Dear All-
Happy Monday!
We are just writing to update you on our progress on OMERO-Beta4.0. This is a big step for us– in Beta4, we are making major changes in the way the OMERO server and clients work, how they communicate with one another, and most importantly, the level of functionality that OMERO delivers. This has been a very ambitious release, based on feedback we’ve had from the community, and most importantly, positions us for the functionality we are scheduling over the next year. Some highlights:
– we have switched our clients completely over to using the ICE framework and entirely removed any dependency on JBOSS. This is a big change, removes a substantial amount of overhead, and simplifies our communications.
– we are releasing a brand new client, OMERO.web. This is our first step in developing and releasing a fully functional web browser-based client.
– we have worked very hard on data import, providing a command line data import facility, full metadata support for Zeiss LSM510, Zeiss ZVI, Leica LEI, API DeltaVision, Metamorph STK files, and substantial acceleration of the data import process.
– we are releasing another new client of OMERO, called OMERO.fs. In its first release, OMERO.fs is a file notification system– it can monitor specified file systems for arriving image files and initiate import for any new files that appear. Currently, this uses our existing import facility– all data is read into and stored within an OMERO server. More sophisticated functionality, including support for multiple repositories and new modes of data import will come in future versions.
– OMERO.insight has been substantially accelerated, includes support for much more metadata, an improved projection interface, and now fully integrates OMERO.editor. OMERO.editor has been substantially updated as well, to support very unstructured experiments (e.g., protocols from existing .doc files).
– for the first time, OMERO will support deleting of images. This is a real “it is truly gone” delete.
As you can imagine, we are now testing Beta4 internally and trying to identify any bugs. You can follow our progress at:
http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4
http://trac.openmicroscopy.org.uk/shoola/milestone/OMERO-Beta4
As we have accelerated and stress-tested OMERO (e.g., working with 1000’s of images at once), we have seen some problems. Most have been fixed, but one of the most insidious is described at:
http://trac.openmicroscopy.org.uk/shoola/ticket/845
Note that this is all due to fundamental problems in Java, which affect a number of parts of OMERO.server and OMERO clients. These bugs were first reported months ago and Sun seems to think they are low priority. We, like others, have spent many hours tracking these problems, only to track them to Java’s underlying libraries. We are examining alternative solutions. This problem appears as “out of memory” errors in OMERO.insight, especially when viewing large numbers of images. We will provide some workarounds in our documentation at release.
Our current timeline shows us packaging a Beta4 release candidate next Monday (March 2) for testing. We’ll announce this on this blog, with links to the latest versions of the OMERO clients, and provide a demo server for Dundee users to play with,
Thanks to all for your patience and feedback– we really do value your comments, and especially any and all constructive criticism.
–jason