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Re: 16bit-TIF with LUT

Posted by ctrueden on Jun 26, 2013; 4:56pm
URL: http://imagej.273.s1.nabble.com/Plugin-for-compiling-all-plugins-tp5003613p5003658.html

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>
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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