Structural analysis and report

The cerebellar-models repository provides a list of analysis and plot that can be performed during or after the BSB reconstruction to extract structural properties of the produced circuit.

The following section will describe in more details all the plots and analysis available through the cerebellar-models reporting.

PlacementTable

This class computes the number and density of each cell type of the BSB scaffold and plot them in a table.

Constructor parameters:

  • scaffold: BSB scaffold object.

  • dict_colors: A Dictionary linking the name of the elements (e.g.: cells, fibers) to plot to their RGBA color

  • dict_abv: Dictionary that links each cell type name to an abbreviation to display

ConnectivityTable

This class computes and plots a Table of the results of the connectivity for BSB Scaffold. This includes for each pair of connected cell types:

  • the number of synapses formed

  • the number of synapses per unique pair of cell.

  • the convergence ratio defined as the mean number of afferent connections created with a single postsynaptic cell

  • the divergence ratio defined as the mean number of efferent connections created with a single presynaptic cell

Constructor parameters:

  • scaffold: BSB scaffold object.

  • dict_colors: A Dictionary linking the name of the elements (e.g.: cells, fibers) to plot to their RGBA color

  • dict_abv: Dictionary that links each cell type name to an abbreviation to display

CellPlacement3D

This class extracts and plots the position of the cells in the scaffold in 3D space. Each soma diameter is based on its cell type radius as defined in the BSB configuration.

Constructor parameters:

  • scaffold: BSB scaffold object.

  • dict_colors: A Dictionary linking the name of the elements (e.g.: cells, fibers) to plot to their RGBA color

  • ignored_ct: List of cell type names to ignore from the scaffold (these cells will not be displayed).

AdjacencyMatrix

This class extracts and plots the adjacency matrix of the scaffold connectome grouped by cell type populations. By default, the matrix is displayed in the logarithm scale.

Constructor parameters:

  • scaffold: BSB scaffold object.

  • dict_colors: A Dictionary linking the name of the elements (e.g.: cells, fibers) to plot to their RGBA color

  • ignored_ct: List of cell type names to ignore from the scaffold (these cells will not be displayed).

  • dict_abv: Dictionary that links each cell type name to an abbreviation to display

StructureReport

This class extends BSBReport and produces a report containing 3 plots with a legend:

  • A table containing the number and densities of placed cells in the final circuit (see section PlacementTable)

  • A 3D plot of the circuit, showing neuron somas placed in the circuit space by BSB (see section CellPlacement3D)

  • A table containing the number of synapses, convergence, divergence ratios for each of the connected cell type pairs (see section ConnectivityTable).

  • A plot of the adjacency matrix, showing counts of synapses per pair of cell types (see section AdjacencyMatrix)

All these plots are saved in a single pdf file.

You can also create this report automatically through the BSB configuration like so (see RunStructureReport).

RunStructureReport

BSB postprocessing node to generate a scaffold StructureReport after running the connectivity jobs. To automatically produce this during BSB scaffold compilation add the following section to your configuration:

after_connectivity:
    print_structure_report:
        strategy: cerebellar_models.analysis.structure_analysis.RunStructureReport
        output_filename: bsb_report_structure.pdf