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

[Kai Schleicher]

Hi Balaji,

thanks for testing - sorry it took me so long to come back to you.

The problem appears when I check "write each timepoint to a separate 
file" and "write each timepoint to a separate file". Whats printed in 
the macro recorder is this:

run("Bio-Formats Exporter", "save=[/home/kai/DATA/Benoit for 
Kai/kaistest/test_export_.tif] write_each_timepoint write_each_channel 
compression=Uncompressed");

I do get single *.tifs, but channels and timepoints are mixed up. This 
becomes clear when you open the resulting images. Channel contains phase 
images while channel two should only be fluorescent images.

Cheers,
Kai

On 09/15/2016 05:03 PM, Balaji Ramalingam (Staff) wrote:
> 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=sers/bramalingam/Desktop/FijiExport/test_5_2_2_export.tif export
> compression=compressed²);
>
> Export as *.ome.tif
> run("Bio-Formats Exporter",
> "save=sers/bramalingam/Desktop/FijiExport/test_5_2_2_tiffexport.tif.ome.t
> if export compression=compressed²);
>
> 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7ba470200e97
>> 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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>