SpikeFun 0.5 - Let's get... brainy :-)

And Now for Something Completely Different ...

SpikeFun v0.5 has just been released, and it contains huge improvements and some quite neat brand new features:

Let's start with the real 3D brain geometry!

If you download SpikeFun v0.50 (and, of course, you can download it here ) you will notice one large file (large as compared to SpikeFun.exe) called "brain_comp.bin". This file contains compressed 3D brain data. If you run any of the "CortexDemo" scripts (or configure your own thalamocortical simulation in SpikeFun settings), SpikeFun will load the said 3D data and create neurons layered on the 3D mesh.

This feature is heavily in development and, right now, it is far from being complete. For example, actual axonal pathways are simple (as well as axons) and do not follow the actual pathways found in the human brain. This will be added in one of the next SpikeFun versions by guiding axons using the white matter DTI (Diffusion Tensor Imaging) MRI data. In addition, thalamus is still a simple sphere (you can see in the center of the brain model) and currently entire 3D model of the brain is treated as cortex. Because 3D model contains thalamus, basal ganglia, brainstem and cerebellum, I will need to partition the 3D mesh and fill the regions with the appropriate neurons... again, this is going to be done in one of the next SpikeFun revisions.

But, even with those shortcomings, the current model is very interesting. Picture below shows it in action with very small number of neurons - even with just ~110000 neurons, it is possible to alternate between delta-wave and gamma-wave activity by switching the stimuli ON and OFF. In this experiment with just ~110K neuron, without stimuli brain will go into typical "spike and wave" pattern similar to the activity found during some epileptic seizures. With much larger number of neurons (~1 million neurons or more), even stimuli-free activity will contain strong gamma-activity for a while.

Apart from the real brain model, SpikeFun v0.5 contains more improvements:

  • AVX optimizations are not requiring separate executable
  • 32-bit and 64-bit builds of SpikeFun are now distributed in one package
  • "Demo view" now contains fMRI BOLD and EEG simulations
  • fMRI BOLD simulation is of higher resolution

Picture below describes the activity mentioned above:


... And this is how the model looks with ~660K neurons: