This is the CZI file:

https://dl.dropboxusercontent.com/u/62347/Count_Cells_DAPI_10_Frames_with_Fiji.czi

The NoSuchMethodError nearly always indicates a mismatch between JAR file versions. Can you please verify that your Fiji is 100% completely up to date?

http://fiji.sc/Frequently_Asked_Questions#How_can_I_verify_that_my_Fiji_is_really_100.25_up_to_date.3F

Also, that Dropbox link gives a 404 for me.

Ok, strange: Here is a link again:

https://db.tt/lJqYrJYI

This links works for me. So I started the updater again and there were some updates for the updater. 

View Uninstalled Files Only: None
View Locally Modified Files Only: None
View Local-only Files: Tons

Most files of the last category are are scripts, macros and some class files from manually added class files. But I am almost 100% sure all those files are also present in the working version of Fiji...

Any ideas?

It might be due to a clash of shadowed files between update sites. Which update sites do you have enabled?

That said, I tested with plain Fiji (only ImageJ + Fiji update sites), Fiji + TrackMate-dev, Fiji + SLIM Curve, and Fiji with lots of stuff (Bio-Formats + Cookbook + FFMPEG + LOCI + ScientiFig + SLIM Curve + Stowers). All of these successfully opened your test file on my system.

From the stack trace, the problem stems from your version of the Bio-Formats plugins library. The library currently lives in bio-formats_plugins.jar; previously, it lived in a file called loci_plugins.jar.

Can you please press L, run the "Find Jar for Class" command, and type in: "loci.plugins.in.ImportProcess"? In a normal installation, the log will say:

    The class loci.plugins.in.ImportProcess is contained in /Applications/Science/Fiji-Default.app/plugins/bio-formats_plugins-5.0.1.jar

Hi Curtis,

There is no "Find JAR for Class" command when pressing L (Find window ...) on my machine. How can I get it?

Sebi

> There is no "Find JAR for Class" command

It is a Beanshell script served from the update site.

Can you please call Help>Update Fiji and make sure that your Fiji is fully up-to-date? I mean, really fully up-to-date (check in advanced mode, view all files, sort by status by clicking on the respective column, verify that there are no "Not Installed" files apart from the platform-dependent launchers).

After that, it would be *really* helpful if you could paste the information auto-generated by Help>Report a Bug. This would prevent a lot of "do you have X" - "yes" - "which version" - "D/M/Y" - "that's not up-to-date" - "it is" - "do you have update site Y enabled" - "yes" - "that explains it" type of conversation (with appropriately patience-taxing delays between responses due to timezone differences).

Created attachment 154
Bug Report Output

All updates site seem to be down (for me) when I tried to check all files again (17pm CET) .... So I cannot check if there any uninstalled filed. But I update my Fiji more or less every day, when I am at work.

I will try this again on Monday.

Sorry for the inconvenience,

Sebastian

Hi,

so I did downloaded a fresh Fiji today (2014_06_02 9am CET) - NoJRE Version tried to open the test dataset using BioFormats Importer

- Fresh Version --> OK, file open correctly

From here on I added my favorite update sites one by one to pin the problem down.

- MosaicTools added --> OK
- BioFormats5 added --> OK
- Trackmate-Dev added (tons of file are installed) --> NOK, here I get the error message, when I try to open the same file as before.

I hope it helps you guys to solve this issue.

Cheers, Sebi

Error Message:

There was a problem with the class loci.common.RandomAccessInputStream which can be found here:
/C:/Users/Public/DOCUME~1/FIJI_N~2/jars/bio-formats/formats-common-5.0.0.jar
/C:/Users/Public/DOCUME~1/FIJI_N~2/jars/formats-common-5.0.0.jar
/C:/Users/Public/DOCUME~1/FIJI_N~2/plugins/Mosaic_ToolSuite/Mosaic_ToolSuite.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: loci.common.RandomAccessInputStream.<init>(Ljava/lang/String;I)V
	at loci.formats.in.ZeissCZIReader.readSegments(ZeissCZIReader.java:942)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:483)
	at loci.formats.FormatReader.setId(FormatReader.java:1319)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:722)

This is no longer happening, correct? There were updates to the MOSAIC update site that should fix this particular problem... (feel free to mark this ticket as resolved if it works now).

Works fine now.