How to import cell masks into ImageJ/QuPath for topographic analysis?

michaellee1 / CellSeg

MIT License

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How to import cell masks into ImageJ/QuPath for topographic analysis? #56

Open SPerrott22 opened 1 year ago

SPerrott22 commented 1 year ago

Hi! Thank you for making Cell Seg, this is an awesome tool! I was wondering if there is a way to import the masks into ImageJ and/or QuPath so that they can overlay on the original tiff and are recognized as masks? (I'm fairly new to QuPath/ImageJ, would really appreciate a tutorial.) Thank you!

charles-xue commented 10 months ago

Hello, I encountered the same confusion, have you solved this problem?

SPerrott22 commented 10 months ago

Hi! I switched to using DeepCell and created this pipeline to facilitate the transfer, hope this helps!