RT Journal Article SR Electronic T1 Suite2p: beyond 10,000 neurons with standard two-photon microscopy JF bioRxiv FD Cold Spring Harbor Laboratory SP 061507 DO 10.1101/061507 A1 Marius Pachitariu A1 Carsen Stringer A1 Mario Dipoppa A1 Sylvia Schröder A1 L. Federico Rossi A1 Henry Dalgleish A1 Matteo Carandini A1 Kenneth D. Harris YR 2017 UL http://biorxiv.org/content/early/2017/07/20/061507.abstract 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.