README.txt

For the dataset "Data for Image-based modelling of skeletal muscle oxygenation"
available at: http://doi.org/10.5258/SOTON/404926

This dataset is related to the publication: 
Zeller-Plumhoff, B. (2017) 'Image-based modelling of skeletal muscle oxygenation', Royal Society Inteface


This file explains the content of the zip-folder Data_Review_Interface

Folder test_case\constant\triSurface contains the .stl mesh files of the muscle cube and red blood cells within (for Figure 8).

The modelling files are created for execution with OpenFOAM (http://openfoam.com/). The LaplacianFoam solver was adapted by Keith Daly.

To execute, OpenFOAM needs to be installed and the folder "test" needs to be transferred to become a subfolder of the "OpenFOAM" 
folder. The solver then needs to be build using the "wmake" command.

The folder "test_case" remains in the parent directory and should be renamed to "test". 

The file "run.sh" can be executed to solve the equations. It may need to be adjusted to suit the executing system.
"test_5090.vtk" is the result file from executing run.sh in the test folder (in the parent directory). It can be opened in Paraview.

Fig9_1860x1524x500_8bit.raw contains the original dataset with which Figure 9 was created. This is the same dataset as displayed 
in Figure 7.
Fig9_1860x1524x500_8bit_segmented.raw is the segmentation of larger blood vessels, bulk muscle tissue and red blood cells 
from this dataset, based on which the isosurface rendering in Figure 9 was created.

This data is made available under a Creative Commons Attribution Share Alike 4.0 licence.


Please contact berit.zeller-plumhoff@hzg.de (ORCiD: 0000-0002-7562-9423) for further questions.