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Fiji opening mvd2 files

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Aromis Storm

Fiji opening mvd2 files

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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

Melissa Linkert-2

Re: Fiji opening mvd2 files

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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

Aromis Storm

答复: Fiji opening mvd2 files

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Thanks to Melissa the problem was solved in the way as it was described.

Many thanks for sharing the experience.

Regards,

Aro

-----邮件原件-----
发件人: Melissa Linkert [mailto:[hidden email]] 代表 Melissa
Linkert
发送时间: Montag, 3. Dezember 2012 23:15
收件人: Aromis
抄送: [hidden email];
[hidden email];
[hidden email]; [hidden email];
[hidden email]
主题: Re: Fiji opening mvd2 files

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:

('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