Documentation for flowtrace, simple visualization of biological fluid flows in MATLAB, Python, and ImageJ
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screenshots
README.md
_config.yml
flowtrace_imagej.md
flowtrace_matlab.md
flowtrace_python.md
gallery.md

README.md

<iframe src="https://player.vimeo.com/video/192180842?title=0&byline=0&portrait=0" width="667" height="500" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>

Vortex arrays generated by starfish larvae. This video won grand prizes in the 2016 Nikon Small World in Motion competition, The 2017 NSF "Vizzies" Visualization Challenge, and the American Physical Society's 69th Annual "Gallery of Fluid Motion" competition.. Our papers using this tool are available here and here

flowtrace

A simple tool for visualizing unsteady flows.

Installation

Flowtrace is currently implemented in Python, MATLAB, and Fiji/ImageJ, please choose your preferred version below for installation and usage instructions

Gallery

The Video Gallery shows our favorite videos generated using flowtrace.

Publications

This tool was created by William Gilpin, Vivek N. Prakash, and Manu Prakash, 2015-2017. For more details and comparison to other tools (such as Finite-Time Lyapunov exponents) please see our paper in Journal of Experimental Biology.

William Gilpin, Vivek N. Prakash, Manu Prakash. "Flowtrace: simple visualization of coherent structures in biological fluid flows" Journal of Experimental Biology, 2017.

If you use the tool in published work, please consider citing the above.

We have also used Flowtrace to generate primary results in our recent study on larval starfish swimming in Nature Physics

William Gilpin, Vivek N. Prakash, Manu Prakash. "Vortex arrays and ciliary tangles underlie the feeding–swimming trade-off in starfish larvae" Nature Physics, 2016.
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