Software and data for "Advection versus diffusion in brain ventricular transport"

This repository contains the code, geometries and data used in the paper

Advection versus diffusion in brain ventricular transport

by Halvor Herlyng, Ada J. Ellingsrud, Miroslav Kuchta, Inyoung Jeong, Marie E. Rognes, Nathalie Jurisch-Yaksi.

The software (code, geometries and data) is licensed under an MIT License.

Contents of this repository:

src.zip
The source code of the model implementation presented in the paper, also available at https://github.com/hherlyng/zebrafish-cilia-csf.

geometries.zip

Computational mesh files (.xdmf format) and surface geometry (.stl) used to generate the ventricular meshes, as well as cylinder meshes used for numerical verification. 

data.zip
The photoconversion and particle tracking data referenced in the paper.

README.md
Readme file describing how to run the software.

LICENSE
The software license.

VideoS1.mp4
Supplementary Video S1 of the paper: A video of zebrafish brain ventricular CSF flow simulated with motile cilia and cardiac pulsatility. Initial view is lateral (xz-plane). Velocity vectors are scaled by magnitude, and colored by the magnitude signed with the x component, such that rostrocaudal flow is red and caudorostral flow is blue. The video spans 24 cardiac cycles at 22 fps rate (half of real-time). 

VideoS2.mp4
Supplementary Video S2 of the paper: Transport of secreted and photoconverted Dendra2 in the zebrafish ventricle. Dual color time-lapse confocal images show the location of unconverted (green) and converted (magenta) signals over time. Acquisition rate: 2.67s per frame. Photoconversion is performed from frame 11 to the end (frame 300).