Can anybody kindly suggest any open source software / application which is used by researchers / doctors / practitioners at hospitals / clinics to visualize patients information?

One example is FreeSurfer which is an application related to brain imagery analysis.

I am interested to know the names of such applications which is widely used in this community that can accept a scan / images of patients as input and generate a detailed visualization. The applications need not be specific to brain only.

  • It might be worth mentioning that a lot of such data is stored in FITS files. Commented Apr 3, 2016 at 5:45
  • Please edit your question and describe scanned images of the patients. As your question is now, it could be any image type, and the question is hardly 'medical'.
    – user416
    Commented Apr 3, 2016 at 9:02

1 Answer 1


I suggest taking a look at MedPy which is a gratis, open source, set of python libraries and command line tools for working with medical images.

To quote: MedPy is a library and script collection for medical image processing in Python, providing basic functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.

It is targeted for Linux systems but there are also docker containers to give you a quick start.

One possible viewer, other than the various python visualisation tools, is itksnap which is also open source and runs on Windows, OS-X & Linux.

enter image description here enter image description here

  • Steve, thanks for your reply. Can I kindly seek clarifications on the following questions. a) How computationally intensive is the MedPy software itself in order to process an image and generate the output? b) What is the approximate running time to perform an imagery analysis assuming that the software is hosted on a physical server having Intel hardware with 32 cores and 64 GB RAM? c) Is the MedPy software multi threaded? d) What are the different kinds of analysis does the software support? For instance, brain imagery. Commented Apr 3, 2016 at 8:21
  • a) & b) it depends on the size, format and complexity of the file and the output required, c) I believe so & d) any that you can imagine but with more work already available in some areas. That is the nature of open source software - the people involved tend to enhance the areas that they specialise in. Commented Apr 3, 2016 at 9:45

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.