The OME Blog Because metadata is worth a thousand pictures

OME Project Status Update

The year so far…

2017 has been a very busy year for the OME team so far with:

  • 2 major OMERO releases plus 6 security or patch releases - introducing ROI Folders, a whole new UI layout for HCS data, a configurable restricted admin user role and many other fixes and improvements
  • 12 Bio-Formats releases to date (and another in the pipeline) - featuring 2 new formats and improved support for many more
  • 4 OME Files C++ releases - improving support for reading and writing OME-TIFF in an open, liberally-licensed, native library
  • 4 OMERO.figure releases - adding support for loading ROIs and choosing look-up tables from OMERO, using markdown syntax for italics and bold labels, setting background colors, plus other fixes and improvements
  • various other web app releases - all now available from PyPI, including OMERO.FPBioimage, a volumetric visualization tool
  • the launch of our new OMERO.iviewer - a web browser-based interactive multidimensional image viewing app that includes ROI drawing and measurement functionality. OMERO.iviewer is approaching a full v1.0 release, a sign of our commitment to maintaining and growing the functionality in this app
  • AND a new website!

Plus of course, our usual Annual User Meeting bringing together members of the community from across the globe (if you couldn’t make it, talks and workshops are available from the event page).

The Image Data Resource (IDR) also continues to go from strength to strength. If you missed it, our Nature Methods paper (or the open access PubMedCentral version) discusses how the IDR can be used to obtain new biological insights from existing datasets, plus an in-depth explanation of how the resource is set up. It also includes information on how you can set up your own IDR.

With all that, hopefully you’ll forgive us for neglecting this blog!

What’s still to come…

We’re running two days of Bioinformatics training at Cambridge University in December. In the run up to this, we’ll be developing new training materials which will all be available via our website for those of you who can’t attend. We’ll also be expanding our collection of Jupyter notebooks providing you with examples of how to carry out image analysis via the OMERO API and likely adding to our collection of how-to movies on our YouTube channel. The IDR will also be updated, publishing several new datasets (our first light sheet fluorescence microscopy dataset is almost ready to go!) and improvements to the Jupyter analysis tools.

In terms of releases, we expect to put out patch releases for OMERO, Bio-Formats and OME Files. As always the content of these will be driven by both the community and our own projects, for example the IDR continues to challenge us in terms of format support and display, and the way our tools connect and interact with analysis packages. You can always keep up with the latest upcoming releases and more via our Trello boards (you can sign up here with just an email address).

Beyond this, we are continuing to push forward our functionality and the scale at which our tools operate. As imaging technology takes huge leaps in scale, this is challenging to say the least and we’ll need the support of the community more than ever. If you have resources to contribute, we’d love you to get involved - write to the mailing lists or forums, check out our contributing developer docs, read our blog posts on helping us support new file formats. Even if you don’t have resources to spare, you can always help us secure grant funding by citing our work in your publications.