We provide open-source code for a variety of applications - from artificial intelligence to biophysical measurements in developing embryos.

All of our code is available on GitHub

We also provide a large repository with several million images of zebrafish, medaka and stickleback embryos on KonDATA under DOI: 10.48606/15 and DOI: 10.48606/50


Uncovering developmental time and tempo using deep learning

Published in Nature Methods

Press release

The software can be accessed at:


Robust phenotyping of developmental defects using convolutional neural networks

Published in Nature Methods

Research briefing about the working principles and applications

Press release

The software can be accessed at:


The program simulates an agent-based model of morphogen diffusion in extracellular space on a two-dimensional grid

The software can be accessed at:


Original publication:
Kuhn T, Landge AN, Mörsdorf D, Coßmann J, Gerstenecker J, Čapek D, Müller P, Gebhardt JCM (2022). Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model. Nature Communications, 13:6101.


Online high-throughput mathematical analysis of reaction-diffusion systems

RDNets performs an automated linear stability analysis to screen for reaction-diffusion network topologies that can form self-organizing spatial patterns. The software is optimized to analyze reaction-diffusion signaling networks with cell-autonomous factors. The analysis can be constrained with qualitative and quantitative data.

The online software can be accessed at:

Original publication:
Marcon L, Diego X, Sharpe J, Müller P. High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals. Elife. 2016 Apr 8;5. pii: e14022. doi: 10.7554/eLife.14022.


Python software to analyze Fluorescence Decay After Photoconversion (FDAP) data sets

Download the PyFDAP software, user guide, and a test data set:

Original publication:
Bläßle A, Müller P. PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments. Bioinformatics. 2015 Mar 15;31(6):972-4. doi: 10.1093/bioinformatics/btu735. Epub 2014 Nov 6.

PyFDAP on GitHub:


Python software to analyze Fluorescence Recovery After Photobleaching (FRAP) data sets

Download the PyFRAP software, user guide, and a test data set:

Original publication:

Bläßle A, Soh G, Braun T, Mörsdorf D, Preiß H, Jordan BM, Müller P (2018). Quantitative diffusion measurements using the open-source software PyFRAP. Nature Communications, doi: 10.1038/s41467-018-03975-6.