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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Save Colored Pixie Masks #1007

Closed srivarra closed 1 year ago

srivarra commented 1 year ago

If you haven't already, please read through our contributing guidelines before opening your PR

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 dataclass to 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 in plot_utils_test.py where 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.

fov0_cell_mask_colored

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