I tested this on my system with a fresh Fiji, and after updating, ran into a similar (but not identical) problem. I am guessing it is a bug in the updater.

To work around, please try this:
1. Help > Update Fiji
2. Click "Advanced mode"
3. Change "View Options" to "View all files"
4. Type "slf" into the search
5. Notice "jars/slf4j-log4j12-1.5.10.jar" on the list
6. My problem was that it was set to "Not installed"
7. Right-click it and set it to "Install it"
8. Click "Apply changes"

After restarting Fiji, if you repeat this process, it should then say "Up-to-date" in the "Status/Action" column.

The "jars/slf4j-api-1.5.10.jar" should also be "Up-to-date" -- if not, install it too.

Please let us know if this solves it for you!

Hi - 

Thanks for your help. This fix didn't work for me: jars/slf4j-log4j12-1.5.10.jar is now "Up-to-date", but when I try to open the .nd2 file, I get another error message. I think this one is different from the original one.

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:680)
Caused by: java.lang.NoSuchMethodError: loci.formats.IFormatReader.addStatusListener(Lloci/formats/StatusListener;)V
	at loci.plugins.importer.Importer.run(Importer.java:229)
	at loci.plugins.LociImporter.run(LociImporter.java:77)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.IJ.runPlugIn(IJ.java:141)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:229)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.IJ.runPlugIn(IJ.java:141)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
	at ij.io.Opener.openImage(Opener.java:288)
	at ij.io.Opener.openImage(Opener.java:309)
	at ij.io.Opener.open(Opener.java:138)
	at ij.io.Opener.open(Opener.java:66)
	at ij.plugin.Commands.run(Commands.java:23)
	at ij.IJ.runPlugIn(IJ.java:158)
	... 8 more




(In reply to comment #1)
> I tested this on my system with a fresh Fiji, and after updating, ran into a
> similar (but not identical) problem. I am guessing it is a bug in the updater.
> 
> To work around, please try this:
> 1. Help > Update Fiji
> 2. Click "Advanced mode"
> 3. Change "View Options" to "View all files"
> 4. Type "slf" into the search
> 5. Notice "jars/slf4j-log4j12-1.5.10.jar" on the list
> 6. My problem was that it was set to "Not installed"
> 7. Right-click it and set it to "Install it"
> 8. Click "Apply changes"
> 
> After restarting Fiji, if you repeat this process, it should then say
> "Up-to-date" in the "Status/Action" column.
> 
> The "jars/slf4j-api-1.5.10.jar" should also be "Up-to-date" -- if not, install
> it too.
> 
> Please let us know if this solves it for you!
> 

So your installation has other files missing too. I believe it a problem with the dependencies of the Bio-Formats plugin. That is, some of the JARs it needs are not being installed.

Until we fix it, here is a more thorough workaround:
1. Help > Update Fiji
2. Click "Advanced mode"
3. Change "View Options" to "View uninstalled files only"
4. Select all files on the list
5. Right-click and set them to "Install it"
6. Click "Apply changes"
7. Restart Fiji

Hopefully that will get your file import working. Let us know how it goes.

Sorry to cause all this trouble - I installed all the files, but I am still getting an error message. I think it is the same as the one below.


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:680)
Caused by: java.lang.NoSuchMethodError: loci.formats.IFormatReader.addStatusListener(Lloci/formats/StatusListener;)V
	at loci.plugins.importer.Importer.run(Importer.java:229)
	at loci.plugins.LociImporter.run(LociImporter.java:77)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.IJ.runPlugIn(IJ.java:141)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:229)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.IJ.runPlugIn(IJ.java:141)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
	at ij.io.Opener.openImage(Opener.java:288)
	at ij.io.Opener.openImage(Opener.java:309)
	at ij.io.Opener.open(Opener.java:138)
	at ij.io.Opener.open(Opener.java:66)
	at ij.plugin.Commands.run(Commands.java:23)
	at ij.IJ.runPlugIn(IJ.java:158)
	... 8 more

OK, I am sorry too, because I should have realized that "NoSuchMethodError" indicated not a *missing* file, but a *mismatched version* of a file.

Is it true that your installation is fully up to date? That is, in the Advanced Mode of the Updater, if you select "View updateable files only" the list is empty, right?

Also in the Advanced Mode of Update Fiji, does it tell you that there are any locally modified files ("View locally modified files only")? If so, you could try flagging those for update as well?

The goal here is to get all your JARs updated to the very latest versions from the update site. There should not be any "NoSuchMethodError" messages if we manage to do that.

Audrey, could you click on Help>Report a Bug and paste the lines in a comment to this bug? This should help us greatly to identify the mismatched file version. Thanks!

Lack of feedback suggests that we can safely close this issue.