neurom.core._neuron¶

Neuron classes and functions.

Functions

`graft_neuron`	Returns a neuron starting at section.
`iter_neurites`	Iterator to a neurite, neuron or neuron population.
`iter_sections`	Iterator to the sections in a neurite, neuron or neuron population.
`iter_segments`	Return an iterator to the segments in a collection of neurites.
`make_soma`	Make a soma object from a MorphIO soma.

Classes

`COLS`	Column labels for internal data representation.
`Neurite`	Class representing a neurite tree.
`NeuriteIter`	Neurite iteration orders.
`NeuriteType`	Type of neurite.
`Neuron`	Class representing a simple neuron.
`Section`	Simple recursive tree class.

class neurom.core._neuron.COLS[source]¶

Bases: object

Column labels for internal data representation.

class neurom.core._neuron.Neurite(root_node)[source]¶

Bases: object

Class representing a neurite tree.

iter_sections(order=<function Section.ipreorder>, neurite_order=<NeuriteIter.FileOrder: 1>)[source]¶

Iteration over section nodes.

Parameters

order – section iteration order within a given neurite. Must be one of: Section.ipreorder: Depth-first pre-order iteration of tree nodes Section.ipreorder: Depth-first post-order iteration of tree nodes Section.iupstream: Iterate from a tree node to the root nodes Section.ibifurcation_point: Iterator to bifurcation points Section.ileaf: Iterator to all leaves of a tree
neurite_order – order upon which neurites should be iterated. Values: - NeuriteIter.FileOrder: order of appearance in the file - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical

class neurom.core._neuron.NeuriteIter(value)[source]¶

Bases: neurom.utils.OrderedEnum

Neurite iteration orders.

class neurom.core._neuron.NeuriteType(value)[source]¶

Bases: enum.IntEnum

Type of neurite.

class neurom.core._neuron.Neuron(filename, name=None)[source]¶

Bases: morphio._morphio.mut.Morphology

Class representing a simple neuron.

transform(trans)[source]¶: Return a copy of this neuron with a 3D transformation applied.

class neurom.core._neuron.Section(morphio_section)[source]¶

Bases: object

Simple recursive tree class.

append_section(section)[source]¶

Appends a section to the current section object.

Parameters: section (morphio.Section|morphio.mut.Section|Section|morphio.PointLevel) – a section

ibifurcation_point(iter_mode=<function Section.ipreorder>)[source]¶

Iterator to bifurcation points.

Parameters: iter_mode – iteration mode. Default: ipreorder.

iforking_point(iter_mode=<function Section.ipreorder>)[source]¶

Iterator to forking points.

Parameters: iter_mode – iteration mode. Default: ipreorder.

ileaf()[source]¶: Iterator to all leaves of a tree.

ipostorder()[source]¶: Depth-first post-order iteration of tree nodes.

ipreorder()[source]¶: Depth-first pre-order iteration of tree nodes.

is_bifurcation_point()[source]¶: Is tree a bifurcation point?

is_forking_point()[source]¶: Is this section a forking point?

is_leaf()[source]¶: Is tree a leaf?

is_root()[source]¶: Is tree the root node?

iupstream()[source]¶: Iterate from a tree node to the root nodes.

neurom.core._neuron.graft_neuron(section)[source]¶: Returns a neuron starting at section.

neurom.core._neuron.iter_neurites(obj, mapfun=None, filt=None, neurite_order=<NeuriteIter.FileOrder: 1>)[source]¶

Iterator to a neurite, neuron or neuron population.

Applies optional neurite filter and mapping functions.

Parameters

obj – a neurite, neuron or neuron population.
mapfun – optional neurite mapping function.
filt – optional neurite filter function.
neurite_order (NeuriteIter) – order upon which neurites should be iterated - NeuriteIter.FileOrder: order of appearance in the file - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical

Examples

Get the number of points in each neurite in a neuron population

>>> from neurom.core import iter_neurites
>>> n_points = [n for n in iter_neurites(pop, lambda x : len(x.points))]

Get the number of points in each axon in a neuron population

>>> import neurom as nm
>>> from neurom.core import iter_neurites
>>> filter = lambda n : n.type == nm.AXON
>>> mapping = lambda n : len(n.points)
>>> n_points = [n for n in iter_neurites(pop, mapping, filter)]

neurom.core._neuron.iter_sections(neurites, iterator_type=<function Section.ipreorder>, neurite_filter=None, neurite_order=<NeuriteIter.FileOrder: 1>)[source]¶

Iterator to the sections in a neurite, neuron or neuron population.

Parameters

neurites – neuron, population, neurite, or iterable containing neurite objects
iterator_type – section iteration order within a given neurite. Must be one of: Section.ipreorder: Depth-first pre-order iteration of tree nodes Section.ipostorder: Depth-first post-order iteration of tree nodes Section.iupstream: Iterate from a tree node to the root nodes Section.ibifurcation_point: Iterator to bifurcation points Section.ileaf: Iterator to all leaves of a tree
neurite_filter – optional top level filter on properties of neurite neurite objects.
neurite_order (NeuriteIter) – order upon which neurites should be iterated - NeuriteIter.FileOrder: order of appearance in the file - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical

Examples

Get the number of points in each section of all the axons in a neuron population

>>> import neurom as nm
>>> from neurom.core import ites_sections
>>> filter = lambda n : n.type == nm.AXON
>>> n_points = [len(s.points) for s in iter_sections(pop,  neurite_filter=filter)]

neurom.core._neuron.iter_segments(obj, neurite_filter=None, neurite_order=<NeuriteIter.FileOrder: 1>)[source]¶

Return an iterator to the segments in a collection of neurites.

Parameters

obj – neuron, population, neurite, section, or iterable containing neurite objects
neurite_filter – optional top level filter on properties of neurite neurite objects
neurite_order – order upon which neurite should be iterated. Values: - NeuriteIter.FileOrder: order of appearance in the file - NeuriteIter.NRN: NRN simulator order: soma -> axon -> basal -> apical

Note

This is a convenience function provided for generic access to neuron segments. It may have a performance overhead WRT custom-made segment analysis functions that leverage numpy and section-wise iteration.

neurom.core._neuron.make_soma(morphio_soma)[source]¶

Make a soma object from a MorphIO soma.

Parameters: morphio_soma (morphio.Soma) – soma instance of MorphIO