neuror.unravel

The unravel module

Unravelling is the action of “stretching” the cell that has been shrunk because of the dehydratation caused by the slicing

Functions

_get_principal_direction

Return the principal direction of a point cloud.

_unravel_section

Unravel a section using number of adjacent points as window_half_length.

unravel

Return an unravelled neuron.

unravel_all

Repair all morphologies in input folder.

unravel_plane

Return a new CutPlane object where the cut-leaves position has been updated after unravelling.
neuror.unravel.unravel(filename, window_half_length=None, legacy_behavior=False, use_path_length=True)[source]

Return an unravelled neuron.

Segment are unravelled iteratively Each segment direction is replaced by the averaged direction in a sliding window around this segment, preserving the original segment length. The start position of the new segment is the end of the latest unravelled segment

Note

Based initially on: DOI: 10.7551/mitpress/9780262013277.001.0001

Section: 9.2 Repair of Neuronal Dendrites

Parameters:

  • filename (str) – the neuron to unravel

  • window_half_length (int) – path length that defines half of the sliding window

  • legacy_behavior (bool) – if yes, when the soma has more than one point, the first point of the soma is appended to the start of each neurite.

  • use_path_length (bool) – if False, the argument window_half_length will be recasted to an int and correspond to number of points on each side of the window.

Returns:

a tuple where first item is the unravelled morphology and the second one is the mapping of each point coordinate before and after unravelling

Return type:

tuple[morphio.mut.Morphology, pandas.DataFrame]

neuror.unravel.unravel_all(raw_dir, unravelled_dir, raw_planes_dir, unravelled_planes_dir, window_half_length=None)[source]

Repair all morphologies in input folder.

neuror.unravel.unravel_plane(plane, mapping)[source]

Return a new CutPlane object where the cut-leaves position has been updated after unravelling.

Parameters: