Learning Context Cues for Synapse Segmentation
This code implements a synapse segmentation algorithm, as introduced in . This is based on the first version available at http://cvlab.epfl.ch/software/synapse
Please check http://cvlab.epfl.ch/software/synapse for updated instructions on how to use this code.
xx WARNING xx: THIS IS A BETA VERSION and DOES NOT FULLY IMPLEMENT THE METHOD IN . xx WARNING xx: If you want to run the approach of , download the original version xx WARNING xx: from http://cvlab.epfl.ch/software/synapse
You need CMake to compile the code. So far, only Linux is supported.
First create a build folder, for example:
cd <where_iiboost_is> mkdir build
Now configure with ccmake:
Choose to build the Python Wrapper (
BUILD_PYTHON_WRAPPER set to
specify the path to ITK 4.5 (
ITK_DIR) and set
(Make sure ITK was compiled with
-fPIC in CXXFLAGS)
Finally, if you are using ILASTIK, set
PYTHON_BASE_PATH to the path where ilastik is.
Otherwise, point it to your root usr folder (eg
You can now compile with
make, and try the python wrapper with
For more information about the synapse segmentation algorithm, please check the following article:
 Learning Context Cues for Synapse Segmentation C. Becker, K. Ali, G. Knott and P. Fua. IEEE Transactions on Medical Imaging (TMI) 2013
 Learning Context Cues for Synapse Segmentation in EM Volumes. C. J. Becker, K. Ali, G. Knott and P. Fua. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Lecture Notes in Computer Science, 2012.
Please mail email@example.com for bug reports, comments and questions.