Retrieve CellProfiler pipelines for the Cell Painting datasets

shntnu commented 4 years ago

For the analysis pipeline

[x] Identify one plate barcode per cell line @gwaygenomics
[x] Retrieve the Experiment.csv file for any one image in each of the 3 plates e.g. https://imaging-platform.s3.us-east-1.amazonaws.com/projects/2015_07_01_Cell_Health_Vazquez_Cancer_Broad/workspace/analysis/CRISPR_PILOT_B1/SQ00014610/analysis/A01-1/Experiment.csv @gwaygenomics
[x] Extract the pipeline from the CSV file by hand (e.g. see SQ00014610.txt; this was extracted from the CSV above)
[x] Compare the 3 pipelines; they are very likely identical, in which case keep just one and name it analysis.cppipe else name each by the cell type e.g. analysis_u2os.cppipe
[x] Compare with https://github.com/broadinstitute/imaging-platform-pipelines/blob/master/cellpainting_a549_20x_phenix_bin1/analysis.cppipe and if it is identical, then just use this version instead (there will be some difference wrt load path etc, which can be ignored)

For the illum pipeline

[x] I'm 100% sure it's the same pipeline we've used for LINCS Cell Painting Pilot https://github.com/broadinstitute/imaging-platform-pipelines/blob/master/cellpainting_a549_20x_phenix_bin1/illum.cppipe so there's nothing to be done here @gwaygenomics

hkhawar commented 4 years ago

@gway @shntnu Only single pipeline is used for all three different cell lines. I have have compared pipelines from following plates

Here below is the the final analysis pipeline.

This pipeline is identical to https://github.com/broadinstitute/imaging-platform-pipelines/blob/master/cellpainting_a549_20x_phenix_bin1/analysis.cppipe. Only difference is ordering of couple of modules are different. We can use this version of pipeline as well.

shntnu commented 4 years ago

Thanks @hkhawar!

We are all set @gwaygenomics; here's what we need:

shntnu commented 4 years ago

Version of CellProfiler used is available in the Experiment.csv file (extracted into the SQ00014610.txt file below):

Extract the pipeline from the CSV file by hand (e.g. see SQ00014610.txt; this was extracted from the CSV above)

CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:20160916141640
GitHash:7a8b7d5

Looking up the GitHash, this turns out to be v2.2.0

bethac07 commented 4 years ago

It is indeed 2.2.0

broadinstitute / cell-health