Connectivity module

exception bsb.connectivity.AdapterError(*args, **kwargs)
class bsb.connectivity.AllToAll[source]

All to all connectivity between two neural populations

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.ArborError(*args, **kwargs)
exception bsb.connectivity.AttributeMissingError(*args, **kwargs)
exception bsb.connectivity.CastConfigurationError(*args, **kwargs)
exception bsb.connectivity.CastError(*args, **kwargs)
exception bsb.connectivity.CircularMorphologyError(*args, **kwargs)
exception bsb.connectivity.ClassError(*args, **kwargs)[source]
exception bsb.connectivity.CompartmentError(*args, **kwargs)
exception bsb.connectivity.ConfigurableCastError(*args, **kwargs)
exception bsb.connectivity.ConfigurableClassNotFoundError(*args, **kwargs)
exception bsb.connectivity.ConfigurationError(*args, **kwargs)
exception bsb.connectivity.ConfigurationFormatError(*args, **kwargs)
exception bsb.connectivity.ConfigurationWarning[source]
class bsb.connectivity.ConnectionStrategy[source]
exception bsb.connectivity.ConnectivityError(*args, **kwargs)
exception bsb.connectivity.ConnectivityWarning[source]
class bsb.connectivity.ConnectomeAscAxonPurkinje[source]

Legacy implementation for the connections between ascending axons and purkinje cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeBCSCPurkinje[source]

Legacy implementation for the connections between basket cells,stellate cells and purkinje cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeDcnGlyGolgi[source]

Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeDcnGolgi[source]

Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeDcnGranule[source]

Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGapJunctions[source]

Legacy implementation for gap junctions between a cell type.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGapJunctionsGolgi[source]

Legacy implementation for Golgi cell gap junctions.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGlomerulusGolgi[source]

Legacy implementation for the connections between Golgi cells and glomeruli.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGlomerulusGranule[source]

Legacy implementation for the connections between glomeruli and granule cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGolgiGlomerulus[source]

Legacy implementation for the connections between glomeruli and Golgi cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGolgiGranule[source]

Legacy implementation for the connections between Golgi cells and granule cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeGranuleGolgi[source]

Legacy implementation for the connections between Golgi cells and glomeruli.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeIOMolecular[source]

Legacy implementation for the connection between inferior olive and Molecular layer interneurons. As this is a spillover-mediated non-synaptic connection depending on the IO to Purkinje cells, each interneuron connected to a PC which is receving input from one IO, is also receiving input from that IO

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeIOPurkinje[source]

Legacy implementation for the connection between inferior olive and Purkinje cells. Purkinje cells are clustered (number of clusters is the number of IO cells), and each clusters is innervated by 1 IO cell

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeMossyDCN[source]

Implementation for the connection between mossy fibers and DCN cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomeMossyGlomerulus[source]

Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomePFInterneuron[source]

Legacy implementation for the connections between parallel fibers and a molecular layer interneuron cell_type.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomePFPurkinje[source]

Legacy implementation for the connections between parallel fibers and purkinje cells.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.ConnectomePurkinjeDCN[source]

Legacy implementation for the connection between purkinje cells and DCN cells. Also rotates the dendritic trees of the DCN.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.ContinuityError(*args, **kwargs)
class bsb.connectivity.Convergence[source]

Implementation of a general convergence connectivity between two populations of cells (this does not work with entities)

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.DataNotFoundError(*args, **kwargs)
exception bsb.connectivity.DataNotProvidedError(*args, **kwargs)
exception bsb.connectivity.DatasetNotFoundError(*args, **kwargs)
exception bsb.connectivity.DeviceConnectionError(*args, **kwargs)
exception bsb.connectivity.DynamicClassError(*args, **kwargs)
class bsb.connectivity.ExternalConnections[source]

Load the connection matrix from an external source.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.ExternalSourceError(*args, **kwargs)
class bsb.connectivity.FiberIntersection[source]

FiberIntersection connection strategies voxelize a fiber and find its intersections with postsynaptic cells. It’s a specific case of VoxelIntersection.

For each presynaptic cell, the following steps are executed:

  1. Extract the FiberMorphology

  2. Interpolate points on the fiber until the spatial resolution is respected

  3. transform

  4. Interpolate points on the fiber until the spatial resolution is respected

  5. Voxelize (generates the voxel_tree associated to this morphology)

  6. Check intersections of presyn bounding box with all postsyn boxes

  7. Check intersections of each candidate postsyn with current presyn voxel_tree

intersect_voxel_tree(from_voxel_tree, to_cloud, to_pos)[source]

Similarly to intersect_clouds from VoxelIntersection, it finds intersecting voxels between a from_voxel_tree and a to_cloud set of voxels

Parameters
  • from_voxel_tree – tree built from the voxelization of all branches in the fiber (in absolute coordinates)

  • to_cloud (VoxelCloud) – voxel cloud associated to a to_cell morphology

  • to_pos (list) – 3-D position of to_cell neuron

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.FiberTransform[source]
exception bsb.connectivity.IncompleteExternalMapError(*args, **kwargs)
exception bsb.connectivity.IncompleteMorphologyError(*args, **kwargs)
exception bsb.connectivity.IntersectionDataNotFoundError(*args, **kwargs)
exception bsb.connectivity.InvalidDistributionError(*args, **kwargs)
exception bsb.connectivity.KernelLockedError(*args, **kwargs)
exception bsb.connectivity.KernelWarning[source]
exception bsb.connectivity.LayerNotFoundError(*args, **kwargs)
exception bsb.connectivity.MissingMorphologyError(*args, **kwargs)
exception bsb.connectivity.MissingSourceError(*args, **kwargs)
exception bsb.connectivity.MorphologyDataError(*args, **kwargs)
exception bsb.connectivity.MorphologyError(*args, **kwargs)
exception bsb.connectivity.MorphologyRepositoryError(*args, **kwargs)
exception bsb.connectivity.MorphologyWarning[source]
exception bsb.connectivity.NestError(*args, **kwargs)
exception bsb.connectivity.NestKernelError(*args, **kwargs)
exception bsb.connectivity.NestModelError(*args, **kwargs)
exception bsb.connectivity.NestModuleError(*args, **kwargs)
exception bsb.connectivity.NeuronError(*args, **kwargs)
exception bsb.connectivity.OrderError(*args, **kwargs)[source]
exception bsb.connectivity.ParallelIntegrityError(*args, **kwargs)
exception bsb.connectivity.PlacementError(*args, **kwargs)
exception bsb.connectivity.PlacementWarning[source]
exception bsb.connectivity.QuiverFieldWarning[source]
class bsb.connectivity.QuiverTransform[source]

QuiverTransform applies transformation to a FiberMorphology, based on an orientation field in a voxelized volume. Used for parallel fibers.

transform_branch(branch, offset)[source]

Compute bending transformation of a fiber branch (discretized according to original compartments and configured resolution value). The transformation is a rotation of each segment/compartment of each fiber branch to align to the cross product between the orientation vector and the transversal direction vector (i.e. cross product between fiber morphology/parent branch orientation and branch direction): compartment[n+1].start = compartment[n].end cross_prod = orientation_vector X transversal_vector or transversal_vector X orientation_vector compartment[n+1].end = compartment[n+1].start + cross_prod * length_comp

Parameters

branch (Branch object) – a branch of the current fiber to be transformed

Returns

a transformed branch

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.ReceptorSpecificationError(*args, **kwargs)
exception bsb.connectivity.RelayError(*args, **kwargs)
exception bsb.connectivity.RepositoryWarning[source]
exception bsb.connectivity.ResourceError(*args, **kwargs)
class bsb.connectivity.SatelliteCommonPresynaptic[source]

Connectivity for satellite neurons (homologous to center neurons)

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.ScaffoldError(*args, **kwargs)
exception bsb.connectivity.ScaffoldWarning[source]
exception bsb.connectivity.SimulationNotFoundError(*args, **kwargs)
exception bsb.connectivity.SimulationWarning[source]
exception bsb.connectivity.SourceQualityError(*args, **kwargs)
exception bsb.connectivity.SpatialDimensionError(*args, **kwargs)
exception bsb.connectivity.SuffixTakenError(*args, **kwargs)
class bsb.connectivity.TouchDetector[source]

Connectivity based on intersection of detailed morphologies

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

class bsb.connectivity.TouchingConvergenceDivergence[source]
validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.TransmitterError(*args, **kwargs)
exception bsb.connectivity.TreeError(*args, **kwargs)
exception bsb.connectivity.TypeNotFoundError(*args, **kwargs)
exception bsb.connectivity.UnionCastError(*args, **kwargs)
exception bsb.connectivity.UnknownDistributionError(*args, **kwargs)
exception bsb.connectivity.UnknownGIDError(*args, **kwargs)
exception bsb.connectivity.UserUserDeprecationWarning[source]
class bsb.connectivity.VoxelIntersection[source]

This strategy voxelizes morphologies into collections of cubes, thereby reducing the spatial specificity of the provided traced morphologies by grouping multiple compartments into larger cubic voxels. Intersections are found not between the seperate compartments but between the voxels and random compartments of matching voxels are connected to eachother. This means that the connections that are made are less specific to the exact morphology and can be very useful when only 1 or a few morphologies are available to represent each cell type.

validate()[source]

Must be implemented by child classes. Raise exceptions when invalid configuration parameters are received.

exception bsb.connectivity.VoxelTransformError(*args, **kwargs)
exception bsb.connectivity.VoxelizationError(*args, **kwargs)
bsb.connectivity.report(*message, level=2, ongoing=False, token=None, nodes=None, all_nodes=False)[source]

Send a message to the appropriate output channel.

Parameters
  • message (string) – Text message to send.

  • level (int) – Verbosity level of the message.

  • ongoing – The message is part of an ongoing progress report. This replaces the endline (n) character with a carriage return (r) character

bsb.connectivity.warn(message, category=None)[source]

Send a warning.

Parameters
  • message (str) – Warning message

  • category – The class of the warning.