morphoclass.transforms.extract_tmd_neurites module

Extract TMD neurites.

class morphoclass.transforms.extract_tmd_neurites.ExtractTMDNeurites(neurite_type, from_tmd_neuron=False)

Bases: object

Extract neurite trees in TMD Tree format.

Parameters

• neurite_type (str) – Type of neurite to extract (apical, axon, basal, all)

• from_tmd_neuron (bool) – If set to true the neurite will be extracted from the TMD neuron in the tmd_neuron field of data. Otherwise, the MorphIO neuron object in the morphology field of data will be converted to a TMD neuron first, from which the neurite will be extracted.

morphio_types = {'all': <SectionType.all: 32>, 'apical': <SectionType.apical_dendrite: 4>, 'axon': <SectionType.axon: 2>, 'basal': <SectionType.basal_dendrite: 3>, 'neurites': <SectionType.all: 32>}

tmd_types = {'all': 'neurites', 'apical': 'apical_dendrite', 'axon': 'axon', 'basal': 'basal_dendrite', 'neurites': 'neurites'}