The Python interface can be used to automatize the creations of axonal trajectories within nerves/fascicles to execute EM-Neuronal simulations.
For example, let's assume that the user wants to populate a cylindrical fascicle with R=1mm and L=100mm with N=100 axonal trajectories randomly distributed. In order to maintain the 'Model' panel clean, a 'Axonal Trajectories' folder is created as well.
The following code does the job:
import s4l_v1 as s4l import numpy as np from s4l_v1 import Vec3 # Parameters definition R=1 # Radius (mm) L=100 # Length of the cylinder (mm) N=100 # Number of axons ## Creates a folder in the Model Panel folder=s4l.model.CreateGroup('Axon Trajectories') # Initialization points=; cnt=0 while cnt<N: # Creates Randomly Distributed Points in the cross section x=2*R*(-0.5+np.random.rand()); y=2*R*(-0.5+np.random.rand()) # only the axons within the cylinders are taken if (x*x+y*y<R*R): pin=Vec3(x,y,-0.5*L); pend=Vec3(x,y,-0.5*L) axon=s4l.model.CreatePolyLine([pin,pend]) axon.Name='Axon_'+str(cnt) folder.Add(axon) cnt+=1
The code can be modified to permit arbitrary distributions of fibers within the fascicle entity.