Behavioral algorithms of ontogenetic switching in larval and juvenile zebrafish phototaxis

Authors: Maxim Q. Capelle, Katja Slangewal, Panagiotis E. Eleftheriadis, and Armin Bahl

This code provides analysis and modeling tools for quantifying and simulating phototactic behavior in larval and juvenile zebrafish. The code extracts, compares, and fits behavioral algorithms from experimental data to reveal developmental switches in phototaxis.

If you use this code in your work, please cite our paper: Capelle et al., Behavioral algorithms of ontogenetic switching in larval and juvenile zebrafish phototaxis, iScience, 2026.

All data can be found under the persistent identifier: KonData Repository.

Folder Structure

• figures/ — Scripts for generating figures
• settings/ — Configuration and settings files
• utils/ — Utility modules and helper functions
• requirements.txt — List of required Python packages
• README.md — Project documentation
• prepare_data.py — Script for preparing and processing of raw data
• simulate.py — Script for running simulations based on fitted models

How to Run the Code

1. Install the required packages listed in requirements.txt.
2. Configure the settings in settings/general_settings as needed for your analysis (especially regarding the paths)
3. Run the scripts in the figures/ directory to generate the desired figures. Alternatively, all figures can be generated at once by running figures/run_all_figures.py. The following dependencies between scripts should be noted:
   • fig3.py requires fig3_fit_models.py.
   • fig4B.py requires fig1_and_4_all_agents.py.
   • figS5.py requires fig1_and_4_all_agents.py.
   • figS6.py requires fig2.py and fig3_fit_models.py.
   • figS7.py requires fig1_and_4_all_agents.py.

Each script is named after its corresponding figure in the paper for easy reference.