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.
Note: If you're interested in testing out suite2p during the session, please install it using the instructions at https://github.com/MouseLand/suite2p. If you'd like to test on your own data during the session, download around 1000 frames of your data to your laptop to try it out. We will discuss the results at the end of the session. More information is available at www.suite2p.org .
Jupyter notebook: https://github.com/MouseLand/suite2p/blob/main/jupyter/run_suite2p_colab...
Zoom link: https://mit.zoom.us/j/97702736613?pwd=LzhYcGNlbWl4b0xoR3o5M1lNTXF6UT09