VtkPlotter: 3D renderings of Morpheus simulations

We have re-implemented Morpheus’ VtkPlotter that write multichannel Vtk files. Vtk files can be used to create beautiful 3D rendering to visuaize cells and tissues with tools such as ParaView and VisIt.

The XML interface for the new Analysis plugin is similar to that of the TiffPlotter. You can select a number of channels, each of which is associated with a symbolic reference (to cell properties or fields or whatever). For instance:

<VtkPlotter time-step="100">
   <Channel symbol-ref="cell.id" no-outline="true"/>
   <Channel symbol-ref="act"/>

This will create a single VTK file (every 100 steps) with two channels: one with the cell.id (a cell property) and one with the “act” (a Field). The no-outline option prevents the cell boundary to be plotted, such that the values of the “act” Field will be visible along the cell boundary.

Currently, it exports the simplest possible Vtk file format: the ASCII-based legacy Vtk format. In following releases, the plugin will be improved to write on binary format to reduce read/write time as well as file size.


Cell exported using the TiffPlotter and rendered in BioView3D. Color indicates value of MembraneProperty.


Cell exported using VtkPlotter and rendered using ParaView. Color indicates values of MembraneProperty










If you are interested in the code, take a look at my gitlab repository: