Resources

Our group is committed to contributing developed software and acquired datasets to the scientific community by making it freely available on Github, open source projects, and open data repositories.

Software

• Scattering to diffusion A scattering framework for linking axonal microgeometry to diffusion signal.
• ACSON: A segmentation pipeline of white matter in electron microscopy images.
• DeepACSON: Deep learning-based segmentation of white matter in electron microscopy images.
• gACSON: (developed with Andrea Behanova) A graphical user interface-based software for the segmentation of white matter in electron microscopy images.
• Skeletonize: A Python-based 3D skeletonization algorithm for 3D objects.
• SproutAngio: (developed with Mustafa Beter) An Open-Source Bioimage Informatics Tool for Quantitative Analysis of Sprouting Angiogenesis and Lumen Space.

Open datasets

• Scattering approach to diffusion: Ex-vivo diffusion MRI and cross-sectional geometry of axons in a rat model of traumatic brain injury
• Segmentation of tissue microstructure in 3D high-resolution electron microscopy datasets of white matter
• Segmentation of tissue microstructure in 3D low-resolution electron microscopy datasets of white matter
• Segmentation of tissue microstructure in 3D high-resolution electron microscopy datasets of gray matter