Pipelines for using Cell Profiles to analyze cell painting data from Opera Phenix

I am looking for guidance on how to analyze a large cell painting dataset generated with the Opera Phenix using Cell Profiler.

Any pipelines available?

Hi mtsompana,

I don’t have any pipelines to hand, but have worked with lots of Opera data in CP.

Stuff you might find useful…

The excellent imageijs-Perkin Elmer Operetta CLS, Stitching And Export stitcher plugin at…
https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/perkinelmer-stitching/
It does a good job of preparing the images for CP.

This thread on extracting the metadata from PE image filenames in CP.

This script for parsing PE XML files into a format CP can read.

Hope that helps. Very interested to see how others handle their Opera Phenix data…

John

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