2021_09_01_VarChAMP_Pilot (cpg0020)

[rsenft1]

Segmentation/ Feature extraction is being performed by Cimini lab Profile creation is being performed by Cimini lab Data can be public in RODA Immediately - yes

Update as generated:
Link to profile repo [Link to publication repo]
[cpg0020-varchamp-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)
• [X] Segmentation/Feature extraction complete
• [X] Profiling complete

Transfer to CellPainting Gallery:

• [X] Upload data to RODA (is private by default)
• [ ] Run validation script to ensure completion
• [ ] Update cellpainting-gallery/README.md
• [x] Make RODA entry 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.

[shntnu]

@ErinWeisbart asked:

As per a conversation in check-in last week, I believe that my last task related to this batch is to move it to the cellpainting-gallery. A project for 2021_09_01_VarChAMP_Vidal_Taipale exists in the cellpainting-gallery already (cpg0020-varchamp-pilot) and has the first arrayed batch in it (2022_08_22_Batch_1).

If I'm understanding correctly, this batch (B1A1R1) represents the first production batch, not a pilot batch.

• Should I create a new cpg for production data (starting with this batch)?
• Should I instead rename the gallery identifier to (cpg0020-varchamp) (removing "pilot") and put this batch in the same folder?
• Should I move the other pilot arrayed batch to the gallery as well? (2023_02_23_Batch_3)
• Should I move pooled pilot batches to the gallery as well? (2023_01_11_Batch2 and 2023_06_05_24W_RD3_poscon/ (in progress))

[shntnu]

• Should I instead rename the gallery identifier to (cpg0020-varchamp) (removing "pilot") and put this batch in the same folder?

Please do this; simpler with a one-off overhead of syncing data over across prefixes (just to be sure: instead of renaming, sync it over and then delete the source)

• Should I move the other pilot arrayed batch to the gallery as well? (2023_02_23_Batch_3)

know nothing about this pilot specifically, but it makes for all of them to live together, assuming this is indeed VarCHAMP

• Should I move pooled pilot batches to the gallery as well? (2023_01_11_Batch2 and 2023_06_05_24W_RD3_poscon/ (in progress))

Oh wait – that's unrelated to VarCHAMP, right? (it's pooled rare?)

[ErinWeisbart]

To confirm:

• I will sync arrayed pilot batches 2022_08_22_Batch_1, 2023_02_23_Batch_3 and this first batch of production data B1A1R1 to a new gallery identifier cpg0020-varchamp
• I will then delete the previously created cpg0020-varchamp-pilot
• Pooled batches are considered a different project despite having the same 2021_09_01_VarChAMP_Vidal_Taipale prefix and will not be synced to this prefix