3D network graphs with Python and the mplot3d toolkit

An example of a 3D network graph using Python and the mplot3d toolkit of the Matplotlib library.

The worked example is available on our blog at

We develop methods to study complex structural networks in biological structures (for instance roots or neurons). This kind of structures can be measured using, for instance, Computed Tomography or Optical Projection Tomography. Unlike more general networks (for example social media networks) structural biological networks are inherently 3D.

Understanding the 3D structure is often the key to understanding the function. That is why a lot of work is being done around the world to develop 3D imaging methods.

[YatharthRai]

Thank you so much! Have been looking for something like this for quite some time

[Dent]

Okay, I now have a folder full of PNGs. How do I inspect the graph live?

[ExtraterrestrialIntelligence]

The Russian government is in possession of a coloured 3D network graph of the neural network of the extra universal artificial intelligence codenamed SEXBOT in a parallel universe