Object counting in 3D Images

2017 3 20
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Hello!
I have a lot of CT Scanner output in the form of Tif stacks / diacoms and wondering if I can use matlab for what I currently use imageJ for.
Primarily I have concern over if matlab will be able to run a 3D object count over a segmented image stack. Is this possible and can anyone point out how please?
Many thanks, N.

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