Summer2009:Using cython

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Key Investigators

  • BWH: Julien de Siebenthal, Sylvain Bouix


We are investigating ways of accelerating the stochastic tractography code developed in python and part of the current version of Slicer 3.4.

Approach, Plan

Cython is used to develop a direct way of integrating native C code where python bytecode is too slow and hinders performance of the algorithm.

During the summer week, we will discuss improvements on the current implementation and possibly other approaches that could complement ours.


  • Implemented Cython code for tensor and fiber tracking
  • Performance depends mainly of the nature of the Python code - if numpy adequately used (vectorization...) - no significant difference with C performance