Re: percentile calculation, ImageJ or otherwise?

Posted by Steffen Dietzel on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Live-cell-Imaging-with-fluoview-1000-tp2242987p2285787.html

Dear all,

thanks for all the replies on and off list. The latter included an e-mail by Jerome Mutterer with a short macro that does the job. With his permission, I post it here so that it gets included in the confocal archive together with the question.

Cheers

Steffen

The following ImageJ macro thresholds the upper 5% pixels in your image:

// threshold percentile

p=0.05;

getRawStatistics(nPixels, mean, min, max, std, h)

sum=h[0];i=0;

while (sum<(1-p)*nPixels) { i++; sum+=h[i]; }

setThreshold(i,h.length-1);

// end macro

-- ---------------------------------------------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

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