Hi,
A student recently asked me about (medical) image registration in Python. I had to tell him that there is currently hardly anything like that in Python.
I was frustrated enough about this that I decided to turn a piece of code from my PhD work into a usable library. It’s a thin wrapper around the awesome Elastix image registration toolkit. I figure/hope that because its so thin, it won’t need much maintenance, and/or is easy to maintain by others. The code and docs are on Github: https://github.com/almarklein/pyelastix Further, the package is on conda-forge and Pypi.
Aside from this announcement, I’d like to propose to put together a list of Python packages that do (nonrigid) image registration. Since efforts in Python-based image registration have only resulted in relatively small and unknown packages, it would be good to have an overview. What would be a good place for this? Maybe a wiki-page on scikit-image’s Gitub repo?
Two entries I would add:
- Kasper Marstal’s SimpleElastix: https://github.com/kaspermarstal/SimpleElastix (also based on Elastix, but compiled against it instead of wrapping the CLI). It’s hard to compile, but Kasper is currently working on putting it on conda-forge.
- During my PhD I developed PIRT (https://bitbucket.org/almarklein/pirt), which uses Cython. It’s a bit idiosyncratic, so it will need work to make “generally useful”. I don’t have the time to do this, let alone maintain it when people start using it.
Regards,
Almar
Is you multivariate interpolation implementation is scalable ? For example I couldn't apply an elastic transform on image larger than 2048x1024 with scipy. If your able to to so, maybe you should contribute to scipy and improve the interpolation module which is currently the biggest bottleneck for Image Registration.
For Ndimage, you can find an example of geometric_transform, but it doesn't work for me, map_coordinate is not suited for a full image mapping.
The list of Python projects related to image registration is up!
It’s implemented as a single index.md file in a github repo. I filled in the projecs that were mentioned in this thread. If you have more to add, or suggestions for improvement, go ahead and make a PR. I think that the description about skimage’s support for image registration needs some improvement.
Regards,
Almar
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