cpg0029-chroma-pilot

[shntnu]

Imaging Platform project tag = 2023_08_31_Chromalive
Segmentation/ Feature extraction is being performed by (Cimini lab / Carpenter-Singh lab)
Profile creation is being performed by (Cimini lab / Carpenter-Singh lab)
Data can be public in RODA Immediately

Update as generated:
[Link to profile repo]
[Link to publication repo]
cellpainting-gallery identifier: cpg0029-chroma-pilot

• Metadata collection form filled out by collaborator or Imaging Platform member (https://airtable.com/shrVxz9DcoMlDoCBI)
• Metadata completely filled out in Project Profiler Database (Imaging Platform internal use only)
• Segmentation/Feature extraction complete
• Profiling complete

Transfer to CellPainting Gallery:

• Upload data to RODA (is private by default) --> public in this case
• Run validation script to ensure completion (https://github.com/jump-cellpainting/data-validation)
• Update cellpainting-gallery/README.md
• Make RODA entry public --> will already be public

If data is being published, prepare for publication:

• Run Distributed-BioFormats2Raw to create .ome.zarr files
• Upload (meta)data to IDR (images remain hosted in cellpainting-gallery).

Once published:

• Make IDR entry public
• Update cellpainting-gallery/README.md and open-data-registry/cellpainting-gallery.yml to reflect publication
• Move this Issue from cellpainting-gallery-private to cellpainting-gallery. This step can be performed at an earlier point if it needs inputs from an external collaborator.

[ErinWeisbart]

One suggestion about naming of this dataset, is this only ever going to include pilot data? If so, then chroma-pilot is appropriate, but we have found with other datasets that started as an upload of the pilot data that then included production/published data, we needed to rename to remove the pilot suffix. So perhaps better to start with just chroma?

[shntnu]

It was named chroma at first but Alán said this:

May I suggest adding something suggesting it is an explorative approach? (e.g,. explorechroma), Just in case it is used for other projects in the future.

I'd agree with Alán here: if end up with multiple chroma datasets, we'd want to have labeled this one as a pilot (this is different from Varchamp, where there is only one)

[bethac07]

Thanks @ErinWeisbart and @sugan89 for getting this uploaded!

Can we add maybe a minimal readme file with what is in each batch in terms of what dyes are present in each plate? I think that's all we need to do to make this "currently usable".

[sugan89]

Hi Beth!
Sorry for not adding it earlier.
DetailsOfBatchesCPG.txt
Please let me know if the attached information will be sufficient for the readme file. Thanks!

[bethac07]

That looks perfect! Great job.

[ErinWeisbart]

Copying Suganya's README text here for quick browse ability:
The images are for comparison of different set of dyes in the cell painting assay. Each batch has been treated with same set of compounds but are stained with different dyes.

Batch1:
BR00122250 - The plate has been treated with standard cell painting dyes (Perkin Elmer)

• Hoechst 405
• ConcavalinA 488
• Nucleic acid 512
• WGA 555
• Phalloidin 568
• Mitotracker 647
  Contains images from 9 fields in a single well

BR00122246 - The plate has been stained with Tocris MitoBrilliant in place of MitoTracker. Rest of the dyes were from Perkin Elmer

• Hoechst 405
• Concavalin A 488
• Nucleic acid 512
• WGA 555
• Phalloidin 568
• Tocris MitoBrilliant 647
  Contains images from 9 fields in single well

Batch2:
BR00122247 - This plate has been stained with Phalloidin 400LS (long stoke shifted) in place of Phalloidin.

• Hoechst 405
• Phalloidin 400LS
• ConcavalinA 488
• Nucleic acid 512
• WGA 555
• Mito 647
  Contains images from 9 fields in a single well.

Batch3:
BR00122248 - This batch contains the images of standard cell painting dyes. The cells were intially stained with Saguaro dyes, imaged live(these images exist in Batch6), fixed and later stained with standard cell painting dyes.

• Hoechst 405
• ConcavalinA 488
• Nucleic acid 512
• WGA 555
• Phalloidin 568
• Mitotracker 647
  Contains images from 9 fields in a single well.

Batch4:
BR00122245 - Images are from live cells. This batch is stained with the following,

• DRAQ7
• Cas 3/7
  Contains images from 9 fields in a single well.

Batch5:
BR00122249 - Images are from live cells. This batch has been stained with Saguaro dyes

• ChromaLive 488 Yellow (CL488Y)
• ChromaLive 561 Yellow (CL561Y) Ex561, Em570-630
• ChromaLive 488 Red (CL488R) Ex488, Em630-750
  Contains images from 9 fields in a single well.

Batch 6, 7 and 8 contains images taken from live cells at different time points.

Batch6:
This batch contains images from three time points and following are the dyes used,

Saguaro

• ChromaLive 488 Yellow (CL488Y)
• ChromaLive 561 Yellow (CL561Y) Ex561, Em570-630
• ChromaLive 488 Red (CL488R) Ex488, Em630-750
• DRAQ7
• Cas3/7

04h Live - BR00122248__2023-03-22T19_03_51-Measurement1 - contains images from 4 fields
24h Live - BR00122248__2023-03-23T17_11_00-Measurement2 - contains images from 4 fields
48h Live - BR00122248__2023-03-24T12_49_58-Measurement3 - contains images from 1 field

Batch7:
This batch contains from images three time points and following are the dyes used,

• DRAQ7
• Cas3/7

04h Live - BR00122245__2023-03-22T22_13_07-Measurement1 - contains images from 4 fields
24h Live - BR00122245__2023-03-23T15_57_45-Measurement2 - contains images from 4 fields
48h Live - BR00122245__2023-03-24T12_32_25-Measurement3 - contains images from 1 field

Batch8:
This batch contains from images three time points and following are the dyes used,

Saguaro dyes

• ChromaLive 488 Yellow (CL488Y)
• ChromaLive 561 Yellow (CL561Y) Ex561, Em570-630
• ChromaLive 488 Red (CL488R) Ex488, Em630-750

04h Live - BR00122249__2023-03-22T20_03_43-Measurement1 - contains images from 4 fields
24h Live - BR00122249__2023-03-23T14_50_32-Measurement2 - contains images from 4 fields
48h Live - BR00122249__2023-03-24T12_14_34-Measurement3 - contains images from 1 field