We are pleased to announce the latest release of OMERO Plus. This release adds support for OME-Zarr 0.5 and Zarr v3, expanded public data-mining workflows, and release of omero-label for label image registration. It also ships with the latest versions of PathViewer and Glencoe’s Bio-Formats.

Specific version information for all components is detailed below.

OME-Zarr: Extending Support for NGFF Specification 0.5 and Zarr Version 3

OMERO Plus now supports importing OME-Zarr data that follows the NGFF 0.5 specification, using Zarr v3. This includes support for images and high-content screening plates from local storage and S3-compatible object storage, including NGFF 0.5-compliant label images.

OMERO Plus remains backwards compatible with NGFF specification 0.4 for the data types described above.

These changes give organisations a path to adopt current NGFF workflows and features such as sharding while continuing to work with their existing OME-Zarr data. You can read more about OME-Zarr for OMERO Plus here.

Advanced Data Mining in Published Data

Did you know that OMERO Plus can be used to publish your complex imaging data, even while keeping the majority of your organisation’s data private? This now extends to advanced PathViewer workflows such as data mining. Published image segmentation or spatial transcriptomics results can be explored dynamically in PathViewer’s Data tab while preserving the expected restrictions on saving changes.

OMERO.web and OMERO.server

This release of OMERO Plus includes OMERO.server 5.6.18 and the latest security release, OMERO.web 5.33.1. Read the OMERO.server 5.6.18 release announcement. Details of the OMERO.web security fix are available in the security advisory.

Highlights of the OMERO.web improvements include displaying OME-Zarr registration details under “External Information” in the right-hand General tab and adding pagination to tagged collections containing more than 200 images, ensuring that every tagged image can be viewed in the Tags tab.

omero-label: Now Available on PyPI

The omero-label Python library is now available on PyPI, making the OME-Zarr label utilities publicly available for standalone installation. See the PyPI project page for more details and installation instructions.

Users can install the package on their own workstations and use the omero label commands to register label images stored locally or in S3, retrieve their properties, and update their locations in OMERO Plus.

PathViewer

This release of OMERO Plus comes with the new PathViewer 3.17.0. Read the PathViewer 3.17.0 release notes to learn more.

Glencoe’s Bio-Formats

This release of OMERO Plus includes the latest version of Glencoe’s Bio-Formats. Read the Glencoe’s Bio-Formats 8.5.0-882 release notes to learn more.

Versions

  • OMERO.server 5.6.18-285-gs-ice36
  • Glencoe’s Bio-Formats 8.5.0-882
  • omero-ms-image-region 0.14.0
  • omero-ms-pixel-buffer 0.10.0
  • omero-ms-thumbnail 0.7.0
  • omero-plus 0.14.0
  • OMERO.web 5.33.1
  • PathViewer 3.17.0

Upgrading OMERO Plus

To schedule your upgrade of OMERO Plus and take advantage of these new features, reach out to support@glencoesoftware.com.