Open Microscopy Environment

Hi

I followed the installation instructions on http://help.openmicroscopy.org/imagej.html#imagej4 to access OMERO via ImageJ. Then I Plugin > OMERO > Connect .. and get the message "WARNING The plugin requires loci_tools.jar. Download ...." although this jar file in already in the plugin folder of ImageJ.

I did the same for Fiji - and in Fiji it works perfectly (because Fiji has already loci tools installed?)

Can anyone help?


Frank

Hi Frank,

What versions of the plugins have you been using?
I've tried ImageJ 1.47r on OS X 10.8 with the loci_tools.jar from http://downloads.openmicroscopy.org/bio-formats/4.4.10/ and OMERO.insight-ij from http://downloads.openmicroscopy.org/omero/4.4.10/. After saving the plugins in the "plugins" directory in ImageJ, connecting to OMERO worked without any problems.

I'd suggest re-downloading the .jar an .zip files and overwriting the ones that you downloaded before.
If that doesn't help, please get in touch and we will try to help you with this issue.

Regards,
Blazej

Hi Blazej

I use ImageJ 1.47v [Java 1.6.0.24 64-bit] on Scientific Linux. I have overwritten the files. In the plugins is the loci_tools.jar (ca. 9.6 MB) and a folder OMERO.insight-ij-4.4.10-ice35-b112 with two subdirectories and an omero-ij.jar file.

After installation the are two sub-menus in the menu "Plugins": LOCI and OMERO. The WARNING is still the same: "WARNING The plugin requires loci_tools.jar. Download ...." .

I tried to open "Plugins> LOCI > Bio-Format Importer". That works. But if I open "Plugins>LOCI>LOCI Plugins Configuration" there are the following error messages on the console.

Frank

MERO client libraries not found. Please obtain omero-common.jar and omero-client.jar from http://dev.loci.wisc.edu/svn/java/trunk/jar/
loci.common.ReflectException: No such class: ome.system.ServiceFactory
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:162)
at loci.ome.io.OMEUtils.createReflectedUniverse(OMEUtils.java:84)
at loci.ome.io.OMEUtils.<clinit>(OMEUtils.java:71)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at loci.plugins.config.LibraryEntry.<init>(LibraryEntry.java:98)
at loci.plugins.config.LibraryEntry.<init>(LibraryEntry.java:76)
at loci.plugins.config.ConfigWindow.run(ConfigWindow.java:429)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NoClassDefFoundError: org/springframework/beans/BeansException
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:247)
at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:158)
... 8 more
Caused by: java.lang.ClassNotFoundException: org.springframework.beans.BeansException
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
... 11 more

Hi Frank,

I'm sorry to hear that you're still experiencing issues with the ImageJ plugin.
I've tried reproducing your setup and installed Scientific Linux in a VM on top of the OS X host system.
Then I've downloaded ImageJ (1.47v), unzipped and followed the loci_tools.jar installation path as before. I managed to reach the OMERO.insight login screen without any warnings...

Could it be that there are some permissions issues with the OMERO .zip and .jar files? Have you tried using a fresh ImageJ zip from http://imagej.nih.gov/ij/download.html?

Regards,
Blazej

Hi

The permission are:
-rw-r--r-- for loci_tools.jar
drwxr-xr-x for the OMERO folder

I download the jar and zip files on a Windows system and unzipped the zip file under windows - and then transferred it to my Linux system.

Hmmm.... At the moment I will use the Fiji system because it is working. I will try to find the problems. Once I have found them, I can post the solution here in the forum.

Frank