BIOMERO.shallower

🚀 This package is part of BIOMERO 2.0 — For complete deployment and FAIR infrastructure setup, start with the NL-BIOMERO Documentation 📖

A filesystem-only library and CPU container for shallow-Zarr normalization. It compares returned images and labels with the workflow's canonical inputs, replaces verified duplicate arrays with references, and retains new or changed data. No OMERO connection or credentials are required.

BIOMERO.importer uses the Python package locally. BIOMERO core runs the same implementation on Slurm before archiving and transferring results. Deduplication never suppresses result registration in OMERO.

Supports contract 1, NGFF 0.4 / Zarr v2 Images and Plates. Shallow storage is optional; installing this package does not enable it. When shallow storage is enabled, remote normalization is preferred unless explicitly disabled.

Quick start

Python 3.11 or newer:

pip install 'biomero-shallower[identity]'
biomero-shallower --version
biomero-shallower inspect --returned-zarr /results/result.zarr

Container:

docker run --rm --network none cellularimagingcf/biomero-shallower:0.1.0 health

Documentation

• Usage and commands
• Architecture, recovery and Python API
• Development and testing
• Release setup

For local tests, install .[test] in a virtual environment and run python -m pytest tests -q. GitHub Actions runs unit tests, container smoke tests and a strict MkDocs build. GitHub releases publish the package and image.

License

Apache-2.0. See LICENSE. Dependencies retain their own licences.