Synapse specification¶

This page is about parameterizing synapses. See Connectivity concepts for specifying connections (for using an external library see Connection generator interface) and Working with connections for inspecting and modifying SynapseCollections.

The synapse properties can be given as just the name of the desired synapse model as a string, as a dictionary specifying synapse model and parameters, or as a CollocatedSynapse object creating multiple synapses for each source-target pair as detailed in the section on collocated synapses.

n = 10
A = nest.Create('iaf_psc_alpha', n)
B = nest.Create('iaf_psc_alpha', n)
nest.Connect(A, B, syn_spec='static_synapse')

syn_spec_dict = {'synapse_model': 'stdp_synapse',
                 'weight': 2.5, 'delay': 0.5}
nest.Connect(A, B, syn_spec=syn_spec_dict)

If synapse properties are given as a dictionary, it may include the keys synapse_model (default static_synapse), weight (default 1.0), delay (default 1.0), and receptor_type (default 0, see Receptor Types for details), as well as parameters specific to the chosen synapse model. The specification of all parameters is optional, and unspecified parameters will take on the default values of the chosen synapse model that can be inspected using nest.GetDefaults(synapse_model).

Parameters can be either fixed scalar values, arrays of values, or expressions.

One synapse dictionary can contain an arbitrary combination of parameter types, as long as they are supported by the chosen connection rule.

Scalar parameters¶

Scalar parameters must be given with the correct type. The weight for instance must be a float, while the receptor_type has to be of type integer. When a synapse parameter is given as a scalar, the value will be applied to all connections created in the current Connect() call.

n = 10
neuron_dict = {'tau_syn': [0.3, 1.5]}
A = nest.Create('iaf_psc_exp_multisynapse', n, neuron_dict)
B = nest.Create('iaf_psc_exp_multisynapse', n, neuron_dict)
syn_spec_dict ={'synapse_model': 'static_synapse', 'weight': 2.5, 'delay': 0.5, 'receptor_type': 1}
nest.Connect(A, B, syn_spec=syn_spec_dict)

Array parameters¶

Array parameters can be used with the rules one_to_one, all_to_all, fixed_total_number, fixed_indegree, and fixed_outdegree. For details on connection rules, see Connectivity concepts. The arrays can be specified as NumPy arrays or Python lists. As with the scalar parameters, all parameters have to be specified as arrays of the correct type.

One-to-one¶

For rule One-to-one the array must have the same length as there are nodes in A and B.

A = nest.Create('iaf_psc_alpha', 2)
B = nest.Create('spike_recorder', 2)
conn_spec_dict = {'rule': 'one_to_one'}
syn_spec_dict = {'weight': [1.2, -3.5]}
nest.Connect(A, B, conn_spec_dict, syn_spec_dict)

All-to-all¶

When connecting with rule All-to-all, the array parameter must have dimension len(B) x len(A).

A = nest.Create('iaf_psc_alpha', 3)
B = nest.Create('iaf_psc_alpha', 2)
syn_spec_dict = {'weight': [[1.2, -3.5, 2.5], [0.4, -0.2, 0.7]]}
nest.Connect(A, B, syn_spec=syn_spec_dict)

Random, fixed total number¶

For rule Random, fixed total number, the array has to be same the length as the number of connections N.

A = nest.Create('iaf_psc_alpha', 3)
B = nest.Create('iaf_psc_alpha', 4)
conn_spec_dict = {'rule': 'fixed_total_number', 'N': 4}
syn_spec_dict = {'weight': [1.2, -3.5, 0.4, -0.2]}
nest.Connect(A, B, conn_spec_dict, syn_spec_dict)

Random, fixed in-degree¶

For rule Random, fixed in-degree the array has to be a two-dimensional NumPy array or Python list with shape (len(B), indegree), where indegree is the number of incoming connections per target neuron. This means that the rows describe the target, while the columns represent the connections converging on the target neuron, regardless of the identity of the source neurons.

A = nest.Create('iaf_psc_alpha', 5)
B = nest.Create('iaf_psc_alpha', 3)
conn_spec_dict = {'rule': 'fixed_indegree', 'indegree': 2}
syn_spec_dict = {'weight': [[1.2, -3.5],[0.4, -0.2],[0.6, 2.2]]}
nest.Connect(A, B, conn_spec_dict, syn_spec_dict)

Random, fixed out-degree¶

For rule Random, fixed out-degree the array has to be a two-dimensional NumPy array or Python list with shape (len(A), outdegree), where outdegree is the number of outgoing connections per source neuron. This means that the rows describe the source, while the columns represent the connections starting from the source neuron regardless of the identity of the target neuron.

A = nest.Create('iaf_psc_alpha', 2)
B = nest.Create('iaf_psc_alpha', 5)
conn_spec_dict = {'rule': 'fixed_outdegree', 'outdegree': 3}
syn_spec_dict = {'weight': [[1.2, -3.5, 0.4], [-0.2, 0.6, 2.2]]}
nest.Connect(A, B, conn_spec_dict, syn_spec_dict)

Expressions as parameters¶

nest.Parameter objects support a flexible specification of synapse parameters through expressions. This includes parameters drawn from random distributions and depending on spatial properties of source and target neurons. Parameters can be combined through mathematical expressions including conditionals, providing for a high degree of flexibility.

The following parameters and functionalities are provided:

Random parameters
Spatial parameters
Spatially distributed parameters
Mathematical functions
Clipping, redrawing, and conditional parameters

For more information, check out the guide on parametrization or the documentation on the different PyNEST APIs.

n = 10
A = nest.Create('iaf_psc_alpha', n)
B = nest.Create('iaf_psc_alpha', n)
syn_spec_dict = {
    'synapse_model': 'stdp_synapse',
    'weight': 2.5,
    'delay': nest.random.uniform(min=0.8, max=2.5),
    'alpha': nest.math.redraw(nest.random.normal(mean=5.0, std=1.0), min=0.5, max=10000.)
}
nest.Connect(A, B, syn_spec=syn_spec_dict)

In this example, the default connection rule all_to_all is used and connections will be using synapse model stdp_synapse. All synapses are created with a static weight of 2.5 and a delay that is uniformly distributed in [0.8, 2.5]. The parameter alpha is drawn from a normal distribution with mean 5.0 and standard deviation 1.0; values below 0.5 and above 10000 are excluded by re-drawing if they should occur. Thus, the actual distribution is a slightly distorted Gaussian.

If the synapse type is supposed to have a unique name and still use distributed parameters, it needs to be defined in two steps:

n = 10
A = nest.Create('iaf_psc_alpha', n)
B = nest.Create('iaf_psc_alpha', n)
nest.CopyModel('stdp_synapse', 'excitatory', {'weight':2.5})
syn_dict = {
    'synapse_model': 'excitatory',
    'weight': 2.5,
    'delay': nest.random.uniform(min=0.8, max=2.5),
    'alpha': nest.math.redraw(nest.random.normal(mean=5.0, std=1.0), min=0.5, max=10000.)
}
nest.Connect(A, B, syn_spec=syn_dict)

For further information on the available distributions see Random numbers in NEST.

Collocated synapses¶

Some modeling applications require multiple connections between the same pairs of nodes. An example of this could be a network, where each pre-synaptic neuron connects with a static synapse to a modulatory receptor on the post-synaptic neuron and with a plastic synapse to a normal NMDA-type receptor.

This type of connectivity is especially hard to realize when using randomized connection rules, as the chosen pairs that are actually connected are only known internally, and have to be retrieved manually after the call to Connect() returns.

To ease the setup of such connectivity patterns, NEST supports a concept called collocated synapses. This allows the creation of several connections between chosen pairs of neurons (possibly with different synapse types or parameters) in a single call to nest.Connect().

To create collocated synapses, the synapse specification consists of an object of type CollocatedSynapses, whose constructor takes synapse specification dictionaries as arguments and applies the given dictionaries to each source-target pair internally.

nodes = nest.Create('iaf_psc_alpha', 3)
syn_spec = nest.CollocatedSynapses({'weight': 4.0, 'delay': 1.5},
                                   {'synapse_model': 'stdp_synapse'},
                                   {'synapse_model': 'stdp_synapse', 'alpha': 3.0})
nest.Connect(nodes, nodes, conn_spec='one_to_one', syn_spec=syn_spec)
print(nest.GetConnections().alpha)

The example above will create 9 connections in total because there are 3 neurons times 3 synapse specifications in the CollocatedSynapses() object, and the connection rule one_to_one is used.

>>> print(nest.num_connections)
9

In more detail, the connections have the following properties:

3 are of type static_synapse with weight 4.0 and delay 1.5
3 are of type stdp_synapse with the default value for alpha
3 are of type stdp_synapse with an alpha of 3.0.

If you want to connect with different receptor types, you can do the following:

A = nest.Create('iaf_psc_exp_multisynapse', 7)
B = nest.Create('iaf_psc_exp_multisynapse', 7, {'tau_syn': [0.1 + i for i in range(7)]})
syn_spec_dict = nest.CollocatedSynapses({'weight': 5.0, 'receptor_type': 2},
                                        {'weight': 1.5, 'receptor_type': 7})
nest.Connect(A, B, 'one_to_one', syn_spec_dict)

>>> print(nest.GetConnections().get())

You can see how many synapse parameters you have by calling len() on your CollocatedSynapses object:

>>> len(syn_spec_dict)
2

Spatially-structured networks¶

Nodes in NEST can be created so that they have a position in two- or three-dimensional space. To take full advantage of the arrangement of nodes, connection parameters can be based on the nodes’ positions or their spatial relation to each other. See Spatially-structured networks for the full information about how to create and connect such networks.

Connecting sparse matrices with array indexing¶

Oftentimes, you will find yourself in a situation, where you want to base your connectivity on actual data instead of rules. A common scenario is that you have a (sometimes sparse) connection matrix coming from an experiment or from a graph algorithm. Let’s assume you have a weight matrix of the form:

\[\begin{split}W = \begin{bmatrix} w_{11} & w_{21} & \cdots & w_{n1} \\ w_{12} & w_{22} & \cdots & w_{n2} \\ \vdots & \vdots & \ddots & \vdots \\ w_{1m} & w_{2m} & \cdots & w_{nm} \\ \end{bmatrix}\end{split}\]

where \(w_{ij}\) is the weight of the connection with pre-synaptic node \(i\) and post-synaptic node \(j\). In all generality, we can assume that some weights are zero, indicating that there is no connection at all.

As there is no support for creating connections from the whole matrix directly, we will instead just iterate the pre-synaptic neurons and connect one column at a time. We assume that there are \(n\) pre-synaptic nodes in the NodeCollection A and \(m\) post-synaptic nodes in B. We also assume that we have our weight matrix given as a two-dimensional NumPy array W, with \(n\) columns and \(m\) rows.

W = numpy.array([[0.5,  0.0, 1.5],
                 [1.3,  0.2, 0.0],
                 [0.0, 1.25, 1.3]])

A = nest.Create('iaf_psc_alpha', 3)
B = nest.Create('iaf_psc_alpha', 3)

for i, pre in enumerate(A):
    # Extract the weights column.
    weights = W[:, i]

    # To only connect pairs with a nonzero weight, we use array indexing
    # to extract the weights and post-synaptic neurons.
    nonzero_indices = numpy.where(weights != 0)[0]
    weights = weights[nonzero_indices]
    post = B[nonzero_indices]

    # Generate an array of node IDs for the column of the weight
    # matrix, with length based on the number of nonzero
    # elements. The array's dtype must be an integer.
    pre_array = numpy.ones(len(nonzero_indices), dtype=int) * pre.get('global_id')

    # nest.Connect() automatically converts post to a NumPy array
    # because pre_array contains multiple identical node IDs. When
    # also specifying a one_to_one connection rule, the arrays of
    # node IDs can then be connected.
    nest.Connect(pre_array, post, conn_spec='one_to_one', syn_spec={'weight': weights})

Receptor Types¶

Conceptually, each connection in NEST terminates at a receptor on the target node. The exact meaning of such a receptor depends on the concrete type of that node. In a multi-compartment neuron, for instance, the different compartments could be addressed as different receptors, while another neuron model might make sets of different synaptic parameters available for each receptor. Please refer to the neuron models documentation for details.

In order to connect a pre-synaptic node to a certain receptor on a post-synaptic node, the integer ID of the target receptor can be supplied under the key receptor_type in the syn_spec dictionary during the call to Connect(). If unspecified, the receptor will take on its default value of 0. If you request a receptor that is not available in the target node, this will result in a runtime error.

To illustrate the concept of receptors in more detail, the following example shows how to connect several iaf_psc_alpha neurons to the different compartments of a multi-compartment integrate-and-fire neuron (iaf_cond_alpha_mc) that are represented by different receptors.

A1 = nest.Create('iaf_psc_alpha')
A2 = nest.Create('iaf_psc_alpha')
A3 = nest.Create('iaf_psc_alpha')
A4 = nest.Create('iaf_psc_alpha')
B = nest.Create('iaf_cond_alpha_mc')

receptors = nest.GetDefaults('iaf_cond_alpha_mc')['receptor_types']

>>> print(receptors)
{'soma_exc': 1,
 'soma_inh': 2,
 'soma_curr': 7,
 'proximal_exc': 3
 'proximal_inh': 4,
 'proximal_curr': 8,
 'distal_exc': 5,
 'distal_inh': 6,
 'distal_curr': 9,}

nest.Connect(A1, B, syn_spec={'receptor_type': receptors['distal_inh']})
nest.Connect(A2, B, syn_spec={'receptor_type': receptors['proximal_inh']})
nest.Connect(A3, B, syn_spec={'receptor_type': receptors['proximal_exc']})
nest.Connect(A4, B, syn_spec={'receptor_type': receptors['soma_inh']})

In the example above, we retrieve a map of available receptors and their IDs by extracting the receptor_types property from the model defaults. This functionality is, however, only available for models with a predefined number of receptors, while models with a variable number of receptors usually don’t provide such an enumeration.

An example for the latter are the *_multisynapse neuron models that support multiple individual synaptic time constants for the different receptors. In these models, the number of available receptors is not predefined, but determined only by the length of the tau_syn vector that is supplied to the model instance. The following example shows the setup and connection of such a model in more detail:

A = nest.Create('iaf_psc_alpha')
B = nest.Create('iaf_psc_exp_multisynapse', params={'tau_syn': [0.1, 0.2, 0.3]})

print(B.n_synapses)   # This will print 3, as we set 3 different tau_syns

nest.Connect(A, B, syn_spec={'receptor_type': 2})

Synapse Types¶

NEST provides a number of built-in synapse models that can be used during connection setup. The default model is the static_synapse, whose only parameters weight and delay do not change over time. Other synapse models implement learning and adaptation in the form of long-term or short-term plasticity. A list of available synapse models is accessible via the command nest.synapse_models. More detailed information about each of them can be found in the synapse model page.

Note

Not all nodes can be connected via all available synapse types. The events a synapse type is able to transmit is documented in the Transmits section of the model documentation.

All synapses store their parameters on a per-connection basis. However, each of the built-in models is registered with the simulation kernel in a number of different ways that slightly modify the available properties of the connections instantiated from the model. The different variants are indicated by specific suffixes:

_lbl¶: denotes labeled synapses that have an additional parameter synapse_label (type: int), which can be set to a user-defined value. In a common application this label is used to store an additional projection identifier. Please note that using this synapse variant may drive up the memory requirements of your simulations significantly, as the label is stored on a per-synapse basis.
_hpc¶: denotes synapses for high-performance computing scenarios, which have minimal memory requirements by using thread-local target node indices internally. Use this version if you are running very large simulations.
_hom¶: denotes homogeneous synapses that store certain parameters like weight and delay only once for all synapses of the same type and can thus be used to save memory.

The default parameter values of a synapse model can be inspected using the command GetDefaults(), which only takes the name of the synapse model as an argument and returns a dictionary. Likewise, the function SetDefaults() takes the name of a synapse type and a parameter dictionary as arguments and will modify the defaults of the given model.

>>> print(nest.GetDefaults('static_synapse'))
{'delay': 1.0,
 'has_delay': True,
 'num_connections': 0,
 'receptor_type': 0,
 'requires_symmetric': False,
 'sizeof': 32,
 'synapse_model': 'static_synapse',
 'weight': 1.0,
 'weight_recorder': ()}
>>> nest.SetDefaults('static_synapse', {'weight': 2.5})

To further customize the process of creating synapses, it is often useful to have the same basic synapse model available with different parametrizations. To this end, CopyModel() can be used to create custom synapse types from already existing synapse types. In the simplest case, it takes the names of the existing model and the copied type to be created. The optional argument params allows to directly customize the new type during the copy operation. If omitted, the defaults of the copied model are taken.

nest.CopyModel('static_synapse', 'inhibitory', {'weight': -2.5})
nest.Connect(A, B, syn_spec='inhibitory')

Inspecting Connections¶

In order to assert that the instantiated network model actually looks like what was intended, it is oftentimes useful to inspect the connections in the network. For this, NEST provides the function

nest.GetConnections(source=None, target=None, synapse_model=None, synapse_label=None)

This function returns a SynapseCollection object that contains the identifiers for connections that match the given filters. source and target are given as NodeCollections, synapse_model is the name of the model as a string and synapse_label is an integer identifier. Any combination of these parameters is permitted. If nest.GetConnections() is called without parameters it returns all connections in the network.

Internally, each connection in the SynapseCollection is represented by the following five entries: source node ID, target node ID, thread ID of the target, numeric synapse ID, and port.

The result of GetConnections() can be further processed by giving it as an argument to GetStatus(), or, better yet, by using the get() function on the SynapseCollection directly. Both ways will yield a dictionary with the parameters of the connections that match the filter criterions given to nest.GetConnections():

A = nest.Create('iaf_psc_alpha', 2)
B = nest.Create('iaf_psc_alpha')
nest.Connect(A, B)
conn = nest.GetConnections()

>>> conn.get()
{'delay': [1.0, 1.0],
 'port': [0, 1],
 'receptor': [0, 0],
 'sizeof': [32, 32],
 'source': [1, 2],
 'synapse_id': [18, 18],
 'synapse_model': ['static_synapse', 'static_synapse'],
 'target': [3, 3],
 'target_thread': [0, 0],
 'weight': [1.0, 1.0]}

The get() function of a SynapseCollection can optionally also take a string or list of strings to only retrieve specific parameters. This is useful if you do not want to inspect the entire synapse dictionary:

>>> conn.get('weight')
[1.0, 1.0]

>>> conn.get(['source', 'target'])
{'source': [1, 2], 'target': [3, 3]}

Another way of retrieving specific parameters is by getting them directly from the SynapseCollection using the dot-notation:

>>> conn.delay
[1.0, 1.0]

For spatially distributed networks, you can access the distance between the source-target pairs by querying distance on your SynapseCollection.

>>> spatial_conn.distance
    (0.47140452079103173,
33333333333333337,
4714045207910317,
33333333333333337,
925231146709438e-17,
33333333333333326,
4714045207910317,
33333333333333326,
47140452079103157)

You can further examine the SynapseCollection by checking the length of it or by printing it to the terminal. The printout will be in the form of a table that lists source and target node IDs, synapse model, weight and delay:

>>> len(conn)
2
>>>  print(conn)
 source   target   synapse model   weight   delay
-------- -------- --------------- -------- -------
      1        3  static_synapse    1.000   1.000
      2        3  static_synapse    1.000   1.000

A SynapseCollection can be indexed or sliced, if you only want to inspect a subset of the connections contained in it:

>>> print(conn[0:2:2])
 source   target   synapse model   weight   delay
-------- -------- --------------- -------- -------
     1        3  static_synapse    1.000   1.000

Last, but not least, SynapseCollection can be iterated, to retrieve one connection at a time:

>>>  for c in conn:
...      print(c.source)
1
2

Modifying Existing Connections¶

To modify the parameters of an existing connection, you first have to obtain handles to them using GetConnections(). These handles can then be given as arguments to the SetStatus() function, or by using the set() function on the SynapseCollection directly:

n1 = nest.Create('iaf_psc_alpha', 2)
n2 = nest.Create('iaf_psc_alpha', 2)
nest.Connect(n1, n2)
conn = nest.GetConnections()
conn.set(weight=2.0)

>>> conn.get()
{'delay': [1.0, 1.0, 1.0, 1.0],
 'port': [0, 1, 2, 3],
 'receptor': [0, 0, 0, 0],
 'sizeof': [32, 32, 32, 32],
 'source': [1, 1, 2, 2],
 'synapse_id': [18, 18, 18, 18],
 'synapse_model': ['static_synapse', 'static_synapse', 'static_synapse', static_synapse'],
 'target': [3, 4, 3, 4],
 'target_thread': [0, 0, 0, 0],
 'weight': [2.0, 2.0, 2.0, 2.0]}

To update a single parameter of a connection or a set of connections, you can call the set() function of the SynapseCollection with the keyword argument parameter_name. The value for this argument can be a single value, a list, or a nest.Parameter. If a single value is given, the value is set on all connections. If you use a list to set the parameter, the list needs to be the same length as there are connections in the SynapseCollection.

conn.set(weight=[4.0, 4.5, 5.0, 5.5])

Similar to how you retrieve several parameters at once with the get() function explained above, you can also set multiple parameters at once using set(parameter_dictionary). Again, the values of the dictionary can be a single value, a list, or a nest.Parameter.

conn.set({'weight': [1.5, 2.0, 2.5, 3.0], 'delay': 2.0})

Finally, you can also directly set parameters on a SynapseCollection using the dot-notation:

>>> conn.weight = 5.
>>> conn.weight
[5.0, 5.0, 5.0, 5.0]
>>> conn.delay = [5.1, 5.2, 5.3, 5.4]
>>> conn.delay
[5.1, 5.2, 5.3, 5.4]

Note that some parameters like source and target are read-only and cannot be set. The documentation of a specific synapse model will point out which parameters can be set and which are read-only.