The OME Blog Because metadata is worth a thousand pictures

OMERO status update

This is a quick update on the status of various versions of OMERO, and some discussion about our future development plans and aspirations.

Releases, maintenance and deprecation

With the release of OMERO 5.2.0 at the beginning of November 2015, the current situation with OMERO versions is as follows:

  • The last release of the OMERO 5.0.x line was February 2015. This version of OMERO and all earlier ones are now unmaintained - we won’t be updating the 5.0.x line of OMERO; anyone who continues to use them does so at their own risk.

  • OMERO 5.1.x is now in “maintenance” - we will provide updates for major security issues but we won’t be releasing bug fixes or any performance enhancements. To access these, you must upgrade to the 5.2.x line. We expect to continue this level of support until the release of OMERO 5.3 (currently aimed for Spring 2016).

  • OMERO 5.2.x is the new stable line and will be updated with bug fixes and enhancements as point releases at least until OMERO 5.3 is released. We expect to continue to support this line throughout 2016, although this support will drop to maintenance level once OMERO 5.3.0 is released.

The best way to keep up-to-date with our release plans is to follow our public Trello boards

  • ‘Getting Started’ acts as a landing board for discovering more specific issue-based boards that may be of interest to you and gives an overview of upcoming releases with their current estimated timelines. You can view these boards without signing up but will need to register for a free Trello account if you want to subscribe to notifications or comments. You only need to supply a valid email address to sign up.

Our next OMERO release will be 5.2.1, which will feature bug fixes but also focus on improving our sysadmin documentation and installation workflows. We recognise that often groups wishing to use OMERO do not have access to a dedicated sysadmin and are trying to alleviate the burden as much as possible. You can follow progress on the OMERO 5.2.1 board.

What’s next?

With OMERO’s use expanding in numbers and in breadth of domains, we are focussing our efforts on making OMERO even more powerful - ensuring that it provides proper facilities for more and more types of image data and metadata, and that it can be deployed in increasingly complex and heterogeneous configurations. Some of our longer term goals:

  • We have applied for funding to develop OMERO’s “federation” capabilities, to make it possible for multiple OMERO servers to be connected at the level of clients or servers.
  • For some time we have wanted to re-architect the framework we use for our OMERO.web and OMERO.insight clients and are seeking funding to do so.
  • Making Bio-Formats and OMERO work effectively with object stores is a major priority.
  • We aim to re-build OMERO’s image rendering engine, to make it faster, more powerful and able to support the creation of increasingly complex data visualisations.

As always, there is a long list of things to do, and we always appreciate any feedback or comments on our work, goals or directions. All of this work is aimed at improving and expanding OME’s support for the heterogeneous metadata which is the foundation of much of modern science (an early vision of the requirements that drive our work was published by Jim Gray and colleagues). Comments welcome on our Trello boards or via our other community channels.

In the shorter term, the bulk of our work involves improvements to metadata handling, especially for regions of interest (ROIs) and analytic metadata. We have been working with several use cases, especially involving super-resolution localisation microscopy (PALM, STORM, dSTORM, etc), high content screening (HCS) and digital pathology, to define common requirements for handling the metadata generated by manual and automatic processing of image data from these different modalities. A discussion of super-resolution data storage (e.g. this thread on the ome-devel mailing list) has helped drive this, as has our ongoing work on publishing large image datasets on the BBSRC-funded Image Data Resource (IDR)1) and participation in several ongoing data-focussed projects (e.g. MULTIMOT and CORBEL). We have already built defined tools for metadata import into the IDR (see the code repository) and will aim to harmonize these with other projects that are collecting metadata on scientific datasets (e.g. BioStudies). Import of metadata from spreadsheets and other text-based tabular formats will be supported, but we will also be supporting more modern, powerful data formats (e.g. HDF5). We will use new resources that provide online services for controlled vocabularies (e.g. EBI’s Ontology Lookup Service).

But next, we want to make ROIs first class citizens in OME’s applications. This means we will add an ‘ROI Folder’ concept, which will allow users and analytic tools to cluster ROIs just like they already do with images and tags. All of these new capabilities will start to appear in OMERO 5.3 (currently scheduled for Spring 2016) and in several point releases through 2016.

  1. At the time of publication, this was referred to as the ‘Image Data Repository’.