[ome-users] LOCI plugins with ND2

[Curtis Rueden]

Hi Michael,


> Bio-Formats... simply does not work with the ND2 files.


Sorry to hear you are frustrated. We do our best to keep Bio-Formats
working, including a rigorous testing process for every release that covers
a huge collection of user-provided sample data. That said, Nikon has
repeatedly changed the ND2 format. It is a game of catch-up to keep things
working with new files, while also avoiding breakage of old files.


> The fix works for a few releases and then gets broken.


Note that you can download old versions of Bio-Formats from the web site:
    http://loci.wisc.edu/software/bio-formats/archive


> p.s.  And what is even more frustrating is that the release from Oct 18,
> 2011 that used to work fine with the Nikon format now crashes.


Did you test with an older ND2 file that you know worked before, or with a
new file? If it was a newer file, this suggests that it is a different in
the ND2 file rather than a mysterious change in Bio-Formats's behavior. If
it was an older file, the breakage could be due to any of several other
factors that changed in the meantime, such as your OS's version of Java
(did you test on the same machine?).

As always, we would be happy to investigate the issue, if you can send a
test file along with details on what went wrong, error message, etc.

Thanks,
Curtis

P.S. In the future, please report problems to the ome-users mailing list
rather than writing private mails.


On Wed, Sep 12, 2012 at 12:52 PM, Cammer, Michael <
Michael.Cammer at med.nyu.edu> wrote:

>  Dear Melissa,****
>
> ** **
>
> This is getting very frustrating.  You know we really appreciate the LOCI
> importer plugins and have been very patient with the problems with the
> Zeiss and Nikon importers, but the importer goes through cycles of working
> and then getting broken again.  We don't find there are problems until we
> need to use the software.  Then it doesn't work and we have to wait for a
> fix.  The fix works for a few releases and then gets broken.  This is a
> recurring cycle.****
>
> ** **
>
> The LOCI tools ****
>
> 4.4.2 (stable release)****
>
> 2012 August 24****
>
> loci_tools.jar <http://loci.wisc.edu/files/software/loci_tools.jar>****
>
> simply does not work with the ND2 files.  Over the last two days we
> collected time lapse at four different stage positions with 2 channels.
> The LOCI importer does not see the stage positions.****
>
> ** **
>
> I have macros to work around this but they have to be tweaked for each
> reordering of the images and we have a large lab of people who either find
> this inconvenient or simply are not computer facile enough to do this.  **
> **
>
> ** **
>
> Can we count on you to make the ND2 importer stable or should we try to
> find another solution?****
>
> ** **
>
> Regards,****
>
> ** **
>
> Michael****
>
> ** **
>
> ________________________________________________________****
>
> Michael Cammer, Assistant Research Scientist****
>
> Skirball Institute of Biomolecular Medicine****
>
> Lab: (212) 263-3208  Cell: (914) 309-3270****
>
> ** **
>
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