[ome-devel] Fiji opening mvd2 files

[Melissa Linkert]

Hi Aro,

[Please forgive the cross-posting, the original message was forwarded to
multiple mailing lists and I wish to help everyone at once.]

> I used to use Fiji to open the mvd2 files generated by Volocity and things
> worked well. However after a 'comprehensive' update of Fiji the software
> told me that there is no  'reader plugin' for the file and it can not open
> mvd2 anymore. I checked the plugin list the 'loci' plugin in ('Bio-formats'
> the one that could open mvd2 files) is still there and is now a higher
> version. 
> 
> Does anyone of you know what caused the problem and might have a solution?

The error message that you mention suggests that some of the things needed by
Bio-Formats are not installed in Fiji; it also looks very similar to this bug
report on Fiji's issue tracker:

http://fiji.sc/bugzilla/show_bug.cgi?id=488

I was able to duplicate the same behavior by downloading Fiji Madison, and
running the updater ("Help > Update Fiji") until no more updates were available.
Starting the updater once more and searching for "slf4j-log4j" with
"View uninstalled files only" selected should bring up one file; if you
install that and restart Fiji then Bio-Formats should be working again.

The bug report above explains the cause in more detail, but the
important point is that this is not a problem in Bio-Formats, so once
you install the missing .jar you should not need a new version.

Alternatively, you could download one of the "continuous release" builds of
Fiji from:

http://fiji.sc/wiki/index.php/Downloads

...as the bug report above mentions that this was recently fixed.

Regards,
-Melissa

On Sun, Dec 02, 2012 at 07:59:24PM +0100, Aromis wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
> 
> Hello Everyone:
> 
> I used to use Fiji to open the mvd2 files generated by Volocity and things
> worked well. However after a 'comprehensive' update of Fiji the software
> told me that there is no  'reader plugin' for the file and it can not open
> mvd2 anymore. I checked the plugin list the 'loci' plugin in ('Bio-formats'
> the one that could open mvd2 files) is still there and is now a higher
> version. 
> 
> Does anyone of you know what caused the problem and might have a solution?
> 
> Thank you very much for your help in advance.
> 
> Regards,
> 
> Aro