Experiences in Python for Medical Image Analysis

A session at SciPy 2013

Thursday 27th June, 2013

6:20pm to 6:40pm (CST)

Upon entering graduate school and selecting radiology informatics as my topic of study, a broad survey of open source options for scientific work was conducted. There were three main criteria:

robust numerical and scientific capability,
strong user community with continuing updates and long term support, and
ease of use for students transitioning from other languages.
Among several strong options that satisfied criteria #1, Python with NumPy and SciPy was the clear winner due to the latter two criteria.

My work focuses on supervised segmentation of soft-tissue abdominal MRI images, extracting novel image features from these segmented regions of interest, and applying machine learning techniques to evaluate features for predictive ability. This presentation will provide an overview of the key computational tasks required for this work, and outline the challenges facing a medical image researcher using Python. Most notably, medical image volumes are rarely isotropic, yet often algorithms for 3-D NumPy arrays inherently assume isotropic sampling. Thus, generalizing or extending various algorithms to handle anisotropic rectangular sampled data is necessary. Our improvements to one such algorithm were recently contributed back to the community, and are presently incorporated in the random walker segmentation algorithm in Scikit-Image.

Another significant challenge is visualization of algorithm output for large volumetric datasets. An extensible tool we call volview was developed, allowing fast visualization of an entire volume and an arbitrary number of colored, alpha-blended overlays, combining the abilities of NumPy, Pyglet, and PygArrayImage. This improved speed and quality of algorithm development, and facilitated review of our results by clinicians.

About the speaker

This person is speaking at this event.
Joshua Warner

MD/PhD Candidate at Mayo Clinic bio from LinkedIn

Coverage of this session

Sign in to add slides, notes or videos to this session

Tell your friends!


Time 6:20pm6:40pm CST

Date Thu 27th June 2013

Short URL


View the schedule


See something wrong?

Report an issue with this session