Table of Contents:
General Set-Up
Converting CZI
Installing CaImAn GUI
Program Insights
Technical Insights
Helpful Links:
Link to the original GitHub:
https://github.com/flatironinstitute/CaImAn
Link to the Caiman documentation: https://caiman.readthedocs.io/en/latest/
Link to CaImAn GUI:
https://github.com/kantarcilab/caiman_gui
What is the CaImAn GUI program?
CaImAn GUI is an add-on to the CaImAn package, developed by Eunsu Kim, for single-cell calcium and voltage imaging. It provides an interactive PyQt5-based interface for setting parameters, performing automatic or manual ROI segmentation, extracting and quantifying spike properties, and automatically generating CSV files and figures. The program is built with Python 3.11.
Things to Know Before Starting
- Folder-based analysis - The program processes TIFF files located directly in the specified folder and ignores TIFFs in subfolders. A summary CSV is generated at the end of the analysis. It is recommended to store TIFF files in separate folders based on experimental conditions.
- Consistent image dimensions required - All TIFF files in a folder must have the same pixel dimensions. Mixing sizes (e.g., 128 x 128 with 64 x 64) will cause errors. To avoid this, separate images into folders by pixel dimensions.
Types of Modes:
- Automatic Mode - Uses the original CaImAn ROI creation pipeline, adapted for batch processing multiple files.
- Manual Mode - Allows ROI creation by brush-drawing masks, which are then used to generate traces for the CaImAn pipeline. (Currently available only for calcium imaging.)
- CZI to TIFF Conversion - An ImageJ/Fiji macro plugin is provided to batch-convert CZI files to TIFF format for use with the program.
Citations:
Andrea Giovannucci, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon L Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L Gauthier, Pengcheng Zhou, Baljit S Khakh, David W Tank, Dmitri B Chklovskii, Eftychios A Pnevmatikakis (2019) CaImAn an open source tool for scalable calcium imaging data analysis eLife 8:e38173