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-tp2242987p2245073.html

At 14:56 30.01.2009, you wrote:
>You can set the threshold at your chosen value
>and check the "Limit to threshold" box in Set
>Measurements. Then Analyze - Measure.

That's the solution to a different problem. What
I'd like to get an answer for is the question "At
which level do I have to set the threshold so
that 5% of all image pixels are above threshold?"

Steffen

>-----Original Message-----
>From: Confocal Microscopy List
>[mailto:[hidden email]] On Behalf Of Steffen Dietzel
>Sent: Friday, January 30, 2009 5:25 AM
>To: [hidden email]
>Subject: percentile calculation, ImageJ or otherwise?
>
>Dear all,
>
>I have a stack of images (16bit) for which I need
>some measurement of the average signal intensity,
>to describe signal loss with increasing depth.
>Since the particular signal is sort of repetitive
>(Collagen matrix), I thought of just going for
>the 5-percentile (5% of all pixels in an image
>plane have the grayvalue X or higher).
>
>ImageJ readily calculates the median
>(50-percentile) but I didn't find an option for
>other percentiles in the program or on the
>plug-ins web page. It is probably easy to program
>it if one knows how and I am sure others have
>done it before but programming isn't one of my capabilities.
>
>Other suggestions to solve this problems also would be welcome
>
>Best regards
>
>Steffen
>
>--
>---------------------------------------------------------------------------------------------------
>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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