PT  - JOURNAL ARTICLE
AU  - Pachitariu, Marius
AU  - Stringer, Carsen
AU  - Dipoppa, Mario
AU  - Schröder, Sylvia
AU  - Rossi, L. Federico
AU  - Dalgleish, Henry
AU  - Carandini, Matteo
AU  - Harris, Kenneth D.
TI  - Suite2p: beyond 10,000 neurons with standard two-photon microscopy
AID  - 10.1101/061507
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 061507
4099  - http://biorxiv.org/content/early/2017/07/20/061507.short
4100  - http://biorxiv.org/content/early/2017/07/20/061507.full
AB  - 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.