As the year comes to a close, Glencoe Software is looking back on the progress made in 2022 and how this lays the foundation for an exciting product roadmap for 2023. First, we summarize some key challenges and how our technology developments in 2022 aim to address them. Then, we propose our product roadmap for 2023 and its basis in these core technologies. As always, we look forward to your feedback.

Challenges addressed in 2022

First and foremost, Glencoe Software is motivated to solve the challenges faced by our customers in managing bioimaging data at scale:

  • Multi-site, global deployments are becoming industry standard, and often image acquisition, processing and analysis do not happen in the same geographical location. OMERO Plus must enable image management, annotation, visualization, processing and analysis across continents with globally distributed data.
  • Many organizations are shifting towards cloud-native deployments with object storage as the primary storage mechanism. These same organizations require consistent user authentication and authorization by institution-wide SSO providers.
  • The scope of OMERO Plus is expanding beyond core image and metadata management. OMERO Plus provides the opportunity to manage analytical data, including image processing parameters, mask and label image overlays, and tabular data, alongside the original images. Further, OMERO Plus is uniquely suited for the orchestration of reproducible image processing tasks at scale.

In the past year, Glencoe Software has made large updates to OMERO Plus to address these challenges:

  • OMERO Plus has native support for cloud architectures, including support for object storage, which can offer lower storage costs per GB per month. Support for object storage is based in the development and adoption of Next-Generation File Formats (OME-NGFF). Read more about OME-NGFF here.
  • OMERO Plus supports SSO, including SAML 2.0 protocol.
  • Server-side processing is safer and more scalable with the new OMERO Plus workflow and processing engines. These provides background task management for workflows including stitching, file conversion, image and metadata import, image segmentation, and ingestion of third-party analysis results. OMERO Plus now offers scalable and automated workflows from image import to cell phenotyping.
  • OMERO Plus Segmentation Connectors enable the generation of cell and nuclear segmentation with popular AI/ML models across image collections. These results can be managed alongisde the original imges and results from other image analysis platforms like CellProfiler and Visiopharm. Segmented objects are paired with measured morphometric, intensity and spatial features. Both segmented objects and their metrics can be visualized in PathViewer overlaid with the original image. Read more about these visualizations here. Processing tools are deployed using containerization technologies for easy deployment and upgrade. Read more about how OME-NGFF makes scalable image processing possible here.

Glencoe Software 2023 Product Roadmap

With the above foundations, we are excited to announce the following products in 2023:

OMERO Plus Administration and Monitoring

The new OMERO Plus Admin Dashboard will provide monitoring of system usage and background tasks. This will include notifications and views for specific roles:

  • Data managers: Monitor current and historical system usage statistics across users and groups, check the status of automated imports, and manage import profiles.
  • OMERO system administrators: Get notifications on storage or database issues and monitor running services.
  • Data analysts: Monitor background tasks such as image processing.

Image Processing and Data Mining in OMERO Plus

With fully integrated image processing for both Digital Pathology and High-Content Screening domains, OMERO Plus will offer a variety of interfaces and APIs for data mining workflows.

  • Visualize segmented objects, object measurements, and summary heatmaps overlaid with the original image in PathViewer. Filter, color and group objects based on their features within the tissue context. Read more about these visualizations here.
  • Object-level measurements are stored in OMERO.tables, which will be extended for improved support for millions of objects, including support for spatial queries. The OMERO.tables API will be modernized for the data science workflow, including support for popular Python libraries such as Pandas.

  • OMERO.pageant will be a new interface for object-level data mining to support cell and tissue classification workflows. Explore tabular data alongside object-focused image thumbnails with support for single and multi-image collections for Digital Pathology and HCS domains. OMERO.pageant is under development. Screenshot are from the latest development version from 2022.11.06. The UI is a subject to change before production release. Image credit: Prof Jerrold R. Turner Lab; Brigham and Women’s Hospital, Harvard Medical School

  • OMERO.ai will provide a new web interface for AI/ML model training and parameter finetuning, pixel painting for model training input, built-in integrations with popular AI/ML models and image processing platforms (StarDist, Cellpose, CellProfiler, etc.), and large-scale image analysis job submission and task monitoring.

OMERO.ai is currently in the discovery phase. Presented UI is a concept and is a subject to change before production release. Image credit: The BBBC013 images are licensed under a Creative Commons Attribution 3.0 Unported License by Ilya Ravkin.

Embeddable Viewer for Domain-Tailored Solutions

A new embeddable version of the popular viewer PathViewer will soon be available for integration into your favorite data dashboard or portal. PathViewerJS is paired with a fully documented JavaScript API for flexible addition to existing and novel data viewers by internal or contracted development teams at your organization. PathViewerJS serves as a foundation for many of the new applications described above and will increasingly allow Glencoe Software to develop tailored solutions for particular domains, including Digital Pathology and High Content Screening, and data-centered roles, such as Pathologists, Data Scientists, and Data Managers.

Glencoe Software customers make it possible and enjoyable to develop solutions to challenging problems, and we thank you for your continued support and feedback.