BIOMERO Schema¶
biomero-schema is the shared, versioned contract package for BIOMERO
services. It supplies Pydantic models, stable JSON representations, generated
JSON Schema, and a command-line validator.
The package has two deliberately separate responsibilities:
- Workflow descriptors provide the normalized model into which BIOMERO converts supported BIAFLOWS and BILAYERS provider descriptors.
- Cross-service contracts describe BIOMERO-owned hand-offs, including canonical Zarr sources, pixel identities, shallow Zarr collections, importer lifecycle operations, and remote shallowing reports and receipts.
This separation matters. A FAIR workflow provider can continue using the supported external BIAFLOWS or BILAYERS specification. BIOMERO's normalized model and storage optimization records are internal contracts between services and are not additions to BILAYERS or OME-NGFF.
Choose a starting point¶
| I want to… | Read… |
|---|---|
| install the package or validate a descriptor | Getting started |
| describe a workflow | Workflow descriptors |
understand .biomero-shallow.json |
Zarr contracts |
interpret dataCode, instanceCode, or another identity field |
Pixel identity |
| request importer-owned shallowing | Import lifecycle |
| exchange remote shallowing reports and receipts | Remote shallower contracts |
| integrate another BIOMERO service | Versioning and compatibility and the Python API |
Experimental shallow-Zarr contracts
The shallow-Zarr and pixel-identity models capture BIOMERO's current implementation while OME-NGFF collections and RFC-8 evolve. They are explicitly versioned and require migrations for breaking changes, but should not be presented as an adopted OME-NGFF interchange format.