Posted by
Elyse Aurbach on
URL: http://imagej.273.s1.nabble.com/help-with-outdated-macro-tp5003326p5003329.html
Hi Gabriel,
Thanks so much for your reply! My 'Standard deviation' box is indeed
checked--and when I visually look at the Threshold box, the appropriate
bounds have been placed on the intensity histogram after using the macro.
But the mask doesn't appear over the thresholded image--and if I take a
measurement without manually adjusting the mask, it returns null values. I
really appreciate your help--do you have any other ideas I can try?
Many thanks!
Elyse
On Mon, Jun 10, 2013 at 4:57 PM, Gabriel Landini <
[hidden email]>wrote:
> On Monday 10 Jun 2013 19:56:15 Elyse Aurbach wrote:
> > Hello,
> >
> > My lab uses ImageJ to quantify greyscale images. I joined the lab and
> > inherited the attached macro to help take background measurements The
> macro
> > was written in 2005, and with ImageJ version 1.34h through versions
> > 1.44p-ish, this macro is sufficient to measure what my lab calls the
> > "background" of a selection in the image, then threshold the image such
> > that the "signal" is defined as the mean of the selection plus 3.5 times
> > the standard deviation of the selection. From there, in the earlier
> > versions, the macro then calls the Threshold function to set a mask on
> the
> > image, such that only pixels with an intensity value above the "signal"
> > threshold are included in subsequent measurements. The issue is that this
> > macro does not work the same way in newer versions of ImageJ--the macro
> > works fine to set the threshold value, but the mask is never created. Is
> > this a matter of the source Threshold function changing? Is there a
> second
> > "mask" function that should be called? Is there something I'm not seeing?
>
> You are probably missing the "Standard deviation" box ticked in
> Analyze>Set Measurements.
> If it is not ticked, then the value is not extracted and you cannot compute
> the background value.
>
> Cheers
> Gabriel
>
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http://imagej.nih.gov/ij/list.html>
--
Elyse L. Aurbach
Ph.D. Candidate, Akil Lab
Molecular and Behavioral Neuroscience Institute
Neuroscience Graduate Program
University of Michigan, Ann Arbor, MI
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