Paraview is a free and open source scientific visualization software, that lets us load and analyze vtk rectilinear grid data and vtk polynomial data, and even ome.tiff data files.

For installation, please follow the official documentation.

• https://www.paraview.org/download/

pcdl_make_conc_vtk output

pcdl_make_cell_vtk output

import pcdl

mcdsts = pcdl.TimeSeries('output/')
mcdsts.make_conc_vtk()
mcdsts.make_cell_vtk()

1. View / Pipeline Browser has to be checked!
2. View / Properties has to be checked!
3. File / Open... path/to/PhysiCell/output/output.._conc.vtr [OK]
4. File / Open... path/to/PhysiCell/output/output.._cell.vtp [OK]
5. In the Pipeline Browser, click the closed eyes, so that they open.
6. In the Pipeline Browser, click the output00000000_cell.vtp* and under Properties Coloring select cell_type in the dropdown menu.
7. In the Pipeline Browser, click the output00000000_conc.vtr* and under Properties Coloring select the oxygen in the dropdown menu.

For learning more about how to run the software, please work through the official documentation.

• https://www.paraview.org/resources/

That's it. The rest is analysis within paraview!