Table of Contents
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: Each project has its own individual contributing guidelines, as well.
