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broadinstitute / pooled-cell-painting-profiling-recipe

:woman_cook: Recipe repository for image-based profiling of Pooled Cell Painting experiments
BSD 3-Clause "New" or "Revised" License
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Adding cell quality scoring using the Feldman et al. method to recipe #65

Open gwaybio opened 3 years ago

gwaybio commented 3 years ago

From Feldman et al. 2019:

Adding data per site to capture Figure 2D, and adding a cell quality metric to filter cells as performed in Figure 2E.

Currently, the filtering method is not exactly as Figure 2E. We filter cells that have more than 1 different perfectly matching barcode.

gwaybio commented 3 years ago

Another TODO

Add barcode_col argument to https://github.com/broadinstitute/pooled-cell-painting-profiling-recipe/blob/886a601761ab62f9ee07b4996c6add9689b41077/0.preprocess-sites/1.process-spots.py#L228-L232

Only the Feldman method uses this argument, it defaults to None, but it needs to be specified. Figure out what to specify barcode_col as if any other method besides Feldman is used. Maybe it is harmless to add the Feldman barcode_col to every assign_cell_quality() arg