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Add Crick and N4BI samples #54

Merged
merged 2 commits into from
Oct 9, 2024
Merged

Add Crick and N4BI samples #54

merged 2 commits into from
Oct 9, 2024

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joshmoore
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netlify bot commented Oct 8, 2024

Deploy Preview for euphonious-mochi-664405 canceled.

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🔨 Latest commit 8d8c0d3
🔍 Latest deploy log https://app.netlify.com/sites/euphonious-mochi-664405/deploys/6706304703b39f0008a3fe34

@joshmoore
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See https://deploy-preview-54--euphonious-mochi-664405.netlify.app/?csv=https://raw.githubusercontent.com/ome/ome2024-ngff-challenge/0e14f3376c70a3c524a08bc79d367ec14b549b1a/samples/ngff_samples.csv

image

Minor issues:

  • thumbnails (for bf2raw collections?) aren't loading
  • CSV URLs ending with "/" fail
  • top-level CSV of the current branch isn't used

But those are all outside of this PR.

cc: @will-moore @constantinpape @folterj @JThoennissen

@joshmoore
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with #56 merged, getting this in, then we can re-arrange with the hierarchy browser later.

@joshmoore joshmoore merged commit ea3eebd into ome:main Oct 9, 2024
5 of 6 checks passed
@joshmoore joshmoore deleted the n4bi branch October 9, 2024 07:27
@will-moore
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will-moore commented Oct 14, 2024

NB: https://radosgw.public.os.wwu.de/n4bi-wp1/challenge/n4bi.csv links to https://radosgw.public.os.wwu.de/n4bi-fzj/ome2024-ngff-challenge/fzj.csv which contains https://radosgw.public.os.wwu.de/n4bi-fzj/ome2024-ngff-challenge/BigBrain.zarr which is Not Found 404.
I'll remove that from our copy of fzj.csv...
See 2293fa5

@JThoennissen
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Sorry, I didn't manage to get the conversion working in time for this volume ... Thank you for removing!

@will-moore
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NB: I made local copies of crick.csv and n4bi.csv in order to add extra columns needed in #53.
See https://github.com/ome/ome2024-ngff-challenge/blob/main/samples/crick.csv and https://github.com/ome/ome2024-ngff-challenge/blob/main/samples/n4bi.csv

The script used to add these extra columns is at https://github.com/ome/ome2024-ngff-challenge/blob/main/samples/load_zarr_stats.py

@joshmoore
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Ok. I'm deleting my CSVs files from the S3 bucket then to avoid confusion.

@joshmoore joshmoore mentioned this pull request Oct 23, 2024
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3 participants