OMERO plugin error in Fiji

First-time user of Fiji and downloaded everything afresh. Followed the OMERO instructions for adding the plugins and all seemed fine except I get the following error when trying the plugins->OMERO->Connect to OMERO.

It is complaining that “/Applications/” doesn’t exist which is correct, there is no file with that name in my installation. Can I have some help to fix this, please?


(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_202 [64-bit]; Mac OS X 10.14.6; 110MB of 4085MB (2%)

java.lang.RuntimeException: Failed to initialize the Container in plugin mode.
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(
at ij.IJ.runUserPlugIn(
at ij.IJ.runPlugIn(
at ij.Executer.runCommand(
Caused by: org.openmicroscopy.shoola.env.init.StartupException: Unable to load Container configuration
at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(
at org.openmicroscopy.shoola.env.init.Initializer.doInit(
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(
… 7 more
Caused by: org.openmicroscopy.shoola.env.config.ConfigException: An error occurred while attempting to process /Applications/ (/Applications/ (No such file or directory))
at org.openmicroscopy.shoola.env.config.Parser.rethrow(
at org.openmicroscopy.shoola.env.config.Parser.parse(
at org.openmicroscopy.shoola.env.config.RegistryFactory.fillFromFile(
at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(
… 9 more
Caused by: /Applications/ (No such file or directory)
at Method)
at org.openmicroscopy.shoola.util.file.IOUtil.readConfigFile(
at org.openmicroscopy.shoola.env.config.Parser.parse(
… 11 more

Bump. Anyone know where the problem is here, please?

Hi Chris
When you unzip, you need to copy the entire folder under the plugins directory of Fiji.

We are working on simpler approach. it should be in the next release.



Ah, no. That now brings me to the OMERO login. Thanks! :+1:

However, OMERO logins are failing with Fiji. “Error: System Failure”. OMERO.insight and OMERO.web are working.

Which version of Fiji are you using?

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_202 [64-bit]; Mac OS X 10.14.6;

I downloaded it on Friday.

Checked for updates and everything is up-to-date. There’s also no blitz.jar (or similar) in the plugins directory.

Interestingly after as restart of Fiji the OMERO login first failes with a username/password error, but on retrying gives the “Error: System Failure”. I’m pretty sure I didn’t have any typos either time.

Any other suggestions? Thanks for the help so far.

Could you check the “jars” directory just in case?

I have installed the latest version of Fiji, and the latest version of the OMERO/imageJ plugin and I was able to connect.
Still digging

OK. I started afresh. Deleted Fiji. New download of Fiji, copied OMERO whole directory into Fiji plugins and ran it.

Still got the incorrect username/password first time - it wasn’t - and then system error the second.

Then, I checked for ImageJ updates and 1.52q was pending (1.52p was instaled). Applied the update and now OMERO works fine!

So got there in the end. Thanks for the help.