Usage

The application expects simple .tif files with shape (t, y, x). File i/o is performed using tifffile.
In the main menu it is possible to select either a single tif file, or an entire folder of tif files.

The application contains several parameters, a brief description can be found here. Progress can by tracked inside the command prompt. When using cellpose segmentation, the first iteration might take a bit longer, as the application will be loading in the cellpose package and model. Once loaded, both are cached and will not have to be reloaded again.
When selecting either Analysis or Bleach correction, segmentation must be turned on, as these both need to know which pixels belong to the cell.