Analysis of simulated cell microtubules.

ImageJ macros for quantitative analysis of platelet alpha-granule SIM imaging as described in Swinkels and Hordijk et al (JTH, 2023)

Quick-Start for life scientists willing to use Matlab (for fluorescence microscopy, mass spectrometry, x-ray crystallography, single-particle electron microscopy, kinetics ...).. No background in programming is required.

Quantitative Fluorescent Speckle Microscopy

Analysis scripts for the manuscript "Spindle checkpoint silencing at kinetochores at submaximal microtubule occupancy" by Etemad et al. "

Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes

Complements mitoSim - the simulator of cell mitochondria as a spacelss graph.

NuclQ - an ImageJ plugin to quantify intensity levels by distance to the nuclear membrane.

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Submission of Human Protein Atlas - Single Cell Classification on Kaggle 2021. A weakly supervised multi-label classification problem.

analyzing images of mechanical stimulation on low elastic modulus dishes (mSLED)

Complete analysis code for Bland et al., 2024

Python implementation of the cellular automata model corresponding to Lange, Schmied et. al.

3D vertex model allowing scutoids

Code associated with The Digital Cell

Python scripts to quantiatively describe Arp2/3 complex organization on travelling Actin Waves

PhD thesis: Molecular feedback and self-organisation in the PAR polarity network

Analyze_Blebs is a semi-automated ImageJ/FIJI-based plugin for analysis of blebbing cells designed for users at all experience levels and blebs of all types.