BIOMERO components

BIOMERO is a collection of cooperating services and libraries. For complete deployment instructions, start with the NL-BIOMERO documentation.

  • BIOMERO core (this package) manages Slurm workflows, container acquisition, event-sourced tracking, and analysis views.

  • BIOMERO.scripts integrates workflow execution, result retrieval, and metadata persistence with OMERO. See OMERO workflow scripts for installation and the script reference.

  • BIOMERO.importer prepares and registers imported data with OMERO.

  • OMERO.biomero provides the OMERO.web user and administrator interfaces.

  • BIOMERO Schema defines shared workflow descriptors, canonical Zarr records, and normalization reports and receipts.

  • BIOMERO.shallower provides filesystem-only shallow-Zarr result normalization. The importer uses the shared implementation locally; core can run its CPU-only container on Slurm before result archiving and transfer.

BIOMERO.shallower

The helper compares returned image and label identities with the exact canonical-input snapshot. Verified duplicate arrays are replaced by canonical references, while new or changed data is retained. It does not connect to OMERO or require OMERO credentials, and it does not suppress result registration. Its initial adapter supports NGFF 0.4 / Zarr v2 Images and Plates.

Shallow storage is optional. When it is enabled, remote normalization is the preferred path; administrators can choose local normalization instead. Trusted receipts allow the importer to validate completed remote normalization without hashing the omitted pixels again. Installing the library or helper alone does not enable shallow storage.

For enablement, image acquisition, resource configuration, and recovery, see the remote shallower administration guide. For file formats and service boundaries, see remote shallower contracts. For the shared implementation, command reference, and container releases, see the BIOMERO.shallower documentation.

For core’s execution APIs and the distinction between worker restart, helper recovery and user-requested reruns, see Execution, storage and recovery. Searchable provenance and administrative refresh requests are described in Workflow metadata views.