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

[Stéphane Dallongeville]

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 
> <mailto: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
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