[ome-devel] Bioformats LOCI Plugin for ImageJ

[Melissa Linkert]

Hi Alex,

> I have some questions about the Bioformats LOCI plugin for ImageJ.
> If I run the 'LOCI Plugins Configuration' command I get a dialog
> where I can see all the Libraries. I am missing some libraries and
> would like to add them.
> 
> I would like to get OMERO Client and OMERO Importer to work. I have
> the latest OMERO client jars but do not know what jars to put where
> for the plugin to see them.
> 
> I cannot determine where the plugin is searching for these libraries
> (and what exact jars I need). I have tried various options such as
> the ImageJ plugins/jars folder, the plugins folder, the jre/lib
> folder, the jre/lib/ext folder and some adjustment of the CLASSPATH.
> No luck.

Unfortunately, the Bio-Formats plugins for ImageJ simply cannot read from
OMERO at the moment.  In the past, you would need have needed to place
ome_tools.jar (from http://loci.wisc.edu/bio-formats/downloads) and
omero_client.jar (which is contained in the 'libs' directory of the
OMERO.clients bundle) in your ImageJ plugins folder.

There are two problems at the moment.  The first is that the code that
interfaces between Bio-Formats and OMERO has not been updated for the 4.3.x
versions.  This is documented on our issue tracking system:

http://trac.openmicroscopy.org/ome/ticket/6376

The second problem is that the Bio-Formats plugins for ImageJ are not at
all connected to the code that reads images from OMERO into Bio-Formats.
This is also documented on our issue tracking system:

http://trac.openmicroscopy.org/ome/ticket/6377

Both tickets are on the roadmap for the upcoming 4.3.2 release.  If you
would like to be automatically notified of updates to either ticket,
please let me know and I will CC you.

> My goal is to have an ImageJ instance that can download images
> directly from an OMERO server.

You might also try OMERO.imagej:

http://www.openmicroscopy.org/site/support/omero4/downloads#section-7

This is another plugin for opening OMERO images in ImageJ, and offers an
interface that looks more like OMERO.insight.

Regards,
-Melissa

On Tue, Jul 26, 2011 at 06:35:06PM +0100, Alex Herbert wrote:
> Hi,
> 
> I have some questions about the Bioformats LOCI plugin for ImageJ.
> If I run the 'LOCI Plugins Configuration' command I get a dialog
> where I can see all the Libraries. I am missing some libraries and
> would like to add them.
> 
> I would like to get OMERO Client and OMERO Importer to work. I have
> the latest OMERO client jars but do not know what jars to put where
> for the plugin to see them.
> 
> I cannot determine where the plugin is searching for these libraries
> (and what exact jars I need). I have tried various options such as
> the ImageJ plugins/jars folder, the plugins folder, the jre/lib
> folder, the jre/lib/ext folder and some adjustment of the CLASSPATH.
> No luck.
> 
> My goal is to have an ImageJ instance that can download images
> directly from an OMERO server.
> 
> Thanks,
> 
> Alex
> 
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