Connectivity module¶
- exception bsb.connectivity.AdapterError(*args, **kwargs)¶
- 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.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.ConnectivityError(*args, **kwargs)¶
- class bsb.connectivity.ConnectomeAscAxonPurkinje[source]¶
Legacy implementation for the connections between ascending axons and purkinje cells.
- class bsb.connectivity.ConnectomeBCSCPurkinje[source]¶
Legacy implementation for the connections between basket cells,stellate cells and purkinje cells.
- class bsb.connectivity.ConnectomeDcnGlyGolgi[source]¶
Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and
- class bsb.connectivity.ConnectomeDcnGolgi[source]¶
Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and
- class bsb.connectivity.ConnectomeDcnGranule[source]¶
Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and
- class bsb.connectivity.ConnectomeGapJunctions[source]¶
Legacy implementation for gap junctions between a cell type.
- class bsb.connectivity.ConnectomeGapJunctionsGolgi[source]¶
Legacy implementation for Golgi cell gap junctions.
- class bsb.connectivity.ConnectomeGlomerulusGolgi[source]¶
Legacy implementation for the connections between Golgi cells and glomeruli.
- class bsb.connectivity.ConnectomeGlomerulusGranule[source]¶
Legacy implementation for the connections between glomeruli and granule cells.
- class bsb.connectivity.ConnectomeGolgiGlomerulus[source]¶
Legacy implementation for the connections between glomeruli and Golgi cells.
- class bsb.connectivity.ConnectomeGolgiGranule[source]¶
Legacy implementation for the connections between Golgi cells and granule cells.
- class bsb.connectivity.ConnectomeGranuleGolgi[source]¶
Legacy implementation for the connections between Golgi cells and glomeruli.
- 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
- 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
- class bsb.connectivity.ConnectomeMossyDCN[source]¶
Implementation for the connection between mossy fibers and DCN cells.
- class bsb.connectivity.ConnectomeMossyGlomerulus[source]¶
Implementation for the connections between mossy fibers and glomeruli. The connectivity is somatotopic and
- class bsb.connectivity.ConnectomePFInterneuron[source]¶
Legacy implementation for the connections between parallel fibers and a molecular layer interneuron cell_type.
- class bsb.connectivity.ConnectomePFPurkinje[source]¶
Legacy implementation for the connections between parallel fibers and purkinje cells.
- class bsb.connectivity.ConnectomePurkinjeDCN[source]¶
Legacy implementation for the connection between purkinje cells and DCN cells. Also rotates the dendritic trees of the DCN.
- 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)
- 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.
- 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:
Extract the FiberMorphology
Interpolate points on the fiber until the spatial resolution is respected
transform
Interpolate points on the fiber until the spatial resolution is respected
Voxelize (generates the voxel_tree associated to this morphology)
Check intersections of presyn bounding box with all postsyn boxes
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
- 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.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.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.ParallelIntegrityError(*args, **kwargs)¶
- exception bsb.connectivity.PlacementError(*args, **kwargs)¶
- 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
- exception bsb.connectivity.ReceptorSpecificationError(*args, **kwargs)¶
- exception bsb.connectivity.RelayError(*args, **kwargs)¶
- exception bsb.connectivity.ResourceError(*args, **kwargs)¶
- class bsb.connectivity.SatelliteCommonPresynaptic[source]¶
Connectivity for satellite neurons (homologous to center neurons)
- exception bsb.connectivity.ScaffoldError(*args, **kwargs)¶
- exception bsb.connectivity.SimulationNotFoundError(*args, **kwargs)¶
- 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
- 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)¶
- 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.
- 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