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As mentioned in #20, the latest version of the
deepcellmodule used for segmentation only supports Python versions up to 3.10. Also, the module itself does not seem to be any longer maintained. Therefore, it is preferable to switch to a different model for segmentation.CellPose was chosen to replace Mesmer, as it also offers a simple interface, displays similar performance for nuclei segmentation, and supports all Python versions from 3.9 to 3.13. It is also still actively maintained and improved.
Switching to CellPose only required minor changes in the segmentation-related code, as well as a few updates in the metadata files and the documentation. Also, the GitHub Actions files were updated to test all the supported Python versions on all the latest OS versions (instead of older versions previously).