Flowtrace: simple visualization of coherent structures in biological fluid flows

• Published in: Journal of experimental biology Vol. 220; no. Pt 19; pp. 3411 - 3418
• Main Authors: Gilpin, William, Prakash, Vivek N., Prakash, Manu
• Format: Journal Article
• Language: English
• Published: England The Company of Biologists Ltd 01.10.2017
• Subjects: Algorithms; Animals; Coherence; Computational fluid dynamics; Computer applications; Flight, Animal; Flow pattern; Fluid flow; Hydrodynamics; Insecta - physiology; Insects; Invertebrates; Invertebrates - physiology; Locomotion; Open source software; Rheology - methods; Social Behavior; Software; Source code; Swarms; Swimming; Visualization; Fluid dynamics; Flow field; Streamlines
• ISSN: 0022-0949; 1477-9145; 1477-9145
• DOI: 10.1242/jeb.162511

We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results to more experimentally-difficult and mathematically-sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential “middle ground” allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques. In addition to being informative, the visualizations generated by our tool are often striking and elegant, illustrating coherent structures directly from videos without the need for computational overlays. Our tool is available as fully-documented open-source code available for MATLAB, Python, or ImageJ at www.flowtrace.org.