GUI in MATLAB for automated Calcium transients extraction from imaging experiments.
- Load tiff file with the sequence of images acquired.
- Perform non-rigid (or rigid) motion correction.
- Find cells based on Suite2P algorithm (Pachitariu et al., 2016).
- Evaluate ROIs identified (area, circularity, perimeter, eccentricity and overlapping).
- Extract calcium transients using local neuropil as the basal of fluorescence.
- Evaluate peak signal-to-noise ratio (PSNR).
- Perform spike inference (foopsi; Friedrich & Paninski, 2016).
- Get raster activity, a binary matrix where each row is the activity of a single ROI.
Output of a structure variable with all data analyzed
Jesús Pérez-Ortega