OME-Zarr RFC-4 — Orientation Sample Data
Sample datasets for RFC-4 (Axis Anatomical Orientation) of OME-Zarr (spec · ome/ngff#528). This repo provides the sample datasets the RFC itself lists as missing; the validator and conformance suite live in the companion code repo: 👉 github.com/fideus-labs/ome-zarr-rfc4-validation.
RFC-4 adds one optional field to spatial axes (type: "space"):
{ "name": "x", "type": "space",
"orientation": { "type": "anatomical", "value": "left-to-right" } }
value is one of 24 controlled-vocabulary directions naming the axis's
lowest→highest coordinate direction. This corpus exercises all 24 terms.
Contents (at the repo root)
manifest.csv · generate_phantoms.py
ome-zarr/ OME-Zarr with RFC-4 written: TC-16..TC-19 (.zip) + TC-C/TC-D (invalid)
synthetic/ome-zarr/ TC-16..TC-20 unpacked + vocab-completion-* (Zarr v3, OME 0.5)
real/ome-zarr/ REAL volumes → OME-Zarr with RFC-4 (see real/README.md)
├── mouse_allen_quadruped.ome.zarr quadruped terms (rostral-caudal, dorsal-ventral)
├── foot_cmb_limb.ome.zarr limb terms (distal-proximal, dorsal-plantar)
├── skin_janelia_superficial_deep.ome.zarr subject-local (superficial-to-deep, real EM)
└── heart_janelia_apex_base.ome.zarr subject-local (apex-to-base, real EM)
dicom/ TC-05 HFDR, TC-06 HFDL (IOP = ground truth)
nifti/ TC-10/23 Canon DTI (oblique+axial), TC-11 qform/sform, avg152 LR/RL
nrrd/ MRHead (real 3D Slicer, SHA256-verified)
screenshots/{slicer,itksnap,niivue}/ viewer captures
The dataset spans OME-Zarr, DICOM, NIfTI and NRRD, covers valid and invalid cases, synthetic and real data, and every one of the 24 RFC-4 anatomical terms.
Usage
git clone https://huggingface.co/fideus-labs/ome-zarr-rfc4-data
git clone https://github.com/fideus-labs/ome-zarr-rfc4-validation
cd ome-zarr-rfc4-validation && pip install -r requirements.txt
python validate_rfc4.py --data-dir ../ome-zarr-rfc4-data
Licensing & attribution
Redistributed here under CC BY 4.0 (umbrella). Per component:
| Data | License | Attribution |
|---|---|---|
Synthetic phantoms (synthetic/, ome-zarr/, dicom/, nifti/TC-11) |
CC0 / generated | — |
real/…/mouse_allen_quadruped |
CC BY 4.0 | Wang et al., Cell 2020 (Allen Institute, brain-map.org); packaged by BrainGlobe |
real/…/foot_cmb_limb |
CC BY 4.0 | CMB-MEL collection, The Cancer Imaging Archive (TCIA) |
real/…/skin_janelia_superficial_deep |
CC BY 4.0 | OpenOrganelle jrc_mus-skin-1 (HHMI Janelia); doi:10.25378/janelia.24085269 |
real/…/heart_janelia_apex_base |
CC BY 4.0 | OpenOrganelle jrc_mus-heart-1 (HHMI Janelia); doi:10.25378/janelia.24020919 |
nrrd/MRHead.nrrd |
donated "without any restrictions" | 3D Slicer sample data |
nifti/avg152T1_{LR,RL} |
public domain | MNI / MONAI-extra-test-data |
nifti/TC-10,TC-23 (Canon DTI) |
BSD-2-Clause | dcm_qa_canon_61 (Chris Rorden / neurolabusc); Canon 3T Galan, GHU Paris (C. Debacker) |
See real/README.md for the exact orientation assignments and
provenance of the real volumes.