🖥 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

Links

Atlas Rat

Scripts to generate a microstructure atlas of the rat spinal cord

Source Code (GitHub) Documentation

AxonSeg

Automatic segmentation of axon and myelin from microscopy data

Source Code (GitHub) Documentation

AxonDeepSeg

Segmentation software for microscopy data using deep learning

Source Code (GitHub) Documentation

AxonPacking

Simulation software for arrangements of axons in white matter

Source Code (GitHub) Documentation

Tract Clustering

Data-driven approach for tracts in rat histology

Source Code (GitHub) Documentation

MRI

Name

Description

Links

ivadomed

Comprehensive and open-source repository of deep learning methods for medical data segmentation

Source Code (GitHub) Documentation

Multiclass Segmentation

Code related to the NIH marmoset longitudinal segmentation project

Source Code (GitHub) Documentation

qMRLab

Software for data aimulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.)

Source Code (GitHub) Documentation

Shimming Toolbox

Code for performing real-time shimming using external MRI shim coils

Source Code (GitHub) Documentation

Spinal Cord Toolbox

Comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord

Source Code (GitHub) Documentation

Template

A framework for creating unbiased MRI templates of the spinal cord

Source Code (GitHub) Documentation

Contributing

NeuroPoly welcomes and appreciates contributions. To get started, please check out NeuroPoly's contributing guidelines: NeuroPoly Lab: Software Contributing Guidlines.