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

[Curtis Rueden]

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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