NGFF is an initiative by the bioimaging community to develop imaging format specifications to address issues of scalability and interoperability.

This repository contains the central specification text, a comprehensive list of metadata examples as well as json schemas to validate written ome-zarr image data.

The built documentation including contribution hints can be found here.

Conformance can be tested at several levels.

1. Validating that individual fields of a zarr attributes object are valid.

2. Validating a single zarr attributes object (i.e. containing OME-Zarr metadata)

   • Validates that correct data can be represented, and that internally inconsistent data can be caught
   • Cannot validate references to other objects in the zarr hierarchy
   • Cannot validate conformance to other zarr metadata e.g. array data type, dimensionality

3. Validating a metadata-only zarr hierarchy

   • Can validate references to other objects and other zarr metadata
   • Cannot validate values e.g. the invertibility of an affine matrix defined as a zarr array

4. Validating a zarr hierarchy with data

This repository contains

• JSON schemas which handle level 1
• a set of test zarr attributes JSON for level 2 (./tests/attributes)
• a set of metadata-only zarr hierarchies for level 3 (./tests/zarr)

as well as a tool for feeding these test cases into an external validator.

See ome_zarr_conformance.py.

Run it in either attributes or zarr mode, optionally with filters for test names or types.

Wrap your own OME-Zarr implementation in a "dingus" CLI, which takes as its last argument the path to either

• attributes mode: a JSON file representing zarr attributes (i.e. containing OME-Zarr metadata)
• zarr mode: a zarr hierarchy root on the file system (i.e. a directory containing zarr.json)

The dingus should print to STDOUT a JSON object with the keys:

• "valid": boolean, whether this is valid
• optionally "message": string, free text describing the success/ failure

Call the tool like

python3 ./conformance/ome_zarr_conformance.py attributes -- path/to/my/dingus -dingusArg +argValue 10

Each call to the dingus will then look like

>>> path/to/my/dingus -dingusArg +argValue 10 /home/you/ngff-spec/tests/attributes/spec/valid/custom_type_axes.json

{"valid": true}

ome_zarr_conformance.py will parse the JSON output and format the results of all requested tests in a tab-separated table.

Full usage information is available with ./conformance/ome_zarr_conformance.py --help.

You can use the conformance testing tool to test JSON Schema-based validation with

>>> ./conformance/ome_zarr_conformance.py attributes -- uv run ./conformance/jsonschema_dingus.py attributes

Some failures are expected as JSON Schema can only handle level 1 validation.