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

Script for publication - Matrix topology guides collective cell migration in vivo

hyrdrodynamics methods for kirchhoff graphs

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

class definitions and 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.

PDE inference from limited spatio-temporal data

Code accompanying "Inverse-Dirichlet Weighting Enables Reliable Training of Physics Informed Neural Networks", Maddu et al., 2021

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

Library for producing and processing on the Adaptive Particle Representation (APR)

Small scripts and bits for data processing interoperability with the cluster

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

Implementation of 2D unet. Use as base for user projects.

scripts related to the publication