Posted by
John Alexander-7 on
Mar 31, 2008; 8:39pm
URL: http://imagej.273.s1.nabble.com/Bug-in-the-plot-lanes-tool-tp3696730p3696732.html
I am using 1.40b - but I am certain this has been going on since version
1.38.
So far, I can adjust the contrast, outline the lanes, plot the profile
(which is blank), then reset the contrast, then Analyze->Gels->Re-plot
lanes and I get the correct plot. Annoying, but at least it works.
One other thing I find slightly annoying is that the plots are 8-bit.
This is an issue when comparing bands when there are both strong and
weak bands. I find myself having to plot the lanes of strong bands
first, then plot the lanes of the weak bands. To compare the strong and
the weak, I have to plot a middle strength band with both the strong and
the weak, and determine a "scaling" factor. It would be nice if the I
were able to simply plot all the lanes and not have a "strong" signal
reduce a weak signal to nothing. I figure that would be done by using a
32-bit plot lanes algorithm.
(I think this hasn't been much of an issue in the past because
chemiluminescence usually didn't provide a decent dynamic range, but
fluorescent westerns are easily providing 4 orders of magnitude - well
beyond the 8-bit limit.)
Jonathan Hilmer wrote:
> I see the same behavior, specifically with the Gel Analyzer (but not
> Plot Profile), using version 1.39u.
>
>
> Jonathan
>
> On Mon, Mar 31, 2008 at 12:16 PM, John Alexander <
[hidden email]> wrote:
>> Greetings list,
>>
>> I've had this difficulty off and on for a while and I think I have
>> isolated the specific problem, i.e. I can now reproduce the problem.
>>
>> The plot lane tools only seems to work on images that have not been B&C
>> adjusted.
>>
>> If I load my tiff of my blot and outline the lanes 1,2,3 ... etc, it
>> works fine. The problem is that some of my bands are very very faint in
>> comparison to other strong ones, so, I adjust the contrast so I can see
>> the faint ones. I then outline the lanes again, and when I plot them,
>> the resulting plot is blank. If I then go to B&C and "reset" the image,
>> it works again.
>>
>>
>> John
>>
>
--
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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