normalize part of image according to another part

Posted by Vojtas on Apr 24, 2014; 10:50am
URL: http://imagej.273.s1.nabble.com/normalize-part-of-image-according-to-another-part-tp5007413.html

Dear all,

I have a scanned 16 bit grayscale image that has an artifact - part of the image has lower dynamic range of pixel intensity. I would like to adjust the range of pixel intensity according to a selected part of the image and preserve the "healthy" part of the image.

I am not satisfied with histogram normalization/equalization. I kind of like a plugin Quantile Based Normalization (Fiji), -  http://www.longair.net/edinburgh/imagej/quantile-normalization/ 
but I couldn't make it work the way I wanted. I was not able to apply successfully the mask for the selected part of image. Also, when I tried the plugin on two testing images, I ended up with two processed images both with changed pixel intensity. I wonder if there is a way how to mark one image as "source" of pixel intensity histogram.

Any suggestions how to either make the Quantile Based Normalization work or to adjust the histogram of one part image according to another?

Vojta

"healthy" image part: