Segmentation of 3D image based on intensity

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najlatsw 2015-4-28

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https://ww2.mathworks.cn/matlabcentral/answers/214010-segmentation-of-3d-image-based-on-intensity

评论： Francisco José Torcal-Milla 2019-3-8

Dear all,

I am trying to segment active brain areas. For this, I have a grid in the brain and in each gridpoint I have a certain power or intensity. A scatter plot of the gridpoints with color and size relative to this power can be seen below.

As you can see, there are clearly three or four clusters of higher activity. I would like to automatically segment those clusters. I already tried watershed, but with all connectivity options, almost everything was segmented in the same cluster.

Is there an easy solution to tackle this problem?

Many thanks in advance!

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Answer 1

Image Analyst 2015-4-28

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Do you have a list of x,y,z coordinates? Or an image? If you have a list of coordinates, loop and turn them into an image. Then you can segment based on intensity simply:

binaryImage = grayImage >= lowThreshold & grayImage <= highThreshold;

See my Image Segmentation Tutorial for more details: http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862

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Image Analyst 2015-4-28

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So just figure out what the thresholds should be. It will still be "automatic" - whatever that means. Either YOU or "some algorithm" needs to figure out what the thresholds needs to be. So you either hard code in some constant, or develop a function to figure out what the value needs to be. They will still be labeled correctly even if they touch if you do intensity based thresholding.

[labeledImage, numRegions] = bwlabel(binaryImage);

Francisco José Torcal-Milla 2019-3-8