Suite2p: a multipurpose functional segmentation pipeline for cellular imaging
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.
Non-Telecentric 2P microscopy for 3D random access mesoscale imaging
Ultra-low-cost, easily implemented and flexible two-photon scanning microscopy modification offering a several-fold expanded three-dimensional field of view that also maintains single-cell resolution. Application of our system for imaging neuronal activity has been demonstrated on mice, zebrafish and fruit flies. Website: https://github.com/BadenLab/nTCscope