Details: I am looking at a large structure within human cells over time and I want to obtain a cross-sectional view of the center of the structure. So, I need to first align the data sets so that the structure is at a constant position in 3D space with time. Secondarily, I want to obtain an image of the cross-section with time. This perhaps requires coding in MATLAB or ImageJ which I have no expertise on. Thanks in advance for any inputs!
Great. Thank you. I am new to Matlab. Are these tools intuitive to a biologist?
Aligning of the 3D volumes is the major difficulty. If the cells or cell-structures do not deform, you can use 'rigid registration'. Matlab probably has some functionality built into it for accomplishing that.
If however the cells or cell-structures deform, then you need to use 'deformable registration'. This is not easy, time consuming, and still a topic of much research... The software package 'ITK' provides some solutions, but the learning curve is steep (heavy C++).
Good luck!
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