Refactor APG interface and instance segmentation tests

[constantinpape]

No description provided.

[constantinpape]

This PR takes care of:

• APG for tiled embeddings
• Refactoring of the instance segmentation functionality, including mask_data_to_segmentation, renaming get_amg, and using "instance_segmentation" as default output_mode.
• Parallelization of the main CPU-bound processing steps in APG.

Still to address (in other PRs):

• Mask refinement with derived box prompts
• Switch to APG as default (in the functions and the napari GUI)
• Check inference for large WSIs and debug / speed up if necessary
• Update documentation to include APG in automatic segmentation CLI

cc @anwai98

[anwai98]

I had a quick look at the scripts here, looks good to me! (didn't test the API in detail, but will do once it's close to completion)

Thanks @constantinpape 🥳

[constantinpape]

Thanks for checking this out @anwai98 . I think that the more efficient segmentation is working now. I will quickly check the result tomorrow and merge this if things look as expected.

[constantinpape]

The tiling result looks very good:

I will merge it despite the test failure, I think that one is a one-off.

[anwai98]

Ahha now that's amazing! (I saw the timing improvements too) ;) Thanks @constantinpape! I'll give it a quick shot today afternoon on the WSIs!