Confocal Microscopy List

Re: percentile calculation, ImageJ or otherwise?

Posted by Julio Vazquez on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Live-cell-Imaging-with-fluoview-1000-tp2242987p2246028.html

Hi Steffen, 

there are probably more elegant and/or faster ways, but you could:

1) with ImageJ, plot the Histogram (Analyze > Histogram ) and then get the values as a list. You can paste the list in Excel and use the Excel "Sum" function to determine where the top 5% intensities are. Not elegant, bit will give you an answer.

2) with Photoshop, open your image (in greyscale mode) and use the curves tool. In the Curves window, use the "Options" button for the Auto adjustment to set the minimum at zero and the maximum clipping at 5%. Apply to your image and then look in the curves window where Photoshop set the thresholds.


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Julio Vazquez, PhD
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Fred Hutchinson Cancer Research Center
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On Jan 30, 2009, at 2:25 AM, Steffen Dietzel wrote:

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

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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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