neuron_morphology.features.layer.reference_layer_depths

Module Contents

Classes

ReferenceLayerDepths

Reference (e.g. average across specimens and regions) depths of

class neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths

Bases: typing.NamedTuple

Reference (e.g. average across specimens and regions) depths of cortical layer boundaries. Depths are given from pia. Units are not specified, but the user should ensure they are consistent with other positional and size units (e.g. node positions and radii, point depths). Several features in this package specify defaults in microns; if you provide reference layer depths in other units, you should review features which use these depths and ensure that any default values agree with your units.

Attributes:

pia_side : the (average) depth of the upper surface of the layer

wm_side : the (average) depth of the lower (closer to white matter) surface

of the layer

scale : if True, these depths are taken as describing the upper and lower

surfaces of a real feature of the data. If False, one or both of them is taken to represent a user-selected boundary. In the latter case, features such as the layer histograms will not attempt to rescale point depths based on observed local layer thicknesses.

pia_side :float

wm_side :float

scale :bool = True

thickness

classmethod sequential(cls, names: Sequence[str], boundaries: Sequence[float], last_is_scale=False)

A utility for constructing multiple ordered reference layer depths without intervening space.

Parameters:

names : The name of each layer

boundaries : The pia and wm side depth of each layer. Should be a flat

sequence that has 1 more element than names.

last_is_scale : If True, the last boundary will be interpreted as a

true anatomical boundary. If false, as an arbitrary cutoff.

neuron_morphology.features.layer.reference_layer_depths.DEFAULT_HUMAN_ME_MET_REFERENCE_LAYER_DEPTHS

neuron_morphology.features.layer.reference_layer_depths.DEFAULT_HUMAN_MTG_REFERENCE_LAYER_DEPTHS

neuron_morphology.features.layer.reference_layer_depths.DEFAULT_MOUSE_ME_MET_REFERENCE_LAYER_DEPTHS

neuron_morphology.features.layer.reference_layer_depths.DEFAULT_MOUSE_REFERENCE_LAYER_DEPTHS

neuron_morphology.features.layer.reference_layer_depths.WELL_KNOWN_REFERENCE_LAYER_DEPTHS