help with outdated macro

Posted by Elyse Aurbach on
URL: http://imagej.273.s1.nabble.com/help-with-outdated-macro-tp5003326.html

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?

Many thanks for any and all help with this issue!

All the best,
Elyse Aurbach

--
Elyse L. Aurbach
Ph.D. Candidate, Akil Lab
Molecular and Behavioral Neuroscience Institute
Neuroscience Graduate Program
University of Michigan, Ann Arbor, MI

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html