Missing images (DNA damage screen)

[beatrizserrano]

Hi, I’ve found some missing images in full plates of the DNA damage screen (idr0010):

• None of the images are available for plate 5-12 (ID 5894).
• Only one channel available for plates 47-35 (ID 5937), 69-49 (ID 5938), 96-14 (ID 5939).

[joshmoore]

Hi @beatrizserrano. This matches my records¹ though I additionally have 153-29 listed as being problematic. There are a small number of plates throughout the IDR where the original imaging data is corrupted due to various issues. When possible, we try to go back and fix what we can. In the case of DNA damage, I'd imagine it will require reader fixes to deal with some inconsistency in these plates. The fixes we already put in place to get the screen in can be seen in the bioformats repo, e.g.:

• Updates for Metamorph plates with one file per channel ome/bioformats#2151
• Fix HCS variant of MetaMorph STK ome/bioformats#2411
• Rebase Metamorph changes from metadata ome/bioformats#2912

I don't foresee us being able to correct these 4-5 plates before the users meeting. If there's some other avenue that might help you, we'd certainly appreciate hearing it.

Cheers,
~Josh

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¹ Internal references: vMCDDpwY, vpc8NKAC,

[beatrizserrano]

Thanks, @josh. We are done with the feature calculation, the API worked fine with 192 vCPUs in parallel.
We haven't encountered much problems with the screens we're using:

• CellMorph: 100 % features computed.
• MitoCheck: 100 % features computed.
• YAP activation: 100 % features computed.
• DNA damage: the missing images reported above. I didn't have issues with 153-29 because it seems like it is not on the list of plates anymore.
• Secretion: 99 % features computed, 9744 images missing, we guess this is due to the issue already reported with the last image.

Cheers,

Beatriz

[joshmoore]

I didn't have issues with 153-29 because it seems like it is not on the list of plates anymore.

Ah. In that case, we likely went so far as to remove it. That may be the best way forward with the other plates as well.

cc: @pwalczysko