Posted by
Jeff Brandenburg on
Sep 15, 2005; 3:44pm
URL: http://imagej.273.s1.nabble.com/what-is-the-reason-for-the-difference-seen-here-tp3704870p3704873.html
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)