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MouseLand / cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
https://www.cellpose.org/
BSD 3-Clause "New" or "Revised" License
1.31k stars 376 forks source link

Modifying the Heat-Source #345

Closed mrseekdeep closed 2 years ago

mrseekdeep commented 2 years ago

Hi there, According to CellPose, the cells are initially represented by a Point which is a "heat-source in the middle" then diffusion is applied. Can a Line be used as the heat-source instead of a Point? In cases where the object that i want to segment looks like 136584248-d95a2b74-2324-4119-aaf6-aa3f87b6924f

136583410-5edd26ff-9765-4bec-9906-bb28b9834a6c

kevinjohncutler commented 2 years ago

I've actually been working on essentially that for the last year, and Carsen and I have been incorporating my changes into Cellpose under the '--skel' flag in the last few weeks. We'll post the paper in the project description showcasing the new algorithm once it gets up on biorxiv. For now, there is no built-in model using it, but you can train it on your own data. I'd love to see some examples of your data if you want to post them here!

mrseekdeep commented 2 years ago

In a way, i think Cellpose is creating contour maps using diffusion. My data looks more like the black and white image in my first comment, and the issue is that in my case the center might not be a point, instead its somewhat a rectangle with curved edges.

mrseekdeep commented 2 years ago

@kevinjohncutler What are you looking to introduce in cellpose 2.0? multi-class segmentation, polygonal shape for the center, .....?

kevinjohncutler commented 2 years ago

@kevinjohncutler What are you looking to introduce in cellpose 2.0? multi-class segmentation, polygonal shape for the center, .....?

There are quite a few changes that I am introducing, but luckily you’ll only have to wait a week or two before we post the paper describing it :) You ideas definitely map onto what we have done, except for the latter - that’s closer to what StarDist did, but does not generalize well to long and curved shapes.

mrseekdeep commented 2 years ago

awaiting eagerly for the release, and wishing you good luck