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Catrex GUI

version 1.0.0 (428 KB) by Jesus Perez
Graphical user interface to extract calcium transients from imaging experiments. Get raster of neuronal activity from a raw tiff file.

34 Downloads

Updated 28 Jul 2020

From GitHub

View license on GitHub

GUI in MATLAB for automated calcium transients extraction from imaging experiments.

1. Load tiff file with the sequence of images acquired.
2. Perform non-rigid (or rigid) motion correction.
3. Find cells based on Suite2P algorithm (Pachitariu et al., 2016).
4. Evaluate ROIs identified (area, circularity, perimeter, eccentricity and overlapping).
5. Extract calcium transients using local neuropil as the basal of fluorescence.
6. Evaluate peak signal-to-noise ratio (PSNR).
7. Perform spike inference (foopsi; Friedrich & Paninski, 2016).
8. 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

Cite As

Jesus Perez (2021). Catrex GUI (https://github.com/PerezOrtegaJ/Catrex_GUI/releases/tag/V1.0.0), GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2020a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Acknowledgements

Inspired by: Suite2P, CaImAn

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To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.