Workshops

Two new advanced workshops will be available in 2016. These two workshops will be offered by Dr. Garyfallidis and are designed to bring academics and industrial software engineers up to speed with the latest advancements in Scientific Python and Diffusion Analysis.

Workshop I

Advanced Scientific Programming in Python for Biomedical Engineers

This workshop is tailored for biomedical engineers and medical imagers who are well familiar with at least one programming language (e.g. C++ or Matlab) and they want to switch into using Python in their daily analysis. With Python language being the most popular language for the last two years this maybe one of your greatest investments.

The workshop will not just teach you how to use the Python language and its leading libraries but also learn how to test properly your code and how to release your own packages. The workshop will have short presentations followed by short quick examples where you can try them in your own notebook or workstation and get immediate feedback from the instructor.

Day 1 Dive into the basics

  1. Python’s Useful data structures
  2. Debugging/Testing in Python
  3. Collaborate with Git

Day 2 Processing numerical arrays

  1. Deep into Numpy
  2. Focus in Scipy
  3. Deal with massive data

Day 3 The need for speed - write fast code

Write efficient code using Cython

Day 4 3D/4D Medical Visualization

  1. Visualization with Python-VTK
  2. Create a package and ship it

Day 5 Align 3D data from different modalities

  1. Linear Registration using Dipy
  2. Nonlinear Registration using Dipy
  3. Streamline-based Registration using Dipy

Workshop II

Diffusion Imaging in Python (DIPY)

This workshop is tailored for the Neuroscientists who want to learn the absolute best way of doing analysis of diffusion MRI datasets. This course will teach you all the hidden details which are usually avoided. To attend this talk you need to already be familiar with at least one programming language (e.g. Matlab) and had a course in medical imaging.

The workshop is both hands-on and bring your own data. The workshop will have short presentations followed by short quick examples where you can try them in your own notebook or workstation and get immediate feedback from the instructor.

Day 1 Introduction to the Python ecosystem for Scientific analysis

Familiarize with Python, Numpy, Scipy, Ipython, install Dipy.

Day 2 Signal Reconstruction

  1. Diffusion Tensor Imaging
  2. Diffusion Spectrum Imaging
  3. HARDI and Deconvolution Techniques

Day 3 Fiber tracking

  1. Deterministic
  2. Probabilistic
  3. Global

Day 4 Image Registration

  1. Linear Registration
  2. Nonlinear Registration
  3. Streamline-based Registration

Day 5 Segmentation and statistical analysis

  1. Segmentation of bundles
  2. Tractometry
  3. Statistical analysis along bundles

Dates TBA. For more information or for organizing a workshop send an e-mail directly to Dr. Garyfallidis.