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

[Balaji Ramalingam (Staff)]

Hi Kai,

Thank you for submitting your files to our QA system.
Unfortunately, testing the same locally, I was unable to reproduce the bug
locally.

I did record my exporter options using the macro-recorder,

Export as *.tif,
run("Bio-Formats Exporter",
"save=/Users/bramalingam/Desktop/FijiExport/test_5_2_2_export.tif export
compression=Uncompressed²);

Export as *.ome.tif
run("Bio-Formats Exporter",
"save=/Users/bramalingam/Desktop/FijiExport/test_5_2_2_tiffexport.tif.ome.t
if export compression=Uncompressed²);

And in both cases, the resultant image had 2 channels and 50 time points,
that were organised exactly like the parent stack.

Could you please record your export command via the macro-recorder and
send us the resultant macro. This would allow us to troubleshoot the issue
in better detail.

Best,
Balaji

__________________
Mr Balaji Ramalingam
Software Developer

OME Team
School of Life Sciences
University of Dundee






On 14/09/2016, 14:12, "ome-users on behalf of Kai Schleicher"
<ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
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=817ba470200e97
>65b861241874bd8077
>
>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
>
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