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

[Curtis Rueden]

Hi again Kai,

> I will try to find time to update that to OMERO 5.2.x.

I cut a new release of ImageJ-OMERO (0.4.0) built on OMERO 5.2, and
uploaded it to a newly created OMERO-5.2 update site.

Note that this initial 5.2-compatible version is only very lightly tested.
Please give it a try and let us know how it goes!

Regards,
Curtis

--
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 2:49 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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 branch, and hence had fallen out of date compared to the Bio-Formats 5.2.x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
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>>
>
>
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