PT  - JOURNAL ARTICLE
AU  - Gilpin, William
AU  - Prakash, Vivek N.
AU  - Prakash, Manu
TI  - Flowtrace: simple visualization of coherent structures in biological fluid flows
AID  - 10.1101/086140
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 086140
4099  - http://biorxiv.org/content/early/2016/11/07/086140.short
4100  - http://biorxiv.org/content/early/2016/11/07/086140.full
AB  - 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-diffcult 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 the need to resort 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.