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Object overlap, quality of life updates and new training option

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@lacan lacan released this 08 Nov 09:21
· 78 commits to main since this release

This update fixes an issue in the way objects were being detected and re-added to QuPath.

It now follows much more closely what is done in the StarDist Extension and should result in fewer issues.

Now the Z and T positions are also appended to the names of the exported images. Useful for 3D and T stacks

Adds the min_training_masks option to help avoid cellpose from excluding images with less than 5 annotations during training

Finally, it adds a bit more verbosity. The full command used to run or train is output in such a way that it can be run from the command line by copy-paste

You should unzip the contents of the file below into your extensions directory