Reanimate is a C++ library to simulate fluid and mass transport in microvascular tissue. The main goal of this project is to provide a simple and flexible framework to simulate blood flow, interstitial flow, and tracer or drug delivery in large microvascular networks. These networks are imported as weighted, undirected graphs which represent a network(s) of blood vessels generated either synthetically or by segmenting and skeletonising biomedical images.
Reanimate implements several mathematical models in research literature including:
- Poiseuille's Law for axisymmetric, laminar pipe flow in 1D networks with known boundary conditions.
- Empirical blood viscosity laws to compute bulk blood viscosity as a function of vessel diameter and haematocrit, thereby capturing the Fåhraeus-Lindqvist effect.
- Empirical phase separation law to calculate the disproportion distribution of haematocrit at microvascular bifurcations.
- Numerical update to phase separation law which accounts for cell-free layer disruption and recovery.
- Blood flow estimation model to simulate blood flow in a microvascular network with incomplete boundary conditions.
- Interstitial flow model which uses a Green's function method to simulate transvascular fluid transport (TO BE IMPLEMENTED).
The Reanimate C++ library is the 2nd generation, user-friendly version of the code which forms the basis of the REANIMATE (Realistic Numerical Image-based Modelling of Biological Tissue Substrates) framework published here and corresponding mathematical methods here.
If you wish to cite the Reanimate library in your work, please use the following references:
Computational fluid dynamics with imaging of cleared tissue and of in vivo perfusion predicts drug uptake and treatment responses in tumours
Angela d'Esposito & Paul W. Sweeney et al.
Modelling the transport of fluid through heterogeneous, whole tumours in silico
Paul W. Sweeney et al.
Reanimate is compatible with C++11, and has been tested on Ubuntu 18.04 LTS and macOS Big Sur. Other distributions of Linux and Windows should work as well.
To install Reanimate from source, download zip file on GitHub page or run the following in a terminal:
git clone https://github.com/psweens/Reanimate.gitThe Reanimate C++ library is an open-source project started by Dr Paul Sweeney during his PhD at University College London under the supervision of Prof. Rebecca Shipley and Prof. Simon Walker-Samuel. The package is maintained by Dr Paul Sweeney on Github. All contributions of all types are most welcome!
Contribution guidelines are available here and a list of feature requests can be found here.
I would like to acknowledge that the Reanimate C++ library utilises several portions of code originally written by Prof. Timothy Secomb but amended to allow integration of the Armadillo C++ library.