Cells#

Cell identifiers and indexes#

The types defined below are used as identifiers for cells and members of cell-local collections.

class arbor.selection_policy#

Enumeration used for selecting an individual item from a group of items sharing the same label.

round_robin#

Iterate over the items of the group in a round-robin fashion.

round_robin_halt#

Halts at the current item of the group until the round_robin policy is called (again).

univalent#

Assert that only one item is available in the group. Throws an exception if the assertion fails.

class arbor.cell_local_label#

For local identification of an item on an unspecified cell.

A local string label tag is used to identify a group of items within a particular cell-local collection. Each label is associated with a set of items distributed over various locations on the cell. The exact number of items associated to a label can only be known when the model is built and is therefore not directly available to the user.

Because each label can be mapped to any of the items in its group, a selection_policy is needed to select one of the items of the group. If the policy is not supplied, the default selection_policy.univalent is selected.

cell_local_label is used for selecting the target of a connection or the local site of a gap junction connection. The cell gid of the item is implicitly known in the recipe.

tag#

Identifier of a group of items in a cell-local collection.

selection_policy#

Policy used for selecting a single item of the tagged group.

An example of a cell member construction reads as follows:

import arbor

# Create the policy
policy = arbor.selection_policy.univalent

# Create the local label referring to the group of items labeled "syn0".
# The group is expected to only contain 1 item.
local_label = arbor.cell_local_label("syn0", policy)
class arbor.cell_global_label#

For global identification of an item on a cell. This is used for selecting the source of a connection or the peer site of a gap junction connection. The label expects a cell_local_label type.

gid#

Global identifier of the cell associated with the item.

label#

Identifier of a single item on the cell.

import arbor

# Create the policy
policy = arbor.selection_policy.univalent

# Creat the local label referring to the group of items labeled "syn0".
# The group is expected to only contain 1 item.
local_label = arbor.cell_local_label("syn0", policy)

# Create the global label referring to the group of items labeled "syn0"
# on cell 5
global_label = arbor.cell_global_label(5, local_label)
class arbor.cell_member#
cell_member(gid, index)#

Construct a cell_member object with parameters gid and index for global identification of a cell-local item.

Items of type cell_member must:

  • be associated with a unique cell, identified by the member gid;

  • identify an item within a cell-local collection by the member index.

Lexicographically ordered by gid, then index.

gid#

The global identifier of the cell.

index#

The cell-local index of the item. Local indices for items within a particular cell-local collection should be zero-based and numbered contiguously.

An example of a cell member construction reads as follows:

import arbor

# construct
cmem = arbor.cell_member(0, 0)

# set gid and index
cmem.gid = 1
cmem.index = 42
class arbor.cell_kind#

Enumeration used to identify the cell kind, used by the model to group equal kinds in the same cell group.

cable#

A cell with morphology described by branching 1D cable segments.

lif#

A leaky-integrate and fire neuron.

spike_source#

A proxy cell that generates spikes from a spike sequence provided by the user.

benchmark#

A proxy cell used for benchmarking.

An example for setting the cell kind reads as follows:

import arbor

kind = arbor.cell_kind.cable

Cell kinds#

class arbor.lif_cell

See LIF cells.

class arbor.spike_source_cell

See Spike source cells.

class arbor.benchmark_cell

See Benchmark cells.

class arbor.cable_cell

See Cable cells.