[ome-users] Change LUT in OMERO.insight

[Curtis Rueden]

Hi Jan,

> FWIW, I justed tried to setup my own omero update site

Thanks for giving that a shot.

> If you know a workaround for the second issue, I'd be happy to hear it

Nope, the OMERO plugin code needs to be changed, to conform to the ImageJ
updater's requirements.

For now, my first priority will be getting the OMERO-5.0 update site
serving the ImageJ-OMERO code -- I think I won't worry about the
OMERO.insight ImageJ plugin for the time being.

Regards,
Curtis


On Thu, Apr 3, 2014 at 10:22 AM, Jan Eglinger <jan.eglinger at gmail.com>wrote:

> Dear Josh,
>
> thanks for your reply.
>
>
> On 03.04.2014, 1:19 PM, Josh Moore wrote:
>
>> On Apr 2, 2014, at 5:19 PM, Jan Eglinger wrote:
>>
>>> 2) May I suggest to create a Fiji update site [1] for OMERO? Currently,
>>> there is the Bio-Formats update site, but for installing the OMERO plugin,
>>> you still need to manually copy the folder into ./Fiji.app/plugins
>>>
>>
>> It's something we've been wanting to do for quite some time. I filed
>> another ticket and CC'd you so that you'll get a notification of when it's
>> done:
>>
>> http://trac.openmicroscopy.org.uk/ome/ticket/12167
>>
>>
> Oh, Curtis has kindly marked this as a duplicate of this existing ticket:
> http://trac.openmicroscopy.org.uk/ome/ticket/9342
>
> FWIW, I justed tried to setup my own omero update site to serve some
> computers in our lab, and I hit two issues:
>
> 1) In the downloaded OMERO.insight-ij folder, there are a bunch of jar
> files in ./lib that duplicate Fiji's own dependencies. I was able to delete
> the following jars whose versioned counterparts are in Fiji.app/jars/ (and
> therefore would not be necessary on the update site):
>
>         commons-codec.jar
>         commons-io.jar
>         ij.jar
>         jcommon.jar
>         jfreechart.jar
>         JHotDraw.jar
>         jna.jar
>         joda-time.jar
>         JWiz.jar
>         kryo.jar
>         native-lib-loader.jar
>         netcdf.jar
>         perf4j.jar
>         slf4j-api.jar
>         xalan.jar
>
> (There might be more however. commons-lang.jar is a special case, since
> the package name 'org.apache.commons.lang3' in the current Fiji version
> differs from the older version in omero-ij 'org.apache.commons.lang')
>
> 2) The xml files in ./config are ignored by the updater, since only java
> and script files are recognized in subdirectories of plugins/ . A solution
> might be to serve the config files in Fiji.app/lib/ , but this would
> require a change in the config file loading mechanism. The other option is
> to allow xml files in subdirectories of plugins/ , but it would require
> changing the updater, and is against the current policy of allowing only
> plugin and script files there.
>
> If you know a workaround for the second issue, I'd be happy to hear it : )
>
> Cheers,
> Jan
>
>
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