GENESIS Reference Manual August 1, 1997: Synaptic Connections

14. Synaptic Connections

Synaptic connections to neurons are established by sending a SPIKE message from a spiking class element to a synchannel class element. Typically, this means using a spikegen element to convert action potentials to delta-function ``spike events'' and establishing a SPIKE message to a synchan element. The propagation delays and synaptic weighting for each synaptic connection are stored in the synchan.

For example, to send somatic action potentials in cell1 to ``Ex_channel'' in the dendrite compartment of cell2, one might use:

  create spikegen /cell1/soma/spike
  setfield /cell1/soma/spike thresh 0 abs_refract 0.010 output_amp 1
  addmsg  /cell1/soma  /cell1/soma/spike  INPUT Vm

  addmsg /cell1/soma/spike /cell2/dend/Ex_channel SPIKE
  setfield /cell2/dend/Ex_channel synapse[0].weight 10 synapse[0].delay 0.005

Here, this synaptic connection is labeled as ``synapse[0]'', as it was the first (of possibly several) to be established with the SPIKE message. A more detailed example is given in Scripts/tutorials/tutorial4.g, and is discussed in Chapter 14 of ``The Book of GENESIS''. The Scripts/orient_tut directory contains examples of routines for setting up networks of synaptically connected cells. Further details of the construction of neural circuits and networks are given in Chapter 17 of ``The Book of GENESIS''.

The following GENESIS routines are used for establishing and working with synaptic connections:

Routine Description
getsynindex Returns the synapse index in a synchan element
given the source element.
getsyncount Returns the number of synapses or SPIKE messages
for synchan and spikegen objects.
getsynsrc Returns the source path of a synapse given the
destination and the synapse index.
getsyndest Returns the destination path or index of a synapse
given the source path and number of the SPIKE message.

planarconnect Connects one group of elements in a plane to another,
using source and destination element lists and masks.
volumeconnect Connects one group of elements in a volume to another,
using source and destination element lists and masks.

planardelay Sets delays of a group of synapses receiving input
from a list of presynaptic elements in a plane.

volumedelay Sets delays of a group of synapses receiving input
from a list of presynaptic elements in a volume.
syndelay Sets up delays of a group of postsynaptic objects.

planarweight Sets weights of a group of synapses receiving input
from a list of presynaptic elements in a plane.
volumeweight Sets weights of a group of synapses receiving input
from a list of presynaptic elements in a volume.
normalizeweights Sets the cumulative synaptic weight on a synaptic
channel to a given or randomly selected value.

resetsynchanbuffers Shrinks the event buffer down to its original size
for synchan2 objects.

Earlier versions of GENESIS used a different method of establishing synaptic connections by means of axon objects (projections) which hold the delays and weights for each connection. This approach, which is not recommended for new simulations, is illustrated in the Scripts/MultiCell simulation.

The following obsolete routines (available in the Connection Compatibility Library) are used with old-style axonal connections:

Routine Description
connect Creates connection between a projection and a segment,
using connection element of a specified type.
delete_connection Deletes a connection between a projection and a
segment.
getconn Returns axon connection weight and delay.
setconn Sets axon connection weight and delay.
showconn Prints out weight or delay of a specified axonal
connection.

cstat Displays information about connections off of a
projection.

region_connect Connects one group of elements in a plane to another,
using source and destination element lists and masks.
volume_connect Connects one group of elements in a volume to another,
using source and destination element lists and masks.

scaleweight Adjusts the weight of a connection by a given scaling
factor.
expweight Sets weights of efferents from arrays of neurons
created with createmap and connected with
region_connect.
normalize_synapses Sets the cumulative weight of axonal connections to
a channel to a given or randomly selected value.
radialdelay Sets delays of a group of synapses receiving input
from a list of presynaptic elements in a plane.
expsum Returns exponentially weighted sum of connection
weights according to the radial distance.
affweight Calculates weights of projections along a path which
decay exponentially in strength with distance.
affdelay calculates an aggregate delay between elements
separated by two paths, one fast-conducting and
one slow-conducting

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Routine	Description
getsynindex	Returns the synapse index in a synchan element
	given the source element.
getsyncount	Returns the number of synapses or SPIKE messages
	for synchan and spikegen objects.
getsynsrc	Returns the source path of a synapse given the
	destination and the synapse index.
getsyndest	Returns the destination path or index of a synapse
	given the source path and number of the SPIKE message.

planarconnect	Connects one group of elements in a plane to another,
	using source and destination element lists and masks.
volumeconnect	Connects one group of elements in a volume to another,
	using source and destination element lists and masks.

planardelay	Sets delays of a group of synapses receiving input
	from a list of presynaptic elements in a plane.

volumedelay	Sets delays of a group of synapses receiving input
	from a list of presynaptic elements in a volume.
syndelay	Sets up delays of a group of postsynaptic objects.

planarweight	Sets weights of a group of synapses receiving input
	from a list of presynaptic elements in a plane.
volumeweight	Sets weights of a group of synapses receiving input
	from a list of presynaptic elements in a volume.
normalizeweights	Sets the cumulative synaptic weight on a synaptic
	channel to a given or randomly selected value.

resetsynchanbuffers	Shrinks the event buffer down to its original size
	for synchan2 objects.


Routine	Description
connect	Creates connection between a projection and a segment,
	using connection element of a specified type.
delete_connection	Deletes a connection between a projection and a
	segment.
getconn	Returns axon connection weight and delay.
setconn	Sets axon connection weight and delay.
showconn	Prints out weight or delay of a specified axonal
	connection.

cstat	Displays information about connections off of a
	projection.

region_connect	Connects one group of elements in a plane to another,
	using source and destination element lists and masks.
volume_connect	Connects one group of elements in a volume to another,
	using source and destination element lists and masks.

scaleweight	Adjusts the weight of a connection by a given scaling
	factor.
expweight	Sets weights of efferents from arrays of neurons
	created with createmap and connected with
	region_connect.
normalize_synapses	Sets the cumulative weight of axonal connections to
	a channel to a given or randomly selected value.
radialdelay	Sets delays of a group of synapses receiving input
	from a list of presynaptic elements in a plane.
expsum	Returns exponentially weighted sum of connection
	weights according to the radial distance.
affweight	Calculates weights of projections along a path which
	decay exponentially in strength with distance.
affdelay	calculates an aggregate delay between elements
	separated by two paths, one fast-conducting and
	one slow-conducting