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Simple thresholding measurements

Hi again!

This time I am analyzing an ~2Gb monocolor fluorescent image, which takes a lot of time.  All I really want is the percentage of pixels in each of three intensity bins (background, dim, bright).  However, currently I am stuck based on my understanding of the software with performing a "Count" which dramatically slows things down performing needless operations (count ends up being well over a million).  Is it possible to export just the area under the curve in the thresholding window, or perform a non-segmentation based measurement which might be faster (I split the work between two computers, one is still running after more than 14 hours).  Unfortunately due to the nature of the sample, filtering or downsampling could impact the distribution of the data between samples. 

If there is any way to just get a 3 bin (specifically defined bins) histogram of the pixels, that would be great!  Select-Threshold does something like what I want, and quickly, but I do not see a way to get the pixel/area data out.

Best Answer

  • Accepted Answer
    I've just attached it to the first answer.


  • edited May 2018
    If you need just 3 intensity bins, you don't need Count, you can get these values directly from intensity histogram (much faster).
    I've attached the app that makes it easier: define 3 ranges in the Threshold dialog and it will report you area percentage of every class.

  • Hi, that sounds perfect!  How do I get the app?
  • And it is perfect!  And works instantly.
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