map_singlecell_inputs¶

singlecell_input_mapper.udvary2022.map_singlecell_inputs(cellName, cellTypeName, nrOfSamples=50, numberOfCellsSpreadsheetName=None, connectionsSpreadsheetName=None, ExPSTDensityName=None, InhPSTDensityName=None, boutonDensityFolderName=None)¶

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 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=None¶

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

Returns:¶

None.

Writes the results to disk, at the same location as the input cellName. Results consist of a .syn, .con file, and a .csv file containing the amount of connected presynaptic cells per cell type, and per anatomical area.