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

[mtsompana (Maria Tsompana)]

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?

[JohnH]

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.

Operetta images - metadata extraction regulare expressions

Hey Guy~ My HCS device is also Operetta system from Perkin Elmer, but My filename is like this: r02c02f01p01rc1-ch1sk1fk1fl1.tiff thanks for the help from clolalan7, now I can extract the metadata from this filename by using regulare expressions. like this ^r(?P[0-9]{2})c(?P[0-9]{2})f(?P[0-9]{2})p(?P[0-9]{2})rc(?P[0-9]) [quote=“BlueALH”]Hi I am trying to process some images generated on the Operetta system from Perkin Elmer to eventually put into FCS Express 4 and generate picture and he…

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

broadinstitute/pe2loaddata

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

John