Hi Sebastian,

 Which update sites do you have enabled? It seems odd that the scifio jars are all listed as "Local-only" in your ImageJ Updater window. For me, they all display as "Up-to-date". Fiji/jars/bio-formats/scifio.jar is provided by the Fiji update site (http://fiji.sc/update/)

 I have the ImageJ and Fiji update sites enabled, and after updating everything to the latest versions I'm able to run the Bio-Formats importer with no problems.

 So, there are two different scifio jars:

- in Fiji/jars this is the SCIFIO core (from https://github.com/scifio/scifio)
- in Fiji/jars/bio-formats this is actually the open source Bio-Formats core (from https://github.com/openmicroscopy/bioformats) which unfortunately also has the name scifio, as this is where development of SCIFIO started. This is the jar that should be used by the Bio-Formats importer.

 Also, the jars/bio-formats/scifio.jar should be versioned with the other Bio-Formats jars. In my local /Fiji/jars/bio-formats, I have "scifio-4.4.9.jar".

 Would you mind verifying the Fiji update site is enabled, and then updating those jars? Or if you prefer, you can manually download scifio.jar from http://downloads.openmicroscopy.org/bio-formats/4.4.9/ and put it in Fiji/jars/bio-formats to ensure you have the correct version.

 If that doesn't help, let us know!

- Mark

Sebastian, I suspect your Fiji installation is messed up somehow.

Please see the FAQ entry:
http://fiji.sc/Frequently_Asked_Questions#How_can_I_verify_that_my_Fiji_is_really_100.25_up_to_date.3F

And also try downloading a fresh copy of Fiji from http://fiji.sc/Downloads and double check whether the problem happens with that version as well.

Hi,
I just updated today (2013_12_17) again and the error message is gone. Nevertheless I checked my Fiji folder and found inside: ...\Fiji\jars\

jai_imageio-4.4.9.jar
scifio.jar
specification.jar
turbojpeg.jar

And in ...\Fiji\jars\ I can also find scifio-0.7.1.jar as well.

Here I have the Fiji, Bio-Formats 5 and LOCI update site enabled (among others), but Bio-Formats 4, Bio-Formats daily builds and NewBio-Formats 5 daily Updates are disabled.

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In a fresh installation inside the same folder I have:

jai_imageio-4.4.9.jar
scifio-4.4.9.jar

And in ...\Fiji\jars\ I can also find scifio-0.7.1.jar as well.

Here I have only the ImageJ & Fiji update site enabled.

Having two scifio JARs (one inside bio-formats and outside) is normal. They are actually two different libraries. Yes, I know it is confusing. But there isn't much we can do about it in the short term.

Since this bug report was filed, the Bio-Formats JAR libraries have been renamed to be more clear in their function. There should no longer be two different "scifio" JAR libraries. The only SCIFIO is now the one from https://github.com/scifio/scifio as you might expect.

As for the error message, I assume this problem has long evaporated? So I am closing the bug. But if this is still an issue, please reopen with details of the current situation.

Thanks!