3D Cell Shapes


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3 months ago by
Hi,

I wonder if it is possible not only to draw 3D shapes but also keep them during growth and mitosis events?
Does lay around every cell a rectangular box or is it possible to select a different shape for a 3D simulation?

Thank you,
Thorsten
Community: CompuCell3D

1 Answer


1
3 months ago by
your best bet if you want to have control over cell shape is to use compartmentalized cells.

See

http://www.compucell3d.org/BinDoc/cc3d_binaries/Manuals/CompuCell3D_Reference_Manual_v.3.7.4.pdf

page 27

and check chapter of length constraint plugin that follows.

As far as mitosis this should help you get started:

http://pythonscriptingmanual.readthedocs.io/en/latest/dividing_clusters.html





2
To add more to my previous answer. The shape of a single cell could be controlled by choosing properly contact energy (NeighborOrder parameter in the Contact plugins plays actually and important role so make sure it is not 1 but bigger to avoid rectangular lattice-related artifacts). Additionally you would control contact energy coefficients and also you may include surface and volume constraints. You may also play with Length constraints. I would suggest that when doing 3D simulation, to start with a single cell and get the parameters right first. Then slowly keep adding components to your simulation and see how things behave. For example you could study what happens at the mitosis stage starting with just one cell. Also to mak simulation run faster start with smaller lattice and increase the size as you add more components. this way you will not waste time by probing the lattice regions that have no cells. Let me know if this answers your questions
written 3 months ago by Maciek Swat  
Thanks for the extensive answer. It definitely helped.

I'm still wondering how the volume and surface of each single cell is calculated?
Is it the calculation for a cuboid, since in 3D we have voxels to display, or is more deeply and than the amount of lattices sites within each cell?
written 3 months ago by Thorsten Mueller  
1
In a 2D CC3D model the "cell surface" is actually a length and the "cell volume" is actually an area. The units are pixels and pixels^2, respectively.

In a 3D CC3D model the "cell surface" is a true area and the "cell volume" is a true volume. The units are pixels^2 and pixels^3, respectively.

Area and volume, in both 2D and 3D, are always integers.

In both 2D and 3D the measurement is over the actual set of pixels (or voxels) and no smoothing or interpolation of the surface is done. As a result, the surfaces tend to be larger than they would be on a smooth surface since the lattice based surface "staircases".
written 3 months ago by James Sluka  
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