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@d33bs d33bs commented Apr 8, 2025

Description

This PR adds DeepProfiler compatibility to CytoTable with necessary adjustments to existing functions. Largely this is about converting NPZ files generated from DeepProfiler into concatenated Parquet data. I used the existing test data from Pycytominer (output data only) as reference data.

Thanks for any feedback!

Closes #15

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  • Bug fix (fixes an issue).
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  • Breaking change (fix or feature that would cause existing functionality to not work as expected).
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@d33bs d33bs marked this pull request as ready for review April 8, 2025 21:00
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@gwaybio gwaybio left a comment

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This looks great @d33bs !

d33bs and others added 5 commits April 10, 2025 10:21
Co-authored-by: Gregory Way <gregory.way@gmail.com>
Co-Authored-By: Gregory Way <gregory.way@gmail.com>
Co-Authored-By: Gregory Way <gregory.way@gmail.com>
Co-Authored-By: Gregory Way <gregory.way@gmail.com>
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d33bs commented Apr 10, 2025

Thanks @gwaybio ! I made some changes based on your comments. I left one comment open which I hope to double check on before we move forward with a merge here.

@d33bs d33bs requested a review from gwaybio April 10, 2025 16:58
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@falquaddoomi falquaddoomi left a comment

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Nice work! This is a pretty complex addition, and it looks like you approached it in a structured way, so kudos for that. I left a few comments mostly about typing and style.

d33bs and others added 3 commits April 16, 2025 09:36
Co-Authored-By: Gregory Way <gregory.way@gmail.com>
Co-Authored-By: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Co-Authored-By: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
d33bs and others added 2 commits April 16, 2025 09:42
Co-Authored-By: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Co-Authored-By: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
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d33bs commented Apr 16, 2025

Thank you @gwaybio and @falquaddoomi for your reviews! After incorporating changes based on your comments into the code I'll now merge this in.

@d33bs d33bs merged commit 632d64c into cytomining:main Apr 16, 2025
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@d33bs d33bs deleted the deepprofiler-compat branch April 16, 2025 18:53
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Add DeepProfiler .npz as input for conversion to other formats

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