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

Marius Pachitariu, Carsen Stringer, Mario Dipoppa, Sylvia Schröder, L. Federico Rossi, Henry Dalgleish, Matteo Carandini, Kenneth D. Harris
doi: https://doi.org/10.1101/061507
Marius Pachitariu
1UCL Institute of Neurology, London WC1N 3BG, UK.
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6BT, UK.
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  • For correspondence: marius10p@gmail.com
Carsen Stringer
3Gatsby Computational Neuroscience Unit, London W1T 4JG, UK.
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Mario Dipoppa
1UCL Institute of Neurology, London WC1N 3BG, UK.
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6BT, UK.
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Sylvia Schröder
4UCL Institute of Ophthalmology, London EC1V 9EL, UK.
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L. Federico Rossi
4UCL Institute of Ophthalmology, London EC1V 9EL, UK.
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Henry Dalgleish
5UCL Wolfson Institute for Biomedical Research, London WC1E 6BT, UK.
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Matteo Carandini
4UCL Institute of Ophthalmology, London EC1V 9EL, UK.
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Kenneth D. Harris
1UCL Institute of Neurology, London WC1N 3BG, UK.
2UCL Department of Neuroscience, Physiology, and Pharmacology, London WC1E 6BT, UK.
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Abstract

Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.

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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 4.0 International license.
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Posted July 20, 2017.
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Suite2p: beyond 10,000 neurons with standard two-photon microscopy
Marius Pachitariu, Carsen Stringer, Mario Dipoppa, Sylvia Schröder, L. Federico Rossi, Henry Dalgleish, 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, Mario Dipoppa, Sylvia Schröder, L. Federico Rossi, Henry Dalgleish, Matteo Carandini, Kenneth D. Harris
bioRxiv 061507; doi: https://doi.org/10.1101/061507

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