Explore projects

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

Improving contrast in confocal data by degrading image with model of light scattering

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

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

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

Sequencing analysis pipeline for our paper "Human liver cholangiocyte organoids capture the heterogeneity of in vivo liver ductal epithelium"

Repository containing the scripts used in Iglesias-Artola et al 2024. Quantitative imaging of species-specific lipid transport in mammalian cells

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 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.

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

class definitions and methods for kirchhoff graphs