broadinstitute / imaging-platform-pipelines Goto Github PK

The entrypoint to the pipelines starting from raw images appears to be JUMP_illum_LoadData_v1.cpproj, which generates illumination correction fn files, and then JUMP_analysis_v3.cppipe for the feature generation, which takes the images and ICF npy files as input.

Both these pipelines require a csv file containing filepaths and metadata. Is the expected format and metadata for this file (columns) documented anywhere, and are there any vendor specific scripts to automatically generate them from default exports?

The youtube Headless CellProfiler/ DistributedCellProfiler Tutorial references loading the images into CellProfiler by drag-n-drop and then exporting the file, but this is not convenient for distributed / cloud use case.

Dear all,

This job is quite helpful. However, I am reaching out for assistance with an issue I encountered while using the JUMP_analysis_v3.cppipe pipeline from the Broad Institute's imaging-platform-pipelines on GitHub (link: JUMP_production).

While processing our own images with this pipeline, I encountered an error at module number 13 (MeasureGranularity). Unfortunately, due to this error, the expected features related to Granularity are missing from the results.

I would greatly appreciate any guidance or support you could provide to help resolve this issue. Thank you very much for your time and assistance.

Looking forward to your response.

Best regards,

Hi,
JUMP_QC_Drag-and-Drop_v1.cppipe is not producing Top Line Per-Object.csv but only
and files without Top Line in the file name, which makes it impossible to run on the fly Knime QC.
Any advice is highly appreciated!
/Nikolai

Changes were made to cellpainting_a549_20x_phenix_bin1 related to the output folders in the ExportToSpreadsheet and SaveImage modules that haven't been reflected in cellpainting_a549_20x_imagexpress

Create pipelines for
cellpainting_a549_20x_with_bf_phenix_bin1 by adding brightfield to pipelines in
cellpainting_a549_20x_phenix_bin1

Create pipelines for
cellpainting_a549_20x_with_bf_with_qcflag_phenix_bin1 by adding FlagImage (appropriately configured to use CPA output) to cellpainting_a549_20x_with_bf_phenix_bin1

Using
https://github.com/broadinstitute/imaging-platform-pipelines/blob/master/cellpainting_a549_20x_phenix_bin1/README.md

as a reference, add REAME.md for

• cellpainting_min6_63x_phenix_bin2
• cellpainting_u2os_63x_phenix_bin2

Do this once this is solved
https://github.com/broadinstitute/cellpainting_scripts/issues/44

See broadinstitute/cmQTL#14 (comment)