Zebrafish Fluid-dynamics Locomotion Optimization Workspace (ZFLOW)

C++ code for running Computational fluid dynamics (CFD) simulation of larval zebrafish, and MATLAB code for preprocessing and postprocessing. See the companion

• Publication Larval zebrafish minimize energy consumption during hunting via adaptive movement selection by Darveniza, T., Wong, R., Zhu, S., Pujic, Z., Sun, B., Levendosky, M., Agarwal, R., McCullough, M. H., & Goodhill, G. (2026). Proceedings of the National Academy of Sciences of the United States of America.
• Preprint Behavioral adaptation to changing energy constraints via altered frequency of movement selection by by Darveniza, T., Zhu, S., Pujic, Z., Sun, B., Levendosky, M., Wong, R., Agarwal, R., McCullough, M. H., & Goodhill, G. for more information.

Overview

To facilitate use of this CFD software by others, we demonstrate how to run a randomly-selected 9 dpf larval zebrafish swim bout through the CFD simulation pipeline.

Preprocessing

Preprocess the swim bout according to steps described in the paper. Following successful preprocessing, the swim bout should be in a similar form to simulation/zebrafish_2D_coords.txt. To better understand this form, run the script preprocess/preSimVis.m.

Simulation

See simulation/README.md

Postprocessing

1. Following successful simulation, there should be two new folders: ZFISH3d, and examplespline.txt.
   • ZFISH3d contains various IBAMR outputs, including power expenditure
   • examplespline.txt contains tracking points on the 3D fish during simulation, which is used during validation
2. Navigate to postprocess/postprocess.m, and run the post-processing functions

Requirements

This code requires MATLAB (tested on R2021b–R2023b) for the pre/postprocessing, make or cmake and IBAMR library (tested on 0.{8,9,13,14,15}.0, currently 0.15.0 is used) for the main CFD simulation.

Contact

• Robert Wong robert.wong@wustl.edu
• Thomas Darveniza darveniza.t@wustl.edu