Open Microscopy Environment

Hi,

Sorry for the long post. I’m new to the topic and a bit overwhelmed by all the projects and possibilities.

I’m working on a project where the users want to create data, store it alongside the information how it was created and later run analysis on that data. Our processing is potentially very time consuming. So we are also looking into doing that on a cluster.

For the storage we want to use Omero. So I started looking around what solutions for our other problems exist that build on that.

I found hints of an Omero.editor, that could be used to store the experiment information. But that information is from the Omero 4.2.2 documentation. http://www.openmicroscopy.org/site/support/omero422/getting-started/tutorial/omero.editor
Was that project discontinued?

For the integration between Omero and a cluster I found a entry in the mailing list.
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-August/002920.html
That leads to a 2-year-old wiki in a git. There is also a discussion in the forums
https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=1051
Which seems like I'm not the first one with that problem.

Also I found hints of Omero.rapid. Including a very promising set of slides:
http://research.nesc.ac.uk/DIR_seminars/Presentation-OMERO-RAPID.pdf
But reading up on that is a bit confusing. There examples are for chemistry. Everything is very light on the connection to Omero. Their screencast video for microscopy seems to have only basic functionality for Omero. Apparently people must input the image by giving its ID.

So to sum up my questions:
Is there work being done on combining a digital lab book with Omero?
Is there work being done for HPC integration with Omero?

Or is that all just very specific work done for individual projects and/or was already discontinued. Because it seems like those are actually pretty common concerns.

Hi
The omero.editor is no longer supported. Editor files were XML files and its usage was limited to the Desktop client. It has been "replaced" by an editable and searchable key-value pairs annotation for adding experimental metadata in 5.1.0 (April 2015). This structure proved to be more flexible and quite powerful. This can be seen as a "light weight editor" available both in the Web and Desktop clients.
See https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/KeyValuePairs.html
For more advanced requirements, it might be preferable to look into existing digital lab books and see the possible extensions points.

The rapid-omero was discontinued: the people involved no longer worked at Edinburgh University.
The latest rapid-omero code can be found here https://github.com/joskoetsier/rapidomero
Other HPC effort can be found athttps://github.com/jjcorreao/OMERO.HPC.

HPC integration with OMERO is certainly an area we are interested in and having your input on use cases/options will be very valuable.

Regards
Jmarie