Implement QC functions for profiling

shntnu commented 7 years ago

The purpose of this issue is to create a list. Once we settle on a list, we will close the issue and create an issue per QC item. We also need to decide where to implement this – here or in http://github.com/CellProfiler/cytominer

Plot illumination corrections functions
Plot salient features on a plate map to see if there are any trends
- Cell count
- IntegratedIntensity
- PercentMaximal
Show excluded wells on a plate map
Check for rotation of the plate layout
- Plate map with cell counts
- Cluster all the wells across plates

shntnu commented 7 years ago

For each plate show the signature strength/reproducibility metric as a heatmap, so that you can see whether bad/good samples fall on certain plates or certain regions of plates This could also help diagnose metadata problems

mrohban commented 7 years ago

heat map plot for the locations of 2N and 4N peaks in the DNA integrated intensity would help to find out how the segmentation worked

shntnu commented 3 years ago

Histogram of all features from a single well – this one had a few outlier features, post normalization. Should we flag these wells?

broadinstitute / cytominer_scripts

Implement QC functions for profiling #2