angelolab / angelolab/TNBC_python_scripts
Update `validate_panel` normalization method to use cohort-wide constants per channel
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bug
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- Python
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Description
**Describe the bug**
Currently, the `validate_panel` function normalizes each channel separately based on its own 99.9% value. This will accentuate noise for very dim images, which leads to undesirable images.
**Expected behavior**
The normalization value needs to reflect the cohort as a whole, and not just on an individual level. To address, figure out what the best constants to use for each channel are, and use that to normalize all images across a cohort or sub-cohort.
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