The Microvessel project is a Chaste add-on library with functionality for modelling blood flow, angiogenesis and nutrient transport in microvessels. It is overviewed in the pre-print here. Detailed installation instructions are below. Quiries via the are welcome.
Click on the images below to see some example applications.
The project can be used directly as a typical C++ Chaste project. First, Chaste dependencies need to be built following the Chaste Install Guide. The project only supports the development version of Chaste. This can be obtained by doing:
The project code itself can be obtained by doing:
The Microvessel project code needs to be included in the main Chaste source. This can be done with a symbolic link:
The C++ libraries can be built using the Chaste CMake build system. First, create a build directory outside the source tree and proceed as:
This will build the C++ library and all tests. To avoid building tests do:
as the final command. The Chaste CMake build system guide should be consulted for options related to generating optimized builds, running other types of test and installation as a system library.
The source and test code are in the src
and test
folders respectively. Unit tests can be built and run using the Chaste CMake framework as detailed here. It is recommended that the tutorials are followed. To run the first tutorial do:
To run all C++ tests and tutorials do:
A conda Python package for Linux is currently under development. In the meantime this package needs to be built from source as a PyChaste module. First, build PyChaste following the instructions here.
Then, follow the above C++ instructions to build the Microvessel project, but with the additional CMake flag -DBUILD_MICROVESSEL_PYTHON=ON
. The final steps should look like:
The Python package microvessel
will be in $BUILD_DIR
under Chaste/projects/Microvessel/python
. The finished package should be copied into the chaste/projects
module of PyChaste.
The Python source and tests are in the src/python
and test/python
folders. The Python tutorials should be followed next.
To run the Python tutorial do:
To run all Python tests do:
A full list of tutorials is given at the bottom of this page.