[ome-users] ImageJ plugin in 4.4-RC2

[Will Moore]

Hi Harri,

 In 4.4 the OMERO imageJ plugin includes all of Insight.
I think you tried to download the old plugin - I also made the same mistake (I think it needs cleaning up). 

When you double click an Image in the Insight ImageJ plugin, the image opens in ImageJ, so you can do your usual analysis etc.

I believe the idea of including Insight in the plugin is that developers have access to the OMERO Java Gateway code, and users have a better experience of browsing & managing their images, but still have Image for analysis etc. 

 Cheers,

  Will. 



On 12 Jul 2012, at 11:44, Harri Jäälinoja wrote:

> Hi Will,
> 
> thanks, this helped, Insight opens and I can login to OMERO. Sorry, I was just confused about how to install the plugin.
> 
> So basically this is another way to distribute/install the Insight client? I had the idea the plugin would somehow allow you to select images from OMERO for processing.
> 
> Hmm, now if I try to download a project or a dataset or a single image from Insight, the "Download" item I get by right-clicking on the file-tree on the left is not active. I wonder why?
> 
> Thanks,
> Harri
> 
> 
> On 12/07/12 13:19, Will Moore wrote:
>> Hi Harri,
>> 
>> You say "Something happens..." but it's still not working (stack trace), right?
>> 
>> I just downloaded and updated Fiji, then downloaded hudson.openmicroscopy.org.uk/job/OMERO-trunk/lastSuccessfulBuild/artifact/src/target/OMERO.insight-ij-4.4.0-RC2-217-a46c0f5-ice33-b3030.zip
>> and put the entire OMERO.ij-4.4.0-RC2-217-a46c0f5-ice33-b3030 folder into the Fiji plugins folder.
>> 
>> This worked fine for me,
>> 
>>  Hope that helps,
>> 
>>   Will.
>> 
>> 
>> 
>> 
>> On 12 Jul 2012, at 10:12, Harri Jäälinoja wrote:
>> 
>>> 
>>>>> http://hudson.openmicroscopy.org.uk/job/OMERO-trunk/3028/artifact/src/targ
>>>>> et/OMERO.insight-ij-4.4.0-RC2-188-da0c55d-ice33-b3028.zip
>>>>> 
>>>>> You'll still need the new loci_tools.jar.
>>>> 
>>>> And ome-io.jar installed in the ImageJ/Plugins folder in order to work.
>>>> 
>>> 
>>> 
>>> Hi,
>>> 
>>> I first reinstalled Fiji, to be sure, and updated it. Then:
>>> 
>>> hajaalin at dh2-bll10-06:~$ cp Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/omero_ij.jar Fiji.app/plugins/
>>> hajaalin at dh2-bll10-06:~$ cp Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/libs/ome-io.jar Fiji.app/plugins/
>>> 
>>> hajaalin at dh2-bll10-06:~$ wget http://hudson.openmicroscopy.org.uk/view/Bio-Formats/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar
>>> hajaalin at dh2-bll10-06:~$ mv loci_tools.jar Fiji.app/plugins/
>>> 
>>> hajaalin at dh2-bll10-06:~$ Fiji.app/fiji-linux64
>>> Re-executing with correct library lookup path (/home/hajaalin/Fiji.app/lib/linux64)
>>> 
>>> 
>>> Now the OMERO plugin menu item is different, says "Connect to OMERO". When I select it, nothing happens.
>>> 
>>> Then I looked at the jar files in Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/libs/, and I noticed that for example TableLayout.jar and JHotDraw.jar are not in Fiji.app/plugins or Fiji.app/
>>> 
>>> To be sure (or maybe to overdo), I did like this:
>>> hajaalin at dh2-bll10-06:~$ cp Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/libs/* Fiji.app/plugins/
>>> 
>>> Now something happens when I select OMERO plugin, so maybe it's a matter of getting the jars right?
>>> 
>>> Cheers,
>>> Harri
>>> 
>>> 
>>> java.lang.reflect.InvocationTargetException
>>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>> 	at java.lang.reflect.Method.invoke(Method.java:597)
>>> 	at ij.Command.runPlugIn(Command.java:146)
>>> 	at ij.Command.runCommand(Command.java:95)
>>> 	at ij.Executer.run(Executer.java:64)
>>> 	at java.lang.Thread.run(Thread.java:662)
>>> Caused by: java.lang.RuntimeException: Failed to intialize the Container in test mode.
>>> 	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:414)
>>> 	at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:160)
>>> 	at ij.IJ.runUserPlugIn(IJ.java:185)
>>> 	at ij.IJ.runPlugIn(IJ.java:152)
>>> 	... 8 more
>>> Caused by: org.openmicroscopy.shoola.env.init.StartupException: Unable to load Container configuration
>>> 	at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(ContainerConfigInit.java:100)
>>> 	at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:255)
>>> 	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:409)
>>> 	... 11 more
>>> Caused by: org.openmicroscopy.shoola.env.config.ConfigException: An error occurred while attempting to process /home/hajaalin/Fiji.app/plugins/config/container.xml. (/home/hajaalin/Fiji.app/plugins/config/container.xml (No such file or directory))
>>> 	at org.openmicroscopy.shoola.env.config.Parser.rethrow(Parser.java:105)
>>> 	at org.openmicroscopy.shoola.env.config.Parser.parse(Parser.java:173)
>>> 	at org.openmicroscopy.shoola.env.config.RegistryFactory.fillFromFile(RegistryFactory.java:102)
>>> 	at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(ContainerConfigInit.java:84)
>>> 	... 13 more
>>> Caused by: java.io.FileNotFoundException: /home/hajaalin/Fiji.app/plugins/config/container.xml (No such file or directory)
>>> 	at java.io.FileInputStream.open(Native Method)
>>> 	at java.io.FileInputStream.<init>(FileInputStream.java:106)
>>> 	at java.io.FileInputStream.<init>(FileInputStream.java:66)
>>> 	at org.openmicroscopy.shoola.util.file.IOUtil.readConfigFile(IOUtil.java:262)
>>> 	at org.openmicroscopy.shoola.env.config.Parser.parse(Parser.java:156)
>>> 	... 15 more
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>> 
> 
>