neuron_morphology.features.layer.reference_layer_depths module

class neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths

Bases: tuple

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.

Methods

count(self, value, /)	Return number of occurrences of value.
index(self, value[, start, stop])	Return first index of value.
sequential(names, boundaries[, last_is_scale])	A utility for constructing multiple ordered reference layer depths without intervening space.

pia_side

Alias for field number 0

scale

Alias for field number 2

classmethod sequential(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.

thickness

wm_side

Alias for field number 1