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

[Balaji Ramalingam (Staff)]

Hi Kai,

Thank you for explaining your issue in better detail.

I was able to reproduce the issue and have created a ticket for the same,
https://trac.openmicroscopy.org/ome/ticket/13287#ticket

You have been added to the cc list and will be notified when there is a
status change on the ticket.

For the time being,
Export as ome-tiff seems to work without any issues.
Hopefully that can be used as a work-around for the time being.

Hope that helps.

Best,
Balaji



__________________
Mr Balaji Ramalingam
Software Developer

OME Team
School of Life Sciences
University of Dundee






On 22/09/2016, 17:18, "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 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
>>
>


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