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

[Curtis Rueden]

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
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>
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