singlecell_input_mapper ❭ map_singlecell_inputs ❭ map_singlecell_inputs

map_singlecell_inputs

singlecell_input_mapper.map_singlecell_inputs.map_singlecell_inputs(cellName, cellTypeName, nrOfSamples=50, numberOfCellsSpreadsheetName=numberOfCellsSpreadsheetName, connectionsSpreadsheetName=connectionsSpreadsheetName, ExPSTDensityName=ExPSTDensityName, InhPSTDensityName=InhPSTDensityName, boutonDensityFolderName=boutonDensityFolderName)

Map inputs to a single cell morphology.

These inputs need to be organized per anatomical structure. Anatomical structures can be arbitrary spatial regions of the brain tissue, or anatomically well-defined areas, e.g. barrels in a barrel cortex.

Steps:

  1. Loads in the data:

    • Cell morphology

    • Number of cells per cell type

    • Connection probabilities between cell types

    • PST densities for normalization of innervation calculations

  2. Loads in the bouton densities:

    • For each anatomical area

    • For each presynaptic cell type

  3. Creates a scalar field (ScalarField) for each bouton density.

  4. Creates a NetworkMapper object.

  5. Creates a network embedding for the cell using create_network_embedding().

The naming of each anatomical area needs to be consistent between:

  • The number of cells per cell type spreadsheet

  • The bouton folders containing axon traces

Parameters:

  • cellName (str) – path to a .hoc file containing the morphology of the cell.

  • cellTypeName (str) – name of the postsynaptic cell type.

  • nrOfSamples (int) – number of samples to use for the network embedding.

  • numberOfCellsSpreadsheetName (str) – Path to the a spreadsheet, containing each neuropil structures as columns, and celltypes row indices. Values indicate how much of each celltype was found in each neuropil structure.

  • connectionsSpreadsheetName (str) – Path to a spreadsheet, containing the connection probabilities between each presynaptic and postsynaptic cell type.

  • ExPSTDensityName (str) – Path to the PST density file for excitatory synapses.

  • InhPSTDensityName (str) – Path to the PST density file for inhibitory synapses.

  • boutonDensityFolderName – A directory containing the following subdirectory structure: anatomical_area/presynaptic_cell_type/*.am

Returns:

None. Writes the results to disk.