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Re: 16bit-TIF with LUT

Posted by Peter Haub on Jul 07, 2013; 6:05am
URL: http://imagej.273.s1.nabble.com/Plugin-for-compiling-all-plugins-tp5003613p5003799.html

Thanks Nikolay
and Thanks Curtis
for your detailed feedback.

My idea was to use 8bit LUTs in 16bit TIFF files.
Since ImageJ offer 8bit LUT support for displayed 16bit images and since
16bit images are mapped to 8bit during opening in ImageJ I thought that
it could also be possible to save the 8bit LUT in the 16bit TIFF and to
apply it during opening.

Maybe this is already possible and I just mist some ImageJ options.

Regards,
Peter


On 26.06.2013 18:56, Curtis Rueden wrote:

> Hi Nikolay & everyone,
>
>> I don't think it is possible to save TIFF with LUT inside the file.
> You can, but only for 8-bit indices. See the TIFF6 specification [1], Part
> 1, Section 5: "Palette-color Images". You can save such indexed color
> images using ImageJ's File > Save As > TIFF, or using the Bio-Formats
> Exporter plugin [2].
>
> However, if you have 16-bit indices, TIFF does not support that. The funny
> thing is that TIFF's ColorMaps are actually 8-bit indices into 48-bit RGB
> triples (so each of red, green and blue range from 0-65535). But that is
> the "wrong direction" if you want to have a color table with 65536 elements
> mapped to either 24-bit or 48-bit RGB triples.
>
> Unfortunately, I do not know of any general image formats that support
> 16-bit color tables. There are some proprietary microscopy formats that do,
> and Bio-Formats supports importing them, but will not export to such
> formats. Neither of the two most promising common graphics formats, TIFF
> and PNG, support it.
>
> For ImageJ2 we can add some custom metadata to the TIFF (like ImageJ1 does
> for hyperstacks), to preserve the LUTs. But then they would only be written
> & read by SCIFIO-based software [3], not all image processing software.
>
> Regards,
> Curtis
>
> [1] http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf
> [2] http://fiji.sc/Bio-Formats
> [3] http://scif.io/
>
>
> On Wed, Jun 26, 2013 at 7:24 AM, Nikolay Rogoshchenkov
> <[hidden email]>wrote:
>
>> I don't think it is possible to save
>> TIFF<http://en.wikipedia.org/wiki/Tagged_Image_File_Format>with LUT
>> inside the file.
>>
>> --
>> Rogoshchenkov Nikolay
>>
>>
>> On Wed, Jun 26, 2013 at 5:01 AM, Peter Haub <[hidden email]> wrote:
>>
>>> Dear List,
>>>
>>> in ImageJ (1.47q)  I saved a 16bit TIF image with a Color-LUT.
>>>
>>> Problem: The LUT will not be stored in the file.
>>>
>>> Is the a something I can fix with configuration settings, is this feature
>>> not supported in ImageJ or is this not an option in the TIF format?
>>>
>>> Peter
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<
>> http://imagej.nih.gov/ij/list.html>
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>>
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