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Add demo for CellProfiler SQLite export thumbnail data using ExampleHuman #4

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merged 10 commits into from
Oct 23, 2024

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@d33bs d33bs commented Oct 14, 2024

This PR adds a demonstration of using CellProfiler to export a SQLite file which includes mask and image thumbnails from the ExampleHuman dataset. I've uploaded the SQLite file and the translated PNG's of the thumbnails which are found in the dataset under the relevant output dir.

Findings:

  • The thumbnails land in the Per_Image table within the SQLite output meaning they are "per image" and not "per object"
  • The thumbnails must be translated from ASCII format in the database through more complex means (here I opted to add a Python script which assists with this).
  • I found the thumbnails were very small and might not be a good candidate for single-cell analysis.

Thanks for any feedback, please don't hesitate to let me know if you have any questions.

Closes #2
Closes #3

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LGTM! LOVE seeing this process get started!

I left a good amount of comments to address. I think we will need to decide what we expect as the overlay output(s) for coSMicQC, which we can discuss in person if that works!

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d33bs commented Oct 23, 2024

Thanks @jenna-tomkinson for the review here! I made notes throughout and tried to capture possible points of action for future work in #5 . Going to merge this in for now.

@d33bs d33bs merged commit 2e20e65 into WayScience:main Oct 23, 2024
@d33bs d33bs deleted the sqlite-image-thumbnails branch October 23, 2024 19:49
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Add ExampleHuman workflow with SQLite thumbnail output Update license
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