Thursday 4 August 2011

3D simulated cells visualisation.

As part of my ongoing PhD in computational biology I've needed to look at methods of visualising simulated multi-cellular structures (tissue) in 3D.  CompuCell3D (the modelling environment on which I develop) has the facility to render opaque surfaces of clusters of cells of the same type, which can allow you to see broad structural detail, but generally not the behaviour of individual cells.  I developed a visualisation that shows individual cell surfaces, each coloured according to a chosen cell variable (for me, the level of protrusive activity), as seen in this rotation of a model 'engineered epithelial tubule':


Of course you might be interested in a certain region or cell, so I use the VTK cursor widget to allow selection of a point or cell around which cells are displayed, opacity decreasing with distance.  I'm also interested in cell paths, so I incorporated these as well.  This image is of the same tubule showing the region around one cell of interest, along with some other cell paths:


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