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 aarbor.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 thedest
with aweight
anddelay
.
- 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 defaultarbor.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 defaultarbor.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 of1
corresponds to an increase in conductivity in the target mechanism of1
μS (micro-Siemens).
- delay¶
The delay time of the connection [ms]. Must be positive.
Note
An minimal full example of a connection reads as follows: (see network tutorial for a more comprehensive example):
import arbor # Create two locset labels, describing the endpoints of the connection. labels = arbor.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 = arbor.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. src = (2, "detector") # gid and locset label of the source dest = "syn" # gid of the destination is determined by the argument to `connections_on`. w = 0.01 # weight of the connection. Correspondes to 0.01 μS on expsyn mechanisms d = 10 # delay in ms 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 aarbor.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
andc1
requires twogap_junction_connection
objects to be constructed: one wherec0
is thelocal
site, andc1
is thepeer
site; and another wherec1
is thelocal
site, andc0
is thepeer
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 defaultarbor.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 defaultarbor.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]