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

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SPerrott22 opened this issue Jan 20, 2023 · 2 comments
Open

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

SPerrott22 opened this issue Jan 20, 2023 · 2 comments

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@SPerrott22
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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
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Hello, I encountered the same confusion, have you solved this problem?

@SPerrott22
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Hi! I switched to using DeepCell and created this pipeline to facilitate the transfer, hope this helps!

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@charles-xue @SPerrott22