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hammerlab / cytokit

Microscopy Image Cytometry Toolkit
Apache License 2.0
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thoughts on adding cellpose based segmentation #29

Open Reardonlab opened 4 years ago

Reardonlab commented 4 years ago

First, this is a great project and we think it's very powerful. We have had really bad poor segmenation with our own data using cytokit. We have however seen seen fantastic results with cellpose. Is there a way that incorporate a way that a user could specify what segmentation approach is used, and provide an option to add others as they become available?

eric-czech commented 4 years ago

Did you see the custom segmentation section in the README? That's all the documentation there is on that unfortunately, but it's not very difficult. Beyond creating a module and ensuring it is in PYTHONPATH, you only need to make some minor changes to the experiment configuration to enable some custom routine.