Feature Presentation

morphopy.computation.feature_presentation.compute_density_maps(neurontree=None, config_params=None)

function for computing density maps which can be specified by a config and passed with a neurontree several projections are computed (x,y,z,xy,xz,yz)

Parameters:

• neurontree – NeuronTree object wich holds a swc file data
• config_params – configuration params passed as dictionary which was load from file containing all customizable params for density maps

Returns:

returns a dictionary with all density maps computed with all projections (x,y,z,xy,xz,yz)

morphopy.computation.feature_presentation.compute_morphometric_statistics(neurontree=None, format='wide')

Compute various morphometric statistics of a NeuronTree which is passed as an object

Parameters:

• neurontree – NeuronTree instance, holds complete data of an swc file
• format –

  String determines the data format of the returned statistics. Options are ‘wide’(default) and ‘long’. For more information read

  http://www.cookbook-r.com/Manipulating_data/Converting_data_between_wide_and_long_format/

Returns:

pandas dataframe object with dictionary of all statistics

morphopy.computation.feature_presentation.get_persistence(neurontree=None, f=None)

Creates the persistence barcode for the graph G. The algorithm is taken from “Quantifying topological invariants of neuronal morphologies” from Lida Kanari et al (https://arxiv.org/abs/1603.08432).

changed for use with networkx v2 (works also in old version: list(G.neighbors()))

Parameters:

• neurontree – instance of a NeuronTree class which holds the data of the swc file
• f – user defined function for computing persitence (see persistence_functions.py)

Returns:

pandas.DataFrame with entries node_id | birth | death . Where birth and death are defined in radial distance from soma.

morphopy.computation.feature_presentation.plot_density_maps(densities=None, figure=None)

functions to plot density maps from densities dictionary with data from x,y,z,xy,xz,yz projections

Returns:

figure will be returned with all plotted maps from densities

Parameters:

• densities – dictionary which holds all projections for the plots
• figure – you can pass a figure if you want to use a custom plot format