micro-ct

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

See the upstream repo and https://github.com/aliraeini/porescale

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

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.

AI-powered TaxaMask workbench for morphology mask annotation, taxonomic evidence review, 2D/STL datasets, and TIF/CT micro-CT volume workflows with SAM/VLM.

CoralLite: μCT reconstruction of coral colonies from individual corallites (CVBMC @ ICPR 2026)

Porosity REV (Representative Elementary Volume) from a segmented 3D image using random cube sampling.

Deep learning framework for micro-CT projection infilling - recovering missing projections to enable undersampled scanning with reduced radiation dose.

A particle tracking library

Image metric analysis (MTF, NPS, and NEQ) based on micro-CT reconstructions of the mCTP 610 quality assurance phantom (Shelley Automation Inc, Canada)

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

3D surface segmentation of ancient Herculaneum papyrus scrolls from micro-CT scans. Dual-pipeline architecture: V1 (CE+Dice, clDice) and V2 (Focal Loss, Deep Supervision, Skeleton Recall). Built for the Vesuvius Challenge $200K Kaggle competition. CC BY-NC 4.0.