Mitochondria Segmentation Code

Mitochondria Segmentation Source Code

Here you can find the source code for our Mitochondria segmentation approach described in our CVPR 2013 paper.

Updated 19/11/2013.


  • – Linux or Windows.
  • – Large amounts of RAM needed for training, depending on the size of the image stack.

Download and Compile

  • – Get the code from github here
  • – Unzip and read Readme.txt for detailed instructions to compile and run the code.


Multiple Object Tracking using K-Shortest Paths Optimization

J. Berclaz; E. Turetken; F. Fleuret; P. Fua 

IEEE Transactions on Pattern Analysis and Machine Intelligence. 2011. Vol. 33, p. 1806–1819. DOI : 10.1109/TPAMI.2011.21.

Supervoxel-Based Segmentation of Mitochondria in EM Image Stacks with Learned Shape Features

A. Lucchi; K. Smith; R. Achanta; G. Knott; P. Fua 

IEEE Transactions on Medical Imaging. 2012. Vol. 31, num. 2, p. 474-486. DOI : 10.1109/TMI.2011.2171705.


If you have any questions or bug reports, please send an email to [email protected].