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.

To install Microstructure.jl, open Julia and enter the package mode by typing ], then add the package:

julia> ]
(@v1.8) pkg> add Microstructure

You can check if your installation is the latest version by typing status in the package mode and upgrade to the latest version using up in the package mode:

(@v1.8) pkg> up Microstructure

If a newer version isn't being installed using up, you can remove current installation and add the latest version by (replace 0.1.4 with latest version number):

(@v1.8) pkg> rm Microstructure
(@v1.8) pkg> add Microstructure@0.1.4

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.

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