Glencoe Software is pleased to announce a variety of new features added to the latest OMERO Plus release - including improved support for cloud storage, single sign-on, and analytical data mining workflows.

To see specific version information of all components, see the section below.

Feature Highlights

Cloud-native OMERO Plus with OME-NGFF

Since the first release of OMERO.server 5.6.5, Glencoe Software’s OMERO Plus has supported OME-NGFF (using Zarr), enabling the use of object storage for image data. Support for cloud-native workflows in OMERO Plus continues to evolve, especially as we mature the flexibility and usability of how NGFF data is registered in OMERO Plus.

  • The conversion tools to generate OME-NGFF, including the CLI tool bioformats2raw and its GUI application wrapper, NGFF-Converter, have been released, with a number of feature additions and bug fixes. Read the complete release notes here. In particular, the conversion process has been extended to include calculation of various OMERO metadata, including per-channel min/max values, and improve import performance.
  • A new OMERO Plus client for OME-NGFF image data import (omero-importer-ngff) has been released.
  • In the latest release of OMERO Plus, the location of OME-NGFF data, either in object or file storage, is now specified in database-stored properties, enabling OMERO API access to the file path or URI of any image or label image.
  • If OME-NGFF data is stored in object storage like S3, OMERO Plus now supports authorization via access keys stored in local credentials files. OMERO Plus also includes experimental support for authorization via an EC2 instance profile.

For complete documentation of the OME-NGFF import workflow in OMERO Plus, reach out to support@glencoesoftware.com.

Improved SSO integration for non-web OMERO clients

Glencoe Software added support for SAML-based SSO for OMERO.web login in 2022. With the latest OMERO Plus release, this now extends to login for OMERO.insight, OMERO CLI tools, or other API interactions. A new extension for OMERO.web supports the generation of a temporary password for these OMERO clients, with configurability of the timeout. With this feature, customers using our SAML integration have full support for the complete set of OMERO clients.

Experimental support for OIDC/OAuth 2.0 has now been added to OMERO Plus. If your institution is interested in this integration, please reach out to Glencoe Software at support@glencoesoftware.com.

Please note that for both SAML and OIDC support, this covers user authentication and profile metadata exchange, not authorization criteria.

Improved support for mining OMERO.tables data in PathViewer

Image segmentation workflows can routinely produce millions of objects paired with hundreds of measurements, all of which can be managed in OMERO Plus using OMERO.tables. PathViewer supports within-image data mining workflows, described here.

The latest release includes substantial performance improvements in the filtering of objects within a label image visualized in PathViewer, and more broadly for the handling of tables with large numbers of columns.

Controlled annotation workflows supported in PathViewer

For scoring and other annotation workflows that require controlled language, Glencoe Software has made initial efforts to satisfy these workflows with predefined ROI styles. These enable the system-wide configuration of ROI names and styles for reduced errors in slide annotation workflows. See the complete documentation of this support here.

The latest PathViewer release includes a number of new features, such as support for advanced channel rendering options. Read the complete PathViewer release notes here.

Support for Glencoe’s Bio-Formats 6.12.0

OMERO Plus now includes the latest version of Glencoe’s Bio-Formats, highlights of which can be read here.

Versions

OMERO.server 5.6.6-102-gs-ice36
Glencoe's Bio-Formats 6.12.0
omero-ms-image-region 0.7.2
omero-ms-pixel-buffer 0.6.2
omero-ms-thumbnail 0.5.6
omero-plus 0.3.0
OMERO.web 5.19.0
PathViewer 3.6.0

To schedule your upgrade of OMERO Plus, reach out to support@glencoesoftware.com.