Posted by
John Alexander-7 on
Aug 26, 2008; 1:12pm
URL: http://imagej.273.s1.nabble.com/Set-Threshold-records-incorrect-values-16bit-images-Ubuntu-tp3695217p3695246.html
I'm using Suse 10.1 Linux 64-bit with ImageJ 1.41j and Java 1.6.0
I'm not quite sure I understand the problem you're encountering, but, I
just loaded the M51.tif sample 16-bit image.
It has a histogram of gray values between 0 and 10106 - so it is shy of
the full 16-bit range that goes up to 65535
I found that if I "set" the threshold to anything outside of that range,
it re-sets it to be within the range of pixel values. For example: low:
0 and high: 20000 -> resets to low:0 and high: 10106.
If I add 10000 to each pixel (math->add->10000), then the range is 10000
to 20106. Again, if I set low:5000 and high: 25000 -> resets to low:
10000 and high: 20106.
But I don't necessarily think this is a bug in that this is what I would
expect to happen - is this what you are referring to?
If not, see if you can post an image that this happens with or, better
yet, use a File->Open Samples image.
John
Ghislain Bugnicourt wrote:
> Dear Wayne,
>
> Thanks for your response. I'm sorry because I didn't expose it clearly
> enough : the problem with 'Threshold, set' is not present on the Windows and
> Mac ImageJ files.
> Actually, I only found this problem on Ubuntu, and more recently on Debian.
> Therefore, it seems that the linux installing file has a problem. I join my
> previous message to explain what happens.
>
> Thanks a lot for your care.
> Ghislain Bugnicourt
> CNRS - CRETA - France
>
>
>
> Ghislain Bugnicourt wrote:
>> Hi. First of all, thanks for this wonderful customizable imaging tool.
>>
>> My issue is about the "set" option of the "adjust...threshold" tool, on
>> 16-bit grey-scale images. I didn't find such a problem in the archive.
>> In this "set" dialog box, if I enter values that are not available with
>> the scrolling bars, it modifies the values. For instance, 107 becomes 9,
>> 940 becomes 104, 372 becomes 107, following a law I couldn't understand,
>> and depending on the image. The images I obtain (even when doing 'apply')
>> respect those wrong numbers.
>> But what is incredible is that sometimes it works well in exactly the same
>> conditions (1/10 times).
>>
>> Configuration :
>> - Ubuntu 8.04 (There's no problem on Mac and Windows. But I couldn't try
>> another Ubuntu 8.04)
>> - The compiz bug (blank images) linked with Java was previously corrected
>> by canceling the visual effects in Ubuntu.
>> - ImageJ 1.41j, with Java 1.6.0_05
>> - 16-bit images obtained with Metamorph (immuno-fluorescence on neuron
>> cultures)
>>
>
--
John K. Alexander, Ph.D.
Post-Doctoral Fellow
William Green Laboratory
University of Chicago
Dept. Neurobiology, Pharmacology, and Physiology
947 East 58th Street
Abott Hall 402
Chicago, IL 60637
(off) 773-702-9386
(fax) 773-702-3774
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