[ome-users] Preferred color mapping for channels in OME-TIFF

[Dmitry Fedorov]

Thank you guys for a thorough check on my question! I'll start using Color
attribute and also write LUTs. So in most cases things should work fine.
Thank you so much!

-dmitry

On Wed, Apr 29, 2015 at 9:35 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi again Dmitry and everyone,
>
> I spoke with Melissa about the channel coloring issue in ImageJ, and she
> pointed out that this feature should already be working [1].
>
> That is: if you have a Channel Color set in the OME metadata, the
> Bio-Formats Importer in ImageJ should show the associated LUT as expected.
> Please let us know if you experience otherwise.
>
> Regards,
> Curtis
>
> [1] *https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/src/loci/plugins/in/Colorizer.java#L317-L379
> <https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/src/loci/plugins/in/Colorizer.java#L317-L379>*
>
> On Wed, Apr 29, 2015 at 8:09 AM, Stéphane Dallongeville <
> stephane.dallongeville at pasteur.fr> wrote:
>
>>  Hi Curtis,
>>
>> With Icy we were initially relying on the 8/16 bit color table
>> information of Bio-Formats but definitely almost time it's empty or not
>> filled according to the Channel Color field so now we check both
>> informations to provide default image channel color.
>>
>> Best,
>>
>> --
>> Stephane Dallongeville
>> Unité d'Analyse d'Images Biologiques
>> CNRS UMR 3691
>> Institut Pasteur
>> 25 rue du Dr. Roux
>> 75724 Paris cedex 15 (FRANCE)
>>
>> Tel: +33 (0)1 45 68 87 01
>> Fax: +33 (0)1 40 61 33 30
>> http://www.bioimageanalysis.org/
>>
>>
>>
>> Le 29/04/2015 15:01, Curtis Rueden a écrit :
>>
>> Hi Roger,
>>
>> The ImageJ plugin does apply color tables from the reader to the images;
>> see ImageProcessorReader.
>>
>> I think the question is more: does that Channel Color property in the
>> OME-XML get transformed into an 8-bit color table in the relevant
>> Bio-Formats readers? When I checked the code last night I could not find
>> any such logic, but may have missed it.
>>
>> Regards,
>> Curtis
>> On Apr 29, 2015 4:12 AM, "Roger Leigh" <rleigh at dundee.ac.uk> wrote:
>>
>>> On 29/04/15 05:18, Dmitry Fedorov wrote:
>>>
>>>> Hi Roger,
>>>>
>>>> Thank you, the Color property is exactly what I needed! Somehow I missed
>>>> that and I would never have guessed the encoding:) This was super
>>>> helpful! Do you know if bioformats, in ImageJ for example, would pickup
>>>> the stored lookup table and use it for visualization?
>>>>
>>>
>>> Looking at the code in
>>>   components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java
>>> it does get an 8-bit LUT, but then doesn't do anything with it, so it
>>> looks like support on import into ImageJ is unfortunately incomplete at
>>> present, limited to channel colour only.
>>>
>>> We do have a ticket for improving this here
>>>   https://trac.openmicroscopy.org/ome/ticket/12168
>>> as part of the model and code changes needed to improve support for
>>> rendering.
>>>
>>>
>>> Regards,
>>> Roger
>>>
>>> --
>>> Dr Roger Leigh -- Open Microscopy Environment
>>> Wellcome Trust Centre for Gene Regulation and Expression,
>>> College of Life Sciences, University of Dundee, Dow Street,
>>> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>
>>
>> _______________________________________________
>> ome-users mailing listome-users at lists.openmicroscopy.org.ukhttp://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>


-- 
__________________________________

Dmitry Fedorov Levit <dima at dimin.net>
Web: http://www.dimin.net/
__________________________________

Center for Bio-Image Informatics:
  <http://www.bioimage.ucsb.edu/>

Vision Research Lab, Electrical and Computer Engineering:
  <http://vision.ece.ucsb.edu/>

University of California, Santa Barbara
_________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150429/756d9692/attachment.html>