Microstructure.jl is a Julia package for fast and probabilistic microstructure imaging. It features flexible and extendable compartment modeling with diffusion MRI and combined diffusion-relaxometry MRI and provides generic estimators including Markov Chain Monte Carlo (MCMC) sampling methods and Monte Carlo dropout with neural networks.

Microstructure.jl is under active development, testing and optimization and updates will be shared throughout this process. You are welcome to try it out and provide feedback on any issues encountered. Microstructure.jl has a developing documentation website introducing functional API and features of the package. More tutorials and recommendations will be coming soon.

Updates! We have a preprint if you are interested in knowing more: Gong, T., & Yendiki, A. (2024). Microstructure. jl: a Julia Package for Probabilistic Microstructure Model Fitting with Diffusion MRI. arXiv preprint arXiv:2407.06379.

Installation

To install Microstructure.jl, open Julia and enter the package mode by typing ], then add the package, which will install the latest released version:

julia> ]
(@v1.10) pkg> add Microstructure

If you want to keep up to date with the developing version I am working on, remove the current installation and add the repository directly:

(@v1.10) pkg> rm Microstructure
(@v1.10) pkg> add https://github.com/Tinggong/Microstructure.jl.git

Relationship to Other Packages

Microstructure.jl focuses on tissue microstructure estimation. If you are also interested in fiber orientation and tractography, please check out Fibers.jl. Additional, Microstructure.jl uses I/O functions from Fibers.jl for reading and writing NIfTI image files.

Acknowledgements

Development of this package is supported by the NIH National Institute of Neurologic Disorders and Stroke (grants UM1-NS132358, R01-NS119911, R01-NS127353).