Propose top-level BDV metadata

joshmoore commented 1 month ago

See e.g. https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://radosgw.public.os.wwu.de/n4bi-goe/Platynereis-H2B-TL.ome.zarr/setup0/timepoint0

cc: @will-moore @constantinpape

joshmoore commented 4 days ago

As a temporary workaround, I've pushed the following two files to your fileset, @constantinpape:

$ mc cp bf2raw.json n4bi-goe/n4bi-goe/Platynereis-H2B-TL.ome.zarr/zarr.json
/tmp/bf2raw.json:         141 B / 141 B ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.96 KiB/s 0s

$ mc cp OME.json n4bi-goe/n4bi-goe/Platynereis-H2B-TL.ome.zarr/OME/zarr.json
/tmp/OME.json:            618 B / 618 B ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.55 KiB/s 0s

$ bat bf2raw.json OME.json
───────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
       │ File: bf2raw.json
───────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1   │ {"attributes": {
   2   │     "ome": {
   3   │         "version": "0.5",
   4   │         "bioformats2raw.layout" : 3
   5   │     }
   6   │ }, "zarr_format": 3, "node_type": "group"}
───────┴────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
───────┬────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
       │ File: OME.json
───────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1   │ {"attributes": {
   2   │     "ome": {
   3   │         "version": "0.5",
   4   │         "series" : [
   5   │             "setup0/timepoint0",
   6   │             "setup0/timepoint1",
   7   │             "setup0/timepoint2",
   8   │             "setup0/timepoint3",
   9   │             "setup0/timepoint4",
  10   │             "setup0/timepoint5",
  11   │             "setup0/timepoint6",
  12   │             "setup0/timepoint7",
  13   │             "setup0/timepoint8",
  14   │             "setup0/timepoint9",
  15   │             "setup1/timepoint0",
  16   │             "setup1/timepoint1",
  17   │             "setup1/timepoint2",
  18   │             "setup1/timepoint3",
  19   │             "setup1/timepoint4",
  20   │             "setup1/timepoint5",
  21   │             "setup1/timepoint6",
  22   │             "setup1/timepoint7",
  23   │             "setup1/timepoint8",
  24   │             "setup1/timepoint9"
  25   │         ]
  26   │     }
  27   │ }, "zarr_format": 3, "node_type": "group"}

~The validator is temporarily unhappy due to the missing OME/METADATA.xml file. cc: @will-moore~ See below

joshmoore commented 4 days ago

@constantinpape: see https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://radosgw.public.os.wwu.de/n4bi-goe/Platynereis-H2B-TL.ome.zarr/

constantinpape commented 4 days ago

Thanks @joshmoore , I think that is a good solution for now. I will prepare the other data we have accordingly.

ome / ome2024-ngff-challenge

Propose top-level BDV metadata #49