Interconnectivity

class arbor.connection

Describes a connection between two cells, defined by source and destination end points (that is pre-synaptic and post-synaptic respectively), a connection weight and a delay time.

The dest does not include the gid of a cell, this is because a arbor.connection is bound to the destination cell which means that the gid is implicitly known.

connection(source, destination, weight, delay)

Construct a connection between the source and the dest with a weight and delay.

source

The source end point of the connection (type: arbor.cell_global_label, which can be initialized with a (gid, label) or a (gid, (label, policy)) tuple. If the policy is not indicated, the default arbor.selection_policy.univalent is used).

dest

The destination end point of the connection (type: arbor.cell_local_label representing the label of the destination on the cell, which can be initialized with just a label, in which case the default arbor.selection_policy.univalent is used, or a (label, policy) tuple). The gid of the cell is implicitly known.

weight

The weight delivered to the target synapse. It is up to the target mechanism to interpret this quantity. For Arbor-supplied point processes, such as the expsyn synapse, a weight of 1 corresponds to an increase in conductivity in the target mechanism of 1 μS (micro-Siemens).

delay

The delay time of the connection [ms]. Must be positive.

An example of a connection reads as follows:

import arbor

def connections_on(gid):
   # construct a connection from the "detector" source label on cell 2
   # to the "syn" target label on cell gid with weight 0.01 and delay of 10 ms.
   src  = arbor.cell_global_label(2, "detector")
   dest = arbor.cell_local_label("syn") # gid of the destination is is determined by the argument to `connections_on`
   w    = 0.01
   d    = 10
   return [arbor.connection(src, dest, w, d)]
class arbor.gap_junction_connection

Describes a gap junction between two gap junction sites.

The local site does not include the gid of a cell, this is because a arbor.gap_junction_connection is bound to the destination cell which means that the gid is implicitly known.

Note

A bidirectional gap-junction between two cells c0 and c1 requires two gap_junction_connection objects to be constructed: one where c0 is the local site, and c1 is the peer site; and another where c1 is the local site, and c0 is the peer site. If ggap is equal in both connections, a symmetric gap-junction is formed, other wise the gap-junction is asymmetric.

peer

The gap junction site: the remote half of the gap junction connection (type: arbor.cell_global_label, which can be initialized with a (gid, label) or a (gid, label, policy) tuple. If the policy is not indicated, the default arbor.selection_policy.univalent is used).

local

The gap junction site: the local half of the gap junction connection (type: arbor.cell_local_label representing the label of the destination on the cell, which can be initialized with just a label, in which case the default arbor.selection_policy.univalent is used, or a (label, policy) tuple). The gid of the cell is implicitly known.

ggap

The gap junction conductance [μS].

class arbor.spike_detector

A spike detector, generates a spike when voltage crosses a threshold. Can be used as source endpoint for an arbor.connection.

threshold

Voltage threshold of spike detector [mV]