TIFF 12bit / 16bit display / conversion problems

[Guenter Giese]

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]

[Wayne Rasband]

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]
>

[Lambright, Geoffrey]

Hi Group,

I have a quick question about the "Object Tracker" plugin
(Tracker_.class) by Wayne Rasband. Does this determine the position of
the object by center of mass?

Thanks very much,

Geoff