[ImageJ-devel] [ome-devel] ImageJ-OMERO status update

Jason Swedlow j.r.swedlow at dundee.ac.uk
Thu May 22 05:45:53 CDT 2014

Hi Curtis-

Thanks for this update. This is very exciting, and will be hugely useful for the community.

Look forward to seeing you in Paris!!!



Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

Phone:  +44 (0) 1382 385819
email: j.swedlow at dundee.ac.uk<mailto:j.swedlow at dundee.ac.uk>

Web: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org<http://openmicroscopy.org/>

From: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden
Sent: Monday, May 19, 2014 5:43 PM
To: OME-devel mailing list; ImageJ Developers
Cc: Johannes Schindelin; William Moore
Subject: [ome-devel] ImageJ-OMERO status update

Hi everyone,

Here is a quick status update on the ImageJ-OMERO project, which seeks to provide access to ImageJ algorithms from the OMERO server side -- as well as to allow access to an OMERO database from the ImageJ application.

I have overhauled the ImageJ-OMERO installation procedure (for "installing" ImageJ into an OMERO server). The installation is now much simpler and more stable. It downloads the latest Fiji and enables the OMERO-5.0 update site, which always ships known-working JARs. All updates will be pushed via that OMERO-5.0 update site, which is consistent with how everything else in the ImageJ/Fiji world works.

Jython is also no longer necessary. The integration works via Python like other OMERO scripts.

For full installation instructions, see:

Today I will be hammering on some of the more egregious bugs, in the hope of closing out the 0.1.0 milestone and doing the first stable release. I will also be ensuring that it is possible to execute ImageJ scripts and ImageJ 1.x plugins, in addition to only ImageJ2 commands. After that, I'll work on completing integration of ImageJ results tables with OMERO.tables.

Further details on priorities at:

Adventurous developers are welcome to give it a try -- ImageJ2 commands worked from OMERO.web in my tests over the weekend, although there is also a user report of image-related commands not working [1].

I'll send another mail when 0.1.0 has been released.


[1] https://github.com/imagej/imagej-omero/issues/36#issuecomment-43472610

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