Software

Open source projects

Below is a list of software projects created at NeuroPoly or at collaborative institutions. These projects are open source and freely available.

Histology
Name Description Language Links
Atlas Rat Scripts to generate a microstructure atlas of the rat spinal cord. MATLAB Source Code (GitHub) Documentation
AxonSeg Automatic segmentation of axon and myelin from microscopy data. MATLAB Source Code (GitHub) Documentation
AxonDeepSeg Segmentation software for microscopy data using deep learning. Python Source Code (GitHub) Documentation
AxonPacking Simulation software for arrangements of axons in white matter. MATLAB Source Code (GitHub) Documentation
Tract Clustering Data-driven approach for tracts in rat histology. Python Source Code (GitHub) Documentation
MRI
Name Description Language Links
IVADOMED Comprehensive and open-source repository of deep learning methods for medical data segmentation. Python Source Code (GitHub) Documentation
Multiclass Segmentation Code related to the NIH marmoset longitudinal segmentation project. Python Source Code (GitHub) Documentation
qMRLab Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) MATLAB Source Code (GitHub) Documentation
Shimming Toolbox Code for performing real-time shimming using external MRI shim coils. MATLAB, Python Source Code (GitHub) Documentation
Spinal Cord Toolbox Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. Python Source Code (GitHub) Documentation
Template A framework for creating unbiased MRI templates of the spinal cord. Python Source Code (GitHub) Documentation

Contributing

NeuroPoly welcomes and appreciates contributions. To get started, please check out NeuroPoly's contributing guidelines.

Note: The guidelines above are awaiting further discussion, and have not yet been formally accepted by maintainers of each NeuroPoly project. In the meantime, please refer to each project's individual contributing guidelines.