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

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bioRxiv. 2017 Jul 20;:061507. doi: https://doi.org/10.1101/061507

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

Pachitariu M, Stringer C, Dipoppa M, Schröder S, Rossi LF, Dalgleish H, Carandini M, Harris KD

Note: Research in this publication was not performed at Janelia.

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

Note: Research in this publication was not performed at Janelia.

Abstract