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Rewrite the Chung lab demo notebook for the OME-Zarr layout #208

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Rewrite the Chung lab demo notebook for the OME-Zarr layout #208

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Rewrite the Chung lab demo notebook for the OME-Zarr layout
bendichter Aug 23, 2026
a92b953
Draw the slab in micrometers and compare blending across the whole slab
bendichter Aug 23, 2026
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4 changes: 0 additions & 4 deletions .github/notebook-colab-exclusions.txt
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Expand Up @@ -68,10 +68,6 @@ tutorials/cosyne_2023/advanced_asset_search.ipynb
# Multiple missing imports (Parallel from joblib and others beyond pandas).
000039/AllenInstitute/Create_manifest.ipynb

# Dandiset 000108 reorganized: microscopy/ → micr/, .SPIM.h5 → .SPIM.ome.zarr.
# Notebook needs a wholesale rewrite for the current data layout.
000108/chunglab/demo/2021-09-27_dandi-demo.ipynb

# Hardcoded path `../../dandiset/sub-...` to a file no Colab user has.
000363/MAP/demo/browse_map_ephys_data.ipynb

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5 changes: 0 additions & 5 deletions .github/notebook-test-exclusions.txt
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Expand Up @@ -74,11 +74,6 @@ tutorials/cosyne_2023/advanced_asset_search.ipynb
# that aren't imported.
000039/AllenInstitute/Create_manifest.ipynb

# Dandiset 000108's data layout was reorganized after this notebook was
# written: microscopy/ → micr/, .SPIM.h5 → .SPIM.ome.zarr, and the path
# pattern changed. Needs a wholesale rewrite, not an API-shape patch.
000108/chunglab/demo/2021-09-27_dandi-demo.ipynb

# Hardcoded path `../../dandiset/sub-...` to a file no contributor has
# locally; needs a switch to streaming-from-DANDI.
000363/MAP/demo/browse_map_ephys_data.ipynb
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