Dig into alignment flag triggers in 4.image-and-segmentation-qc.py

broadinstitute / pooled-cell-painting-profiling-recipe

:woman_cook: Recipe repository for image-based profiling of Pooled Cell Painting experiments

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Dig into alignment flag triggers in 4.image-and-segmentation-qc.py #29

Closed ErinWeisbart closed 2 years ago

ErinWeisbart commented 4 years ago

Look carefully at alignment in a couple batches of data and determine qc thresholds. Compare to alignment qc thresholds Beth determined with WG screen images. Either:

Develop method for simply setting cutoff and build it into recipe step
Have recipe output .csvs for a few different qc thresholds so that the correct one can be chosen post hoc

ErinWeisbart commented 3 years ago

Notes from a conversation with @bethac07 : If you were going to generate anything, I'd say maybe mean of all correlation metrics, or max correlation metric (assuming that if the max is too low, something is wrong). Min just seems like it would generate a value that seems scary even though there is potentially not anything actually wrong.

I think I wouldn't filter, because we do want to see the ones that DO align well.

I think my vote would be a mean, or a % that fail your cutoff.

ErinWeisbart commented 2 years ago

The code this conversation refers to was removed in #72 2e6e9d2 so I'm closing this issue.