Interconnectivity¶

class arbor.connection¶

Describes a connection between two cells, defined by source and target end points (that is presynaptic and postsynaptic respectively), a connection weight, and a delay time.

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

connection(source, target, weight, delay)¶: Construct a connection between the source and the target 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).

target¶: The target end point of the connection (type: arbor.cell_local_label representing the label of the target 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 and finite.

Note

A minimal full example of a connection reads as follows: (see network tutorial for a more comprehensive example):

import arbor as A
from arbor import units as U

# Create two locset labels, describing the endpoints of the connection.
labels = A.label_dict()
labels['synapse_site'] = '(location 1 0.5)'
labels['root'] = '(root)'

# Place 'expsyn' mechanism on "synapse_site", and a threshold detector at "root"
decor = A.decor()
decor.place('"synapse_site"', 'expsyn', 'syn')
decor.place('"root"', arbor.threshold_detector(-10), 'detector')

# Implement the connections_on() function on a recipe as follows:
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.
   source  = (2, "detector") # gid and locset label of the source
   target = "syn" # gid of the target is determined by the argument to `connections_on`.
   weight = 0.01  # unit/scaling depends on the synapse used; commonly chosen as μS
   d    = 10 * U.ms # delay
   return [arbor.connection(source, target, weight, delay)]

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 target 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.

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 target 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 unit-less weight of the gap junction connection.

class arbor.threshold_detector¶

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

threshold¶: Voltage threshold of threshold detector [mV]

class arbor.network_site_info¶

A network connection site on a cell. Used for generated connections through the high-level network description.

gid¶: The cell index.

kind¶: The cell kind.

label¶: The associated label.

location¶: The local location on the cell.

global_location¶: The global location in cartesian coordinates.

class arbor.network_connection_info¶

A network connection between cells. Used for generated connections through the high-level network description.

source¶: The source connection site.

target¶: The target connection site.

class arbor.network_description¶

A complete network description required for processing.

selection¶: Selection of connections.

weight¶: Weight of generated connections.

delay¶: Delay of generated connections.

dict¶: Dictionary for named selecations and values.

arbor.generate_network_connections(recipe, context=None, decomp=None)¶: Generate network connections from the network description in the recipe. A distributed context and domain decomposition can optionally be provided. Only generates connections with local gids in the domain composition as the target. Will return all connections on every process, if no context and domain decomposition are provided. Does not include connections from the “connections_on” recipe function.