dlmbl / instance_segmentation

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Review 2024 #5

Open neptunes5thmoon opened 2 months ago

neptunes5thmoon commented 2 months ago
pattonw commented 2 months ago

Thanks for the feedback.

As for the affinities section, I have added a few basics that get the affinities up to doing pretty decently. 1) weight balancing for 0/1 affinities, pretty necessary for neighboring affs since its almost all 1s 2) long range affinities (this makes it much easier to see visually that the task is different to a simple foreground/background segmentation) 3) mutex watershed call for getting the final segmentation instead of seeded watershed from distance to boundary, which sort of defeats the purpose of affinities unless you do a second agglomeration step.

I think this section could still use some better images and explanations

neptunes5thmoon commented 2 months ago

I think the magic line doesn't install ipykernel but rather registers the kernel somehow. Not sure exactly though, I just copied it from some other exercise. This seems to corroborate my assumptions: https://ipython.readthedocs.io/en/stable/install/kernel_install.html

Maybe checkpoint right after is a good compromise for the maximum filter part? In Milan people were struggling with this iirc (but also we were pretty rushed).

I'll try to find time to look over the affinities part again tomorrow