[ome-users] Change LUT in OMERO.insight

[Jan Eglinger]

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