http://imagej.273.s1.nabble.com/what-is-the-reason-for-the-difference-seen-here-tp3704870p3704874.html
between the actual values of the pixels and the display values.
limited range of values (256 comes to mind). As a result, ImageJ
will set an output LUT (i.e. the range of display pixels) to display
the range of the data in 1/256 intensity steps. Thus, even if you
use a 16-bit input file, your display will still be 8-bits. This
will not affect your data, just how it appears. You can manually set
the display to a given output scale with the b/c routine.
(although this requires an 8-bit image) and your data is changed.
> On Sep 14, 2005, at 6:58 PM, sean_incali wrote:
>
> >> ImageJ does automatic contrast/brightness adjustment for display
> >> under some circumstances. If you examine the histogram for the
> >> image, you'll find that it's unaltered.
> >>
> >
http://img369.imageshack.us/img369/3179/compare6cb.jpg> >
> >
> > How do you use the histogram to check? Are you comparing the
> > intensity distributions? (I guess that's the only thing I can think
> > of using Histogram to check...)
>
> Here's what I did to verify what I thought I'd seen:
>
> I opened a RAW image file in ImageJ, and noted its range of values (in
> this case, 0-32767 or thereabouts).
>
> I used Process: Math: Divide to divide all pixel values by 16. The
> resulting image was very dark, as I'd expect. I saved this image in a
> new file, again in RAW format.
>
> I re-opened the original file and the divided-by-16 file. Both images
> *appeared* essentially identical as displayed by ImageJ. However,
> while the original image had a range of 0-32767, the new image had a
> range of 0-2047.
>
> I suspect that the image you're examining has no fully-saturated
> pixels, and that LSM browser is displaying it without adjustment,
> while ImageJ is automatically adjusting contrast and brightness to
> maximize visual contrast.
>
> If LSM browser lets you examine the histogram of your image, I'd
> suggest examining the histogram there and in ImageJ. I'm guessing
> that you'll see the same values and the same distribution in both
> cases.
>
> Note that I'm not an LSM user, so I can't vouch for this from personal
> experience.
>
> > Also I have a question about opening a lsm file using LSM plugin vs
> > using an image in Tiff format exported from LSM broswer.
> >
> > If I open the "Tiff file" in ImageJ, is that same as the lsm file
> > opened using the plugin? (same, I mean in terms of intensity in two
> > channels.)
> >
> > If they are different, how different are they? in what respect?
>
> Again, I don't know what LSM does. However, I do believe that ImageJ
> does the same autoscaling behavior with TIFFs that it does with RAW
> data. --
> -jeffB (Jeff Brandenburg, Duke Center for In-Vivo Microscopy)
Joel B. Sheffield, Ph.D.