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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.

MRI

Name
Description
Links
ivadomed
Comprehensive and open-source repository of deep learning methods for medical data segmentation
Multiclass Segmentation
Code related to the NIH marmoset longitudinal segmentation project
qMRLab
Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.)
Shimming Toolbox
Code for performing real-time shimming using external MRI shim coils
Spinal Cord Toolbox
Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord
Template
A framework for creating unbiased MRI templates of the spinal cord

Histology

Name
Description
Links
Atlas Rat
Scripts to generate a microstructure atlas of the rat spinal cord
AxonSeg
Automatic segmentation of axon and myelin from microscopy data
AxonDeepSeg
Segmentation software for microscopy data using deep learning
AxonPacking
Simulation software for arrangements of axons in white matter
Tract Clustering
Data-driven approach for tracts in rat histology

Contributing

NeuroPoly welcomes and appreciates contributions. To get started, please check out NeuroPoly's contributing guidelines: NeuroPoly Lab: Software Contributing Guidelines.
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Open-Source Projects
MRI
Histology
Contributing