Re: 16bit-TIF with LUT

Posted by ctrueden on Jul 10, 2013; 6:22pm
URL: http://imagej.273.s1.nabble.com/Plugin-for-compiling-all-plugins-tp5003613p5003900.html

Hi Peter,

> My idea was to use 8bit LUTs in 16bit TIFF files.
> Maybe this is already possible and I just mist some ImageJ options.

Sorry if my long-winded response made it unclear. In brief:

* It is not possible with ImageJ
* It is not possible with the TIFFs at all
* It is not possible with PNGs, or *any* other graphics format I know of

Regards,
Curtis


On Sun, Jul 7, 2013 at 1:05 AM, Peter Haub <[hidden email]> wrote:

> 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<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<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
>>>>
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>>>> <
>>>>
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