[ome-users] Bio-formats exporter bug with .dv file

[Curtis Rueden]

Hi Kai,

> I realised that updating to the latest version is only possible when
> Java 8 is check in the update manager while at the same time
> bio-formats IS NOT checked. If only bio-formats or both are checked,
> then version 5.1.10 is installed.

The Bio-Formats update site is intended for previewing _unreleased and
hence unstable_ versions of Bio-Formats.

Unfortunately, it was still configured to build the 5.1.x development
branch, and hence had fallen out of date compared to the Bio-Formats 5.2.x
releases which have already taken place.

I have now updated it to build the develop branch (currently 5.2.x). So if
you update your Fiji with the Bio-Formats update site enabled, you should
see (as of this writing) Revision 011d303e, with release listed
as"5.2.2-DEV" (note that unlike Maven SNAPSHOTs, this refers to a state
_after_ the 5.2.2 release).

> Since we are also running OMERO, I am a big fan of the omero-fiji
> connector, which works great for me! As we are currently running OMERO
> 5.2.5, I was wondering whether this connector could also be included
> in an update site for fiji. Currently we find only 5.0 and 5.1.

Are you talking about the OMERO-5.0 and OMERO-5.1 update sites, which ship
the ImageJ-OMERO project [1]?

If so, I will try to find time to update that to OMERO 5.2.x.

Regards,
Curtis

[1] https://github.com/imagej/imagej-omero

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Sep 14, 2016 at 6:12 AM, Kai Schleicher <kai.schleicher at unibas.ch>
wrote:

> Hi,
>
> I encountered a bug when using the bio-formats exporter to save individual
> *.tifs  (per channel as well as per timepoint) from a two channel timelaps
> hyperstack recorded on a Deltavision microscope with softworx (*.dv). I
> have uploaded said image as ID 17340 here:
> https://www.openmicroscopy.org/qa2/qa/feedback/17340/?token=
> 817ba470200e9765b861241874bd8077
>
> In detail I believe that channels and timepoints get mixed up as the image
> for Channel 0 timepoint 1 is actually channel 1 timepoint 0 and so on.
>
> I am using the latest bio-formats version 5.2.2.
>
> Concerning this I realised that updating to the latest version is only
> possible when Java 8 is check in the update manager while at the same time
> bio-formats IS NOT checked.
> If only bio-formats or both are checked, then version 5.1.10 is installed.
>
> This seems a bit counter-intuitive to me, if possible I think it'd be
> easiest from a user perspective to keep updating the bio-formats from the
> respective update site.
> Just as a comment, I was also wondering if it'd be possible to show the
> bio-formats version number in the splash screen of the importer? This way
> it'd easier for our facility users to find out which version they have
> installed.
>
> Since we are also running OMERO, I am a big fan of the omero-fiji
> connector, which works great for me! As we are currently running OMERO
> 5.2.5, I was wondering whether this connector could also be included in an
> update site for fiji. Currently we find only 5.0 and 5.1.
>
> Thanks for your help and cheers,
> Kai
>
> --
>
> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy |
> Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
> Phone: +41 61 267 22 50 | kai.schleicher at unibas.ch |
> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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