Library for performing multiphase simulations (based on the Shan-Chen model) in complicated geometries (i.e. porous media 3D images)

OpenFOAM solver for performing single- and two-phase flow simulations on hybrid-scale porous media.

Deep-Learning for Tidemark Segmentation in Human Osteochondral Tissues Imaged with Micro-computed Tomography

Direct pore-scale simulation of single- and two-phase flow through confined media (alpha-release / experimental)

Reconstruction and image processing of micro-CT/nano-CT data taken at SPring-8 and APS Argonne.

ITK Image IO for Scanco MicroCT .ISQ files

Software for processing output of Scanco uCT machines/ any ISQ or TIF producing machine, and producing data. See instructions.pdf for full explaination.

ITK filters to reduce ring artifacts common in x-ray computed tomography.

GUI-based neuronal network model building

A particle tracking library

The notebook demonstrates the workflow for obtaining pore size distribution from binarized micro-CT images. The general principle involves identifying each pore, estimating the volume of each pore, and ultimately determining the radius of a sphere with an equivalent volume of each pore.

Extract ROIs (e.g. nerves, blood vessels) from multi-terabyte cloud-hosted medical scans.

ImageJ/Fiji macro that crops any given image stack without having to load it into memory first.

Code used to analyze adaptive decoupling in insects.

Converts any image stack to a Stratovan Checkpoint file (*.ckpt) keeping specimen names and voxel sizes.