I am trying to mimic the segment patterning in fruit flies through a CC3D model. Can anyone help me as to how to draw out a 3D paraboloid PIFF file with different cell types along the surface?


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5 months ago by
Currently, I see no options to draw a 3D PIF in Cell Draw. The objective is to show segment width of different cell types (coloured differently) with variable values of the contractility term aka Young's modulus. Also, the environment needs to be bounded, meaning the boundary conditions should be fixed or periodic but can't be open.
Community: CompuCell3D
Hi, as far as I am concerned, the contractility term is a little different from Young's modulus. What's your contractility term, the lambda volume or surface?
written 5 months ago by Yuan  
The contractility term is Lambda surface
written 5 months ago by Abhishek Das  
Yes, when I use the Lambda surface, the cells often tend to be rectangle or so, which is not analogous to the condition of cells. Have you ever meet such things?
written 5 months ago by Yuan  
Yes, in a realistic embryo system of a developing fly the cell shapes are more of polygonal nature with pentagons and hexagons visible but with CC3D if I initialize the system with square cells, ideally the cells will try to get to a circular shape over time due to energy minimisation principle. The catch point is the regional geometrical constraints play a role (i.e. if you dont want your cells to divide and play with a constant number of cells).

Although I must say, even though visibly they look rectangular or squarish from the sim output, performing a Voronoi analysis (after  extracting the center of mass of the cells) showed a distribution of polygonal shapes at steady state!
written 5 months ago by Abhishek Das  
Not very familiar with Cell Draw. But you can use a separate CC3D simulation to generate a PIF file with your initial conditions first and later on export it for other simulations.  (CC3D Gui -> Tools-> Generate a PIF from current snapshot) . Advantage is you can attach your Young's modulus to each cell and adjust it's constraints to describe your system. (Note to construct cells of arbitrary lengths you can use self.cellField)  
written 5 months ago by priyomadhyapok  

1 Answer


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5 months ago by

Expanding on priyomadhyapok’s answer; Sometimes the easiest way to generate a cell layout (2D or 3D) is to just do it directly in CC3D. If you can write the equations for the geometry you can have python place the individual cells exactly where you want them.

The key commands are;

Iterate over all pixels in the model (in the python steppables file);

for x in range (0,self.dim.x):  # x, y and z width of the bounding box
    for y in range (0,self.dim.y):
        for z in range (0,self.dim.z):
            print x,y,z

Create a new cell at a particular location (in the python steppables file);

newcell=self.newCell(self.MYCELL) 

# MYCELL is the all-uppercase name of the cell type you want
SIZE=5.
self.cellField[x:int(x+SIZE-1),y:int(y+SIZE-1),z:int(z+SIZE-1)]=newcell
# the size of cell will be SIZExSIZExSIZE
# if you want to have the new cell centered at the3 pixel you will need something like;
# [int(x-SIZE/2.:int(x+SIZE/2. -1), ...


Write a piff file (goes in the project’s XML file)

<Steppable Frequency="100" Type="PIFDumper">
   <!-- Periodically stores cell layout configuration in a piff format -->
   <PIFName>SphereOfCells</PIFName>
   <PIFFileExtension>piff</PIFFileExtension>
</Steppable>

Note: the piff file (SphereOfCells.piff) is written in the CC3D directory (e.g., C:\CompuCell3D) and not in the project’s directory like it should!

I have attached a zipped CC3D project called SphereOfCells that uses CC3D/Python to create a hollow sphere of cells and saves it as a piff file.

File attached: SphereOfCells.zip (262.91 KB)

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