to inferred spike times. We formulate a generative model of the fluorescence image, incorporating spike times and a spatially smooth neuropil signal, and solve the inference and learning problems using a fast algorithm. This implementation scales linearly with the number of recorded cells, and the complete pipeline runs in approximately one hour for typical two-hour long recordings, on commodity GPUs. Furthermore, this method recovers twice as many cells as a previous standard method. This allowed us to routinely record and detect ~10,000 cells simultaneously from the visual cortex of awake mice using standard two-photon resonant-scanning microscopes. The software is publicly available at github.com/cortex-lab/Suite2P, together with a graphical user interface that allows rapid manual curation of the results.

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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-ND 4.0 International license.
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Posted June 30, 2016.
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Suite2p: beyond 10,000 neurons with standard two-photon microscopy
Marius Pachitariu, Carsen Stringer, Sylvia Schröder, Mario Dipoppa, L. Federico Rossi, Matteo Carandini, Kenneth D. Harris
bioRxiv 061507; doi: https://doi.org/10.1101/061507
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Suite2p: beyond 10,000 neurons with standard two-photon microscopy
Marius Pachitariu, Carsen Stringer, Sylvia Schröder, Mario Dipoppa, L. Federico Rossi, Matteo Carandini, Kenneth D. Harris
bioRxiv 061507; doi: https://doi.org/10.1101/061507

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