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CompuCell3D Advanced Tutorials

Plugin Development Tutorials by Jeremy Fisher

Moved Sample Code to Github

For the tutorial series on Plugin and Wrapper development, I have moved the relevant code to my github repository here.

Happy simulating!

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Making a CompuCell Plugin with a Python Wrapper: Part 3

Welcome to the final part of this tutorial series! In this section, we’ll create a CC3D project. Open Twedit++, and in the menu select CC3DProject > New CC3D Project…I like to separate Python and XML, so we’ll use that format for this section. Continue reading “Making a CompuCell Plugin with a Python Wrapper: Part 3”

Making a CompuCell Plugin with a Python Wrapper: Part 2

Welcome back! At the beginning of this tutorial, you should have set up all the needed files, as well as a method to debug your plugin. By the end, you will know how to program a Change Energy Function, access XML attributes/elements and store additional variables in each cell.

Continue reading “Making a CompuCell Plugin with a Python Wrapper: Part 2”

Making a CompuCell Plugin with a Python Wrapper: Part 1

Introduction

Like the previous tutorial, we will be manipulating the energy term for a pixel flip attempt to make the cells in the simulation circular. However, we will do this in c++, rather than python because

  • It is more efficient by far; and
  • Accessing cell parameters does not cause a crash, as it would if we were to use Python.

Continue reading “Making a CompuCell Plugin with a Python Wrapper: Part 1”

CompuCell Theory

To accomplish a given cellular behavior, CompuCell3D offers many tools, some more suited than others. It is important to understand how these tools are implemented, because each has its pitfalls. For example, don’t try to change individual cell shapes in python — because that part of the software does a poor job of influencing membrane fluctuation; and don’t try to write a c++ plugin to change the cell volume — because it would be redundant and difficult to share.

Continue reading “CompuCell Theory”

Manipulating the Energy Term for a Pixel Flip Attempt in Python

Introduction

In this tutorial, we will be manipulating the energy term for a pixel flip attempt to make the cells in the simulation circular. For now, we’ll do this in python.

Continue reading “Manipulating the Energy Term for a Pixel Flip Attempt in Python”

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