The original Caiman program and CaImAn GUI program both require TIFF files in a specific format for cell analysis.

ImageJ/Fiji is a popular open-source tool for biological image analysis. The CaImAn GUI GitHub repository includes a macro plugin that can batch-convert CZI files into TIFFs automatically for use with the program.

Download Fiji:

https://imagej.net/software/fiji/downloads

Installing the macros plugin

1. Open ImageJ/Fiji.
2. In the menu bar (File, Edit, Image, Process, Analyze), click Plugins → Marcos → Install.
3. In your CaImAn GUI program folder, locate the file CZI to TIFF Converter CaImAn and select it.
4. When prompted, choose the input folder containing the CZI files you want to convert.
5. Choose the output folder where the converted TIFFs will be saved (can be the same as the input folder or a different one).
6. Once the paths are selected, the macro will automatically convert all CZI files in the input folder to TIFF format.