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KnottLab / codex

Pipeline processing CODEX output
MIT License
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outline and documentation #3

Closed nathanin closed 3 years ago

nathanin commented 3 years ago

hey @abs51295 take a look at what is outlined here and see if it makes sense. especially at the proposed a file structure. I do not think we need to stick to this splitting outputs between a 1_data and 3_Segmentation directory.. we can just have an output folder or something. I'm building downstream workflows for cell segmentation/clustering/visualization assuming this is the structure we'll be using for the time being.

I also propose splitting preprocessing functions into separate files for their individual parts, since the image data is being passed around anyway. This merge won't work as-is since I don't have your EDOF fixes.

https://github.com/KnottLab/codex/blob/31c7707da87dddc645ed1384e84cc0ce3bce54d9/src/main.py#L14-L40

abs51295 commented 3 years ago

@nathanin can you just resolve conflicts and I can merge.

nathanin commented 3 years ago

@abs51295 ok this looks good. i left all the print statements / np.save's in there for now since i guess we'll want to just test this once more to make sure i didn't screw everything up