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class definitions and methods for kirchhoff graphs

This repository is all about simulating flow driven pruning in biological flow networks.

This software package implements the identification of robust topological defects.

This repository contains the image analysis pipelines for bile canaliculi analysis and mesenchyme counting associated with the paper "Mouse liver assembloids model periportal architecture and biliary fibrosis"

This repository contains source codes and notebook demos for trainin STENCIL-NET.

Image-based pipeline for solving inhomogeneous reaction-diffusion PDEs in real-world porous geometries. Level-set method (multi-CPU) for reconstruction. Sparse grids (multi-GPU) for diffusion simulation. Parallel data structures from OpenFPM.

Exploring cellpose (deep learning) for segmentation in 2D&3D. Including setup for GPU on cluster or workstation

This is a python implementation of the cycle coalescence algorithm as described by Modes et al, 2016.