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hyrdrodynamics methods for kirchhoff graphs

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"

Hexagonal spring network with pores are stretched. The resulting stress profile is analyzed. The aim is to verify the hypothesis that in the Zebrafish optic cup, ECM with more pores are under more stress than ECM with less pores.

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.

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

Repository of Code used in the Bachelor Thesis "Guanine crystal segmentation and classification imaged in the eye of zebrafish embryos"

Supplementary Jupyter notebook to our article "Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool"

Theory analysis and code for studying Drosophila wing disc eversion

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.

PDE inference from limited spatio-temporal data