SpikeFun 0.57 - DSI Axon Guidance, Multi-Site EEG, Experiments...

SpikeFun v0.57 has just been released... and with this release it is the right time to describe several important changes that had happened since the last post. And there are, indeed, many! So, what are they?

  • Axon routing through white matter by using DSI (Diffusion Tensor Imaging) data - DSI Studio Engine is used for dynamic build-up of DSI tracts (you can select how many tracts to use for a simulation)
  • New and significantly improved algorithm for generation of the cortical network (3-4 times faster)
  • Fixed over-provisioning of neural compartments in cases where there are not enough synaptic candidates to meet the cell requirements
  • Added capability to inject brief depolarizing current into the selected neuron ('I' key)
  • Added capability to adjust the brainstem modulation level of the thalamus as well as artificially-generated sensory stimulus intensity
  • Added multi-site intracranial EEG simulation (F2 key)
  • New "brain view" user interface that also allows viewing of axonal bifurcations
  • Improved cortex and thalamus 3D model (generated by FreeSurfer)
  • Added support for cortical labels (generated by FreeSurfer)
  • New command-line interface (-h for help)
  • Removed "box" simulations as they are quite obsolete by now

Let's start with the improved GUI - below view shows the new "brain view" user interface. As you can see, selected neuron axons are visible, including the white matter portions (DSI data):

Picture 1: BrainView GUI:


Another improvement is multi-site intracranial EEG - it is activated by pressing F2 key during the simulation and it is designed to show EEG activity located in several key regions of the cortex:


Following two videos show SpikeFun 0.57 in action, simulating 1.4 million neurons with ~140 million synapses: