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@TorecLuik TorecLuik released this 26 Mar 12:58
· 22 commits to main since this release
v2.4.0
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BIOMERO v2.4.0

Minor release introducing enhanced workflow organization and ZARR-native plate processing capabilities through improved admin controls and workflow categorization.

What's Changed

  • 🎛️ Enhanced Admin Controls: Redesigned admin panel enables administrators to configure workflow types (image vs plate workflows) and format capabilities (ZARR vs TIFF processing), providing better workflow organization and automatic version checking against GitHub repositories.
  • 📋 Dual Workflow Interface: New tabbed workflow interface separating "Image Workflows" and "Plate Workflows" for improved user experience, with plate workflows featuring native ZARR-to-ZARR processing and direct screen import capabilities.
  • 📦 Screen Import Support: Plate workflows can now import results directly into OMERO screens, enabling comprehensive high-content screening data management.
  • 🔄 Automatic Version Monitoring: Admin panel now checks GitHub repositories for workflow updates, helping maintain up-to-date analysis capabilities. Note that you have to run Slurm Init to install new versions (old versions will remain on Slurm for reproducibility, but you can manually clean these up if desired).

Key Improvements

  • Admin-configurable workflow categorization enables better organization of diverse analysis tools
  • Plate workflows bypass format conversion entirely, maintaining ZARR format throughout processing pipeline
  • Automatic version checking helps administrators keep workflows current
  • Screen import support completes the high-content screening workflow ecosystem

ZARR Workflow Framework

While continuing full support for BIAFLOWS (TIFF-to-TIFF containerized workflows), v2.4.0 introduces experimental ZARR-native workflow capabilities. Administrators can now enable ZARR workflows through the admin interface, supporting containerized analysis that processes ZARR data directly.

Experimental Examples:

Future releases will expand this framework with standardized ZARR workflow descriptors, building on the proven BIAFLOWS foundation. But for now it requires manual configuration per workflow inside BIOMERO admin.

Requirements: ZARR Features

The new native ZARR processing capabilities (ZARR-to-ZARR, ZARR plate-to-plate imports) are only available when using the BIOMERO.importer integration. BIOMERO deployments without the importer continue to use the proven TIFF conversion pipeline and remain fully compatible with existing workflows.

For deployments wanting to leverage the new ZARR-native capabilities, see the analyzer-importer setup guide and consider the full NL-BIOMERO deployment!

Requirements: OMERO.biomero >= v1.3.0

The UI will need to be updated with latest OMERO.biomero (TBD)

Changelogs

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