Axon definition

[inesw]

While working on an implementation of the GoC axon for the GoCtoGoCconnections, the following things were noted:

• The parameter GoC_AxonL from the parameter file is never used
• The parameters GoC_Axon_nseg and GoC_Axon_npts that occur within BREP are not defined in the parameter file. However, in the current BREP version of modelDB, the number of axon segments is set to 1, and the number of points is set to 2, namely the soma point and the end point, which makes those two parameters somewhat meaningless.
• Each axon includes the soma point, i.e. if there are 20 axons, the soma point is searched for 20 times
• The paper says 'The GoC axons were represented as uniformly distributed random points in a rectangular area (boundaries in μm: transverse [-45:45], sagittal [-160:160], vertical [-75:75]) relative to the soma position.'

Until further notice, I will handle the case as follows:

• I will represent each axon as its end point. It will thus follow the definition from the paper and effectively be the same as the current BREP code, however I will represent the soma only once. This means, if there are n axons, there will be n+1 points representing the axons.
• As distance of the connection I will take the distance between the axon endpoint and the soma.