morph_tool.apical_point

Module to retrieve the position of the apical point.

Functions

apical_point_position(neuron[, tuft_percent])

Attempt to find the apical point in 'tufted' neurons.

apical_point_section_segment(neuron[, ...])

Find the apical point's section and segment.

morph_tool.apical_point.apical_point_position(neuron, tuft_percent=20)

Attempt to find the apical point in ‘tufted’ neurons.

Consider a neuron:

    |   /    | Tuft = 20%
    |--/     |
    |   /
    |--/
    |
----.-----

All endpoints in the top ‘tuft_percent’ are found, then their common branch segment, furthest from the soma, is identified.

Using the release from 2012 as the base, apical points were compared from the annotated versions, and using this algorithm. Of 239 morphologies that were annotated, 48 differed in the apical point choice by more than 1um in the y component. Many of the differences were morphologies that shoulnd’t have had apical points in the first place (ie: weren’t pyramidal cells, ex: C050398B-I4).

Parameters
  • neuron (morphio.Morphology) – a neuron morphology

  • tuft_percent – percentage of the ‘height’ of the apical dendrite that would enclose the tuft, only leaves in this volume are considered as endpoints

Returns

a point if it is found, or None otherwise

Return type

neurom.core.dataformat.Point

morph_tool.apical_point.apical_point_section_segment(neuron, tuft_percent=20)

Find the apical point’s section and segment.

Parameters
  • neuron (morphio.Morphology) – a morphology

  • tuft_percent – percentage of the ‘height’ of the apical dendrite that would enclose the tuft, only leaves in this volume are considered as endpoints See apical_point_position for more details

Returns

(NeuroM/MorphIO section ID, point ID) of the apical point. Since NeuroM v2, section ids of NeuroM and MorphIO are the same excluding soma.

Return type

Tuple