List of connection strategies¶

Connection strategies starting whose name start with Connectome are made for a specific connection between 2 cell types, those that do not can be used for connections between any cell type.

Shared configuration attributes¶

class: A string that specifies which connection strategy to apply to the connection type.
from_cell_types: An array of objects with a type key indicating presynaptic cell types and optionally a compartments key for an array of compartment types:
```
"from_cell_types": [
  {"type": "basket_cell", "compartments": ["axon"]},
  {"type": "stellate_cell", "compartments": ["axon"]}
]
```
to_cell_types: Same as from_cell_types but for the postsynaptic cell type.

`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

`TouchingConvergenceDivergence`¶

divergence: Preferred amount of connections starting from 1 from_cell
convergence: Preferred amount of connections ending on 1 to_cell

`ConnectomeGlomerulusGranule`¶

Inherits from TouchingConvergenceDivergence. No additional configuration. Uses the dendrite length configured in the granule cell morphology.

`ConnectomeGlomerulusGolgi`¶

Inherits from TouchingConvergenceDivergence. No additional configuration. Uses the dendrite radius configured in the Golgi cell morphology.

`ConnectomeGolgiGlomerulus`¶

Inherits from TouchingConvergenceDivergence. No additional configuration. Uses the axon_x, axon_y, axon_z from the Golgi cell morphology to intersect a parallelopipid Golgi axonal region with the glomeruli.

`ConnectomeGranuleGolgi`¶

Creates 2 connectivity sets by default ascending_axon_to_golgi and parallel_fiber_to_golgi but these can be overwritten by providing tag_aa and/or tag_pf respectively.

Calculates the distance in the XZ plane between granule cells and Golgi cells and uses the Golgi cell morphology’s dendrite radius to decide on the intersection.

Also creates an ascending axon height for each granule cell.

aa_convergence: Preferred amount of ascending axon synapses on 1 Golgi cell.
pf_convergence: Preferred amount of parallel fiber synapses on 1 Golgi cell.

`ConnectomeGolgiGranule`¶

No configuration, it connects each Golgi to each granule cell that it shares a connected glomerules with.

`ConnectomeAscAxonPurkinje`¶

Intersects the rectangular extension of the Purkinje dendritic tree with the granule cells in the XZ plane, uses the Purkinje cell’s placement attributes extension_x and extension_z.

extension_x: Extension of the dendritic tree in the X plane
extension_z: Extension of the dendritic tree in the Z plane

`ConnectomePFPurkinje`¶

No configuration. Uses the Purkinje cell’s placement attribute extension_x. Intersects Purkinje cell dendritic tree extension along the x axis with the x position of the granule cells, as the length of a parallel fiber far exceeds the simulation volume.