MouseLand/suite2p

cell detection in calcium imaging recordings

What it solves

Suite2p is a pipeline for processing two-photon calcium imaging data. It automates the extraction of neural activity from large-scale imaging recordings, allowing researchers to identify and track the activity of individual neurons (ROIs) in the brain.

How it works

The software processes raw imaging data through a series of modules:

  • Registration: Aligns imaging frames to correct for motion.
  • ROI detection: Identifies regions of interest (neurons) in the data.
  • Signal extraction: Extracts fluorescence traces from the identified ROIs.
  • Signal extraction: Extracts fluorescence traces from the identified ROIs.
  • ROI classification: Distinguishes between actual cells and noise/artifacts using a classifier.
  • Spike detection: Uses a deconvolution algorithm to estimate neural spikes from fluorescence traces.
  • Visualization GUI: Provides a graphical interface to review results, refine ROI selection, and visualize population-level activity.

Who it’s for

It is designed for neuroscientists and researchers working with two-photon calcium imaging data to analyze neural activity at scale.

Highlights

  • End-to-end pipeline: Covers everything from registration to spike detection.
  • Integrated GUI: Allows for manual curation of ROIs and training of custom classifiers to adapt to specific data statistics.
  • GPU acceleration: Supports CUDA for faster processing of long recordings.
  • Comprehensive outputs: Generates fluorescence traces, neuropil traces, and deconvolved spike traces.

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