neurom

NeuroM neurom morphology analysis package.

Examples

Load a morphology

>>> import neurom as nm
>>> m = nm.load_morphology('tests/data/swc/Neuron.swc')

Obtain some morphometrics using the get function

>>> ap_seg_len = nm.get('segment_lengths', m, neurite_type=nm.APICAL_DENDRITE)
>>> ax_sec_len = nm.get('section_lengths', m, neurite_type=nm.AXON)

Load morphologies from a directory. This loads all SWC, HDF5 or NeuroLucida .asc files it finds and returns a list of morphologies

>>> import numpy as np  # For mean value calculation
>>> pop = nm.load_morphologies('tests/data/valid_set')
>>> mean_section_lengths = [np.mean(nm.get('section_lengths', m)) for m in pop]

Apply a function to a selection of neurites in a morphology or morphology population. This example gets the number of points in each axon in a morphology population

>>> import neurom as nm
>>> filter = lambda n : n.type == nm.AXON
>>> mapping = lambda n, section_type : len(n.points)
>>> n_points = [n for n in nm.iter_neurites(pop, mapping, filter)]