Save Colored Pixie Masks #1007
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Save Colored Pixie Masks #1007
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cliu72
reviewed
Jun 3, 2023
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Looks great!
Just a small request: in all three notebooks, can we move the plot_utils.save_colored_masks code block to before the plot_utils.plot_pixel_cell_cluster_overlay code block? I think most people will run these chunks of code for a subset of FOVs to test, and then want to generate the masks and colored masks for all FOVs in the cohort (but not look at all FOVs in the notebook - since that would be a shit ton of scrolling). So I think it would be more intuitive to have the mask generation and colored mask generation code together.
camisowers
approved these changes
Jun 5, 2023
ngreenwald
approved these changes
Jun 6, 2023
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What is the purpose of this PR?
Allows the user to save both, cell phenotype masks and pixel phenotype masks.
How did you implement your changes
Created a
dataclassto store the metacluster / coloring information. Refactored a good chunk of what's there to reduce duplicate lines. For testing, created fixtures and applied them elsewhere inplot_utils_test.pywhere appropriate.Remaining issues
This pr was a good instance to test an alternative / refactored masking procedure specifically for pixie before tackling #857 again in the near future.
Here is an example image, had to convert the format from TIFF to png to upload.