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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.

multiparameter persistence

Sequencing analysis pipeline for our paper "Human assembloids recapitulate periportal liver tissue in vitro"

This is a code-repository for the image-, sequencing and data-analysis performed for the manuscript: Integrated Molecular-Phenotypic Profiling Reveals Tuneable Modulators of Morphological Variation in Stembryos" authored by: Alba Villaronga Luque et al.

hyrdrodynamics methods for kirchhoff graphs

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.

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

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"

class definitions and methods for kirchhoff graphs

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

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