Re: TIFF 12bit / 16bit display / conversion problems

Posted by Wayne Rasband on Apr 07, 2008; 9:18pm
URL: http://imagej.273.s1.nabble.com/TIFF-12bit-16bit-display-conversion-problems-tp3696612p3696613.html

Add these two macros to ImageJ/macros/StartupMacros.txt and you will be
able to set the display range of all open images to 0-4095 by pressing
F1 and generate a 0-4095 histogram by pressing F2.

   macro "Display 0-4095 [f1]" {
      for (n=1; n<=nImages; n++) {
         selectImage(n);
         setMinAndMax(0, 4095);
      }
   }

   macro "Histogram 0-4095 [f2]" {
      setKeyDown("alt");
      run("Histogram", "bins=256 x_min=0 x_max=4095 y_max=Auto");
   }

-wayne


On Apr 7, 2008, at 11:40 AM, Guenter Giese wrote:

> Dear list members,
>
> We record a lot of images with PCO/Cooke CCD cameras (Sensicam QE,
> 12bit).
> The images are acquired as 12bit images (grey value range 0 to 4095)
> and
> saved in 16 bit format. Obviously the 16 bit storage format uses the
> lower
> range 0 to 4095 only thereby not changing the brightness values
> recorded.
>
> When opening these images in ImageJ, the image (display) contrast is
> changed
> / scaled (even when one unchecks the "Edit>Options>Conversion>Scale
> When
> Converting" option before). The values displayed for the pixels under
> the
> mouse cursor still seem to have the "correct" (original 12bit) values,
> but
> the histogram shows that the brightness values are scaled /
> Brightness/Contrast adjusted into the 8 bit display range. Saving as
> 16 bit
> and reloading does not help.
>
> Is there a way to convert the original values linearly from the 12 bit
> to
> the 16 bit range (from 0-4095 to 0-65536) in ImageJ itself or with a
> plugin?
> Maybe during loading?
>
> And is it possible to direct the display and the histogram to
> represent the
> values in respect to the total range (12 bit), or converted to 16 bit
> (for
> display only: linearly scaled to 8 bit without Brightness/Contrast
> adjustment)?
>
> There may be some other programs available to do the conversion job.
> However, many people at our institute would like to do complete
> handling of
> images and image analysis in ImageJ.
>
> Having this option in ImageJ would facilitate our work a lot.
>
>
> Best,
>
> Guenter
>
> ------------------------------------------
> Dr. Guenter Giese
> Light Microscopy Facility Manager
> Dept. of Biomedical Optics
> MPI fuer Medizinische Forschung Jahnstr. 29
> D-69120 Heidelberg, Germany
> Phone [phone] (Fax: -325)
> e-mail: [hidden email]
>