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Parse entire macsima metadata from OME metadata #349

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Parse entire macsima metadata from OME metadata #349

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5c588fc
Parse cycle from ame in tiff metadata, not actual filename
MSHelm Dec 10, 2025
8b49711
Parse additional metadata from filename stored in ome tiff
MSHelm Dec 15, 2025
82d304f
Parse all metadata from ome metadata, nothing from filename
MSHelm Dec 16, 2025
cef7170
Add public OMAP data sets for testing and adjust tests
MSHelm Dec 16, 2025
0aae9ce
Merge branch 'main' into fix/macsima-cycle-parsing
LucaMarconato Dec 28, 2025
904abfc
Emitt warning when duplicate key with different value is found in OME…
MSHelm Jan 5, 2026
334fc55
Harmonize imagetype between format versions. Adjust tests for small d…
MSHelm Jan 9, 2026
2445c76
Add comprehensive metadata test
MSHelm Jan 9, 2026
d721a25
add small OMAP ci datasets
LucaMarconato Jan 9, 2026
885ee41
fix 'on' config for github workflow
LucaMarconato Jan 9, 2026
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11 changes: 10 additions & 1 deletion .github/workflows/prepare_test_data.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@ on:
schedule:
- cron: "0 0 1 * *" # run once a month to prevent artifact expiration
workflow_dispatch:
# uncomment and adjust the branch name if you need to add new datasets to the artifact
# Uncomment and adjust the branch name if you need to add new datasets to the artifact.
# It needs to be a branch in the spatialdata-io origin repository, not from a fork.
# push:
# branches:
# - main
Expand Down Expand Up @@ -57,6 +58,14 @@ jobs:
# Spatial Genomics seqFISH v2
curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip

# -------
# MACSima OMAP datasets are licensed as CC BY 4.0
# OMAP23 for format v1.x.x
curl -o OMAP23_small.zip "https://zenodo.org/api/records/18196452/files-archive"

# OMAP10 for format v0.x.x
curl -o OMAP10_small.zip "https://zenodo.org/api/records/18196366/files-archive"

- name: Unzip files
run: |
cd ./data
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