Fix Cellpose segmentation with masking ROI tables & relabeling

[jluethi]

Checklist before merging

• I added an appropriate entry to CHANGELOG.md

[jluethi]

My new relabeling approach is more robust and should be fine for all real-world cellpose use-cases. But we'll want to offer an abstracted version of this in ngio later, see issue here to track this: #787

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
fractal_tasks_core
masked_loading.py
fractal_tasks_core/tasks
cellpose_segmentation.py					184
Project Total

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[lorenzocerrone]

Overall, it looks good to me.

I don't like that num_labels_tot is a shared global state. To avoid returning the current number of labels, I would have wrapped segment_ROI in a small class.

I think this is totally fine for now, this code will be heavily refactored soon anyway when we have ngio for this task.

[jluethi]

Thanks for reviewing it!

I don't like that num_labels_tot is a shared global state. To avoid returning the current number of labels, I would have wrapped segment_ROI in a small class.

I think this is totally fine for now, this code will be heavily refactored soon anyway when we have ngio for this task.

Agreed, that will be something to improve on with the ngio refactor. But I'll go with this for the time being :)