Python Image Registration Libraries - 3D Medical

What are some Python libraries that have the ability to read CT model files with extensions like .vtk

or .stl

, and do 3D image registration with regular videos. I have found many programs that have this ability, but what I am looking for is not a program but a Python library like Numpy or OpenCV where all I have to do is import numpy

or import cv2


Created example of what I want to do

  • Step 1 - Get the 3D CT model of the human skull.
  • Step 2 - Read CT 3D Model in Python
  • Step 3 - Get a normal video of a person standing still
  • Step 4 - Perform 3D CT and Human Video Registration
  • Step 5 - Displaying the Registration Output

I've found a couple of Python libraries that "seem" to be like this, but don't have enough information in the library description to be sure that this is what I want. I am also open to using multiple libraries. Is there anyone who has done something similar to this, and it would be great if anyone with experience with any libraries could give me some guidance, thanks. If not, I will also consider libraries in other languages.

What I have reviewed so far

  • FW4SPL Libarary in C ++
  • MITK library in C ++
  • MeVisLab software in Python
  • Elastix C ++ Library
  • Python SimpleElastix Library
  • ITK library in C ++
  • SimpleITK library in Python


and MITK

I have not been able to successfully compile the source code due to new errors occurring after debugging old errors. It looks like new bugs won't stop appearing (I've spent a lot of time on this and don't want to continue anymore).

It MeVisLab

's not a Python library like numpy

or opencv

, but it's a graphical interface that is also called programmable.

For Elastix

, SimpleElastix


and SimpleITK

they really are the libraries of C ++ and Python, which seem to be ideal, but I'm not sure that they provide the requirements of my application as described above. Also, I am very confused about attitudes towards each other.


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1 answer

I am playing with vtk and stl files for the first time. Your question piqued my curiosity, but I obviously haven't experienced it. I started looking into this before the above comment. I didn’t understand that we were not in the subject, sorry. Therefore, I am giving you my findings at this stage, as they are designed to be shared.

1) for .vtk files It turns out that most of the library I've seen is for python 2.7, while I prefer the updated version (now 3.5). For 3.5 I finally accepted the "woodscn" version which seems promising, for encoding it seems to me that all the information needed is on Reading a .vtk file with python

2) for .stl files, the "dense package from" conda-forge "looks good, with a typical example at

Then you just need to write import vtk

, and import nestly

in python script.

hope this helps



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