List of connection strategies

VoxelIntersection

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.

• affinity: A fraction between 1 and 0 which indicates the tendency of cells to form connections with other cells with whom their voxels intersect. This can be used to downregulate the amount of cells that any cell connects with.

• contacts: A number or distribution determining the amount of synaptic contacts one cell will form on another after they have selected eachother as connection partners.

Note

The affinity only affects the number of cells that are contacted, not the number of synaptic contacts formed with each cell.

FiberIntersection

This strategy is a special case of VoxelIntersection that can be applied to morphologies with long straight compartments that would yield incorrect results when approximated with cubic voxels like in VoxelIntersection (e.g. Ascending Axons or Parallel Fibers in Granule Cells). The fiber, organized into hierarchical branches, is split into segments, based on original compartments length and configured resolution. Then, each branch is voxelized into parallelepipeds: each one is built as the minimal volume with sides parallel to the main reference frame axes, surrounding each segment. Intersections with postsynaptic voxelized morphologies are then obtained applying the same method as in VoxelIntersection.

• resolution: the maximum length [um] of a fiber segment to be used in the fiber voxelization. If the resolution is lower than a compartment length, the compartment is interpolated into smaller segments, to achieve the desired resolution. This property impacts on voxelization of fibers not parallel to the main reference frame axes. Default value is 20.0 um, i.e. the length of each compartment in Granule cell Parallel fibers.

• affinity: A fraction between 1 and 0 which indicates the tendency of cells to form connections with other cells with whom their voxels intersect. This can be used to downregulate the amount of cells that any cell connects with. Default value is 1.

• to_plot: a list of cell fiber numbers (e.g. 0 for the first cell of the presynaptic type) that will be plotted during connection creation using plot_fiber_morphology.

• transform: A set of attributes defining the transformation class for fibers that should be rotated or bended. Specifically, the QuiverTransform allows to bend fiber segments based on a vector field in a voxelized volume. The attributes to be set are:

  • quivers: the vector field array, of shape e.g. (3, 500, 400, 200)) for a volume with 500, 400 and 200 voxels in x, y and z directions, respectively.

  • vol_res: the size [um] of voxels in the volume where the quiver field is defined. Default value is 25.0, i.e. the voxel size in the Allen Brain Atlas.

  • vol_start: the origin of the quiver field volume in the reconstructed volume reference frame.

  • shared: if the same transformation should be applied to all fibers or not