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

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.

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

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

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

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.

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

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

Henricks script as Python