Table of Contents


List of software created at NeuroPoly or at collaborative institutions. These software are open source and freely available.


  • Atlas Rat: Scripts to generate a microstructure atlas of the rat spinal cord. Written in Matlab.
  • AxonSeg: Automatic segmentation of axon and myelin from microscopy data. Written in Matlab.
  • AxonDeepSeg: Segmentation software for microscopy data using deep learning. Written in Python.
  • AxonPacking: Mingasson, T., Duval, T., Stikov, N., Cohen-Adad, J., 2017. AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter. Front. Neuroinform. 11, 5.
  • Tract Clustering: Data-driven approach for tracts in rat histology. Written in Python.


  • IVADO medical imaging: Comprehensive and open-source repository of deep learning methods for medical data segmentation. Collaboration between MILA and NeuroPoly for the IVADO project on medical imaging. Written in Python.
  • Multiclass Segmentation: Code related to the NIH marmoset longitudinal segmentation project. Written in Python.
  • qMRLab: Software for Data Simulation, Analysis, and Visualization of Quantitative Magnetic Resonance Imaging (Magnetization Transfer, Diffusion etc.) data.
  • Shimming Toolbox: Code for performing real-time shimming using external MRI shim coils. Written in Matlab.
  • Spinal Cord Toolbox: Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord.Written in Python.
  • Template: A framework for creating unbiased MRI templates of the spinal cord. Written in Python.


Config files

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