Create 0.preprocess-sites/n.determine-site-quality

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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Create 0.preprocess-sites/n.determine-site-quality #11

Closed ErinWeisbart closed 4 years ago

ErinWeisbart commented 4 years ago

The CellProfiler analysis pipeline now contains measurements that address the quality of images/data at a given site. It would be nice to have a pipeline that outputs a summary so that it can be viewed at a glance. Such as:

Confluent regions
- list all sites with confluent regions and their % confluent
- map all sites with confluent regions
MeasureImageQuality
- plot power log log slope as a proxy for focus
- plot saturation
Thresholds
- map segmentation thresholds

ErinWeisbart commented 4 years ago

I don't currently see the need to integrate it into flagging/filtering sites in downstream data analysis. But it we chose to in the future, it may allow us to filter and hence use datasets that are even more problematic than those we have been working with (e.g. sets where the autofocus left half the sites out of focus).

ErinWeisbart commented 4 years ago

As I see it right now: 1) It would be helpful for the assay dev team to have when communicating with the wet lab team. 2) If the assay dev team needed to re-run analysis, these are useful metrics for tweaking the pipeline. 3) If profiling doesn't go smoothly or some sites seem to be outliers, this would be an easy first place to look for an explanation.

ErinWeisbart commented 4 years ago

Might also fit nicely in with 8.visualize-plate-layout.ipynb with a renaming?