How to derive quantile value of a particular threshold value

Beginner Questions
1

Hi,

I am using ITK C++, and I have applied Otsu thresholding to derive a threshold for a particular image. Now, I want to know the quantile this threshold is set. What would be the best way to do this? Also, ultimately, I want to use this quantile value to threshold other images, which I believe I should use itk::Histogram. Any suggestions appreciated.

2

You could create a histogram of your image with the same number of bins as Otsu thresholding used. Then translate the Otsu-threshold to a bin index. Sum up all frequencies for bins up to the threshold bin and divide by the total frequency. That should give you the corresponding quantile.

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3

Thank you so much @crossmanith !

Is there an Example that you could recommend to create a histogram of an image? I could only find https://itk.org/Doxygen/html/Examples_2Statistics_2Histogram_8cxx-example.html , which does not show image → histogram conversion as an example.

P.S. Looks like I have to read Book2 the relevant section. Will go through p.482+ and come back!

4

ITK: itk::Statistics::ImageToHistogramFilter< TImage > Class Template Reference

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5

Thank you so much! This helped me to find the relevant example associated to the filter!

https://itk.org/Doxygen/html/Examples_2Statistics_2ImageHistogram3_8cxx-example.html

6

The examples are better viewed on GitHub, as there is access to history and the rest of the source code. This particular example is here: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Statistics/ImageHistogram3.cxx.

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7

Thank you very much! A lot of learning, this is definitely helpful!!!

8

Now that I can compute the percentile and also apply thresholds for each individual z-slices, I am having trouble of assembling that back to a 3D image.

I was basing my program with the following example:
https://examples.itk.org/src/filtering/imagegrid/stack2dimagesinto3dimage/documentation

But that only extracts one slice and paste(?)s. Is there a good example for applying a filter to each slice of a 3D image?

9

SliceBySliceImageFilter

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10

Thank you so much!

Just to make sure I understand this correctly - I have to apply different thresholds for each slices (it maintains the percentile, but not the actual value) - I can calculate these values by extracting the slice, but would it be possible to apply this to the slicebysliceImagefilter?

11

Thank you everyone, just to follow up, I was able to create a custom filter which could be feed in to the slicebysliceImageFilter that @zivy pointed to! (Learned how to make a custom filter!).

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