How can i reconstruct series or sequence of 2D DICOM images into 3D reconstruction?

Beginner Questions
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1

Hello there,
I had a bunch of microscopy image in a .tif or a .czi extension but I manage to convert it into Dicom standard format using pydicom. Moreover, after conversion now I have a sequence of Dicom image like from (0-119, each subject has 1316x1316x120 (x,y,z)) for one subject. My goal is to transform this sequence of 2D .dcm image into 3D using ITK and VTK.

So, my question is: Is it possible to perform 3D reconstruction using ITK and VTK for this kind of image, if yes then how can I perform it?

I read some topic related to my query like 1. Display 3D image using ITK and VTK
2. import 3D volume from itk to vtk
But I didn´t understand it completely. I think these are done in window OS.

I am using macOS and I want to perform all these operations of python if possible.

It would be great if anyone suggests me some steps related to it or suggest me some better idea to perform 3D reconstruction.

2

Are you aware of this example? I think it does what you want. You might also want to try reading the TIFF images directly using this example or another one from IO group.

3

Hello,
Thanks for your reply.
I have gone through your suggestion but I guess these suggestion are to create a 3D volume in a .nrrd format.
But my goal is to perform 3D reconstruction using a series of 2D Dicom image.
Any suggestion for 3D reconstruction and visualizing it after that.
Thanks

4

If you just need to visualize the 3D image instead of writing to disk, try itk::ViewImage class. You will need to enable Module_ITKVtkGlue during CMake configuration step.