neurom.fstΒΆ
NeuroM, lightweight and fast
Examples
Load a neuron
>>> from neurom import fst
>>> nrn = fst.load_neuron('some/data/path/morph_file.swc')
Obtain some morphometrics
>>> ap_seg_len = fst.get('segment_lengths', nrn, neurite_type=fst.NeuriteType.apical_dendrite)
>>> ax_sec_len = fst.get('section_lengths', nrn, neurite_type=fst.NeuriteType.axon)
Load neurons from a directory. This loads all SWC or HDF5 files it finds and returns a list of neurons
>>> import numpy as np # For mean value calculation
>>> nrns = fst.load_neurons('some/data/directory')
>>> for nrn in nrns:
... print 'mean section length', np.mean(fst.get('section_lengths', nrn))
Functions
get |
Neuron feature getter helper |
load_neuron |
Build section trees from an h5 or swc file |
Classes
Neuron |