SynapseMapper¶

class singlecell_input_mapper.udvary2022.synapse_mapper.SynapseMapper(cell: singlecell_input_mapper.udvary2022.cell.Cell, synDist=None, isDensity=True)¶

Bases: object

Assign synapses to neuron morphology from density meshes.

Poisson sample the synapse distribution mesh and assign them to a random point on the morphology that lies within the same voxel.

Parameters:¶

cell : Cell¶

Neuron morphology to map synapses onto.

synDist : ScalarField¶

Synapse distribution mesh.

isDensity : bool¶

If True, synapse distribution is interpreted as an average density. If False, synapse distribution is interpreted as an actual realization, and values are taken as is.

Attributes:¶

cell¶

The postsynaptic neuron.

Type:¶

Cell

synDist¶

Synapse distribution mesh. Can be either a density or a realization (i.e. whole number values per voxel).

Type:¶

ScalarField

isDensity¶

Set to True if synapse distribution is interpreted as an average density. Set to False if synapse distribution is interpreted as an actual realization, and values are whole numbers.

Type:¶

bool

voxelEdgeMap¶

Dictionary mapping synapse distribution mesh coordinates on list with pairs of indices that correspond to the edge and edgePt ID of all morphology points inside that voxel.

Type:¶

dict

Methods:¶

create_synapses(preType)	Creates instantiation of synapses on cell from synapse distribution.
_create_voxel_edge_map()	Fills voxelEdgeMap with voxel indices, and the section and point indices that the voxel contains.
_intersect_bboxes(bbox1, bbox2)	Check if two bounding boxes overlap
_pt_in_box(pt, box)	Check if a point is inside a bounding box.
_compute_path_length(sec, x)	Calculate the path length betwen the soma and location x on section sec