suite2P: a fast and accurate pipeline for automatically processing functional imaging recordings

Carsen Stringer, HHMI Janelia Research Campus


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 are often inefficient and the results hard to interpret. Here we introduce Suite2p: a fast, accurate, parameter-free and complete pipeline that registers raw movies, detects active and/or inactive cells (using Cellpose), extracts their calcium traces and infers their spike times. Suite2p runs faster than real time on standard workstations and outperforms state-of-the-art methods on newly developed ground-truth benchmarks for motion correction and cell detection.

Helpful links:

Suite2p installation instructions: https://github.com/MouseLand/suite2p
Suite2p additional information: http://www.suite2p.org/
Colab notebook: https://github.com/MouseLand/suite2p/...


Speaker Bio:
Carsen Stringer is a group leader at HHMI Janelia Research Campus. She did her postdoctoral work with Marius Pachitariu and Karel Svoboda at Janelia, and did her PhD work with Kenneth Harris and Matteo Carandini at University College London. She develops tools for understanding high-dimensional visual computations and neural representations of behavior.