Re: macro threshold values

Posted by Swayne, Theresa C. on
URL: http://imagej.273.s1.nabble.com/macro-threshold-values-tp5015759p5015769.html

Hi Natalie,


If you want to get the top 2% of the pixel population, there is a possibly related thread on the forum, where the poster is trying to get the top 2% of the pixel population using a cumulative sum.
http://forum.imagej.net/t/thresholding-as-a-percentage-of-intensity-histogram-in-a-macro/923/

However, I agree with Jeremy that differing amounts of positive staining per image will change the shape of the histogram, so the population approach may not be robust.

Philippe’s solution gives you a threshold = 98% of the maximum value in the image, which would seem to be robust to differing amounts of positive signal per image, as well as to inconsistent staining levels.

Hope this helps,
Theresa

On Mar 2, 2016, at 3:19 AM, Philippe CARL <[hidden email]<mailto:[hidden email]>> wrote:

Dear Natalie,
I guess you are looking for a code like this:
nBins = 256;
ratio = 0.5;
run("Blobs (25K)");
getHistogram(values, counts, nBins);
Array.getStatistics(values, valuesMin, valuesMax, valuesMean, valuesStdDev);
setThreshold(0, ratio * valuesMax );
setOption("BlackBackground", true);
run("Convert to Mask");
with in your case ratio = 0.98;
My best regards.
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : [phone]

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Natalie M
Envoyé : lundi 29 février 2016 18:43
À : [hidden email]<mailto:[hidden email]>
Objet : macro threshold values

Hi all,
I am writing a macro to count cells in images I've taken of slides. Does anyone know what code I could use to have the macro threshold each image at the top 2% of each histogram, rather than at a set number value on each histogram?
Thanks in advance,
Natalie Morel
University of Wisconsin

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Theresa Swayne, Ph.D.
Manager
Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center
Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: [phone]
[hidden email]<mailto:[hidden email]>


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