neurom.view

View tools to visualize morphologies.

neurom.view.plot_dendrogram(ax, obj, show_diameters=True)[source]

Plots Dendrogram of obj.

Parameters
  • ax – matplotlib axes

  • obj (neurom.Neuron, neurom.Section) – neuron or section

  • show_diameters (bool) – whether to show node diameters or not

neurom.view.plot_neuron(ax, nrn, neurite_type=<NeuriteType.all: 32>, plane='xy', soma_outline=True, diameter_scale=1.0, linewidth=1.2, color=None, alpha=0.8, realistic_diameters=False)[source]

Plots a 2D figure of the neuron, that contains a soma and the neurites.

Parameters
  • ax (matplotlib axes) – on what to plot

  • neurite_type (NeuriteType|tuple) – an optional filter on the neurite type

  • nrn (neuron) – neuron to be plotted

  • soma_outline (bool) – should the soma be drawn as an outline

  • plane (str) – Any pair of ‘xyz’

  • diameter_scale (float) – Scale factor multiplied with segment diameters before plotting

  • linewidth (float) – all segments are plotted with this width, but only if diameter_scale=None

  • color (str or None) – Color of plotted values, None corresponds to default choice

  • alpha (float) – Transparency of plotted values

  • realistic_diameters (bool) – scale linewidths with axis data coordinates

neurom.view.plot_neuron3d(ax, nrn, neurite_type=<NeuriteType.all: 32>, diameter_scale=1.0, linewidth=1.2, color=None, alpha=0.8)[source]

Generates a figure of the neuron, that contains a soma and a list of trees.

Parameters
  • ax (matplotlib axes) – on what to plot

  • nrn (neuron) – neuron to be plotted

  • neurite_type (NeuriteType) – an optional filter on the neurite type

  • diameter_scale (float) – Scale factor multiplied with segment diameters before plotting

  • linewidth (float) – all segments are plotted with this width, but only if diameter_scale=None

  • color (str or None) – Color of plotted values, None corresponds to default choice

  • alpha (float) – Transparency of plotted values

neurom.view.plot_soma(ax, soma, plane='xy', soma_outline=True, linewidth=1.2, color=None, alpha=0.8)[source]

Generates a 2d figure of the soma.

Parameters
  • ax (matplotlib axes) – on what to plot

  • soma (neurom.core.Soma) – plotted soma

  • plane (str) – Any pair of ‘xyz’

  • soma_outline (bool) – should the soma be drawn as an outline

  • linewidth (float) – all segments are plotted with this width, but only if diameter_scale=None

  • color (str or None) – Color of plotted values, None corresponds to default choice

  • alpha (float) – Transparency of plotted values

neurom.view.plot_soma3d(ax, soma, color=None, alpha=0.8)[source]

Generates a 3d figure of the soma.

Parameters
  • ax (matplotlib axes) – on what to plot

  • soma (neurom.core.Soma) – plotted soma

  • color (str or None) – Color of plotted values, None corresponds to default choice

  • alpha (float) – Transparency of plotted values

neurom.view.plot_tree(ax, tree, plane='xy', diameter_scale=1.0, linewidth=1.2, color=None, alpha=0.8, realistic_diameters=False)[source]

Plots a 2d figure of the tree’s segments.

Parameters
  • ax (matplotlib axes) – on what to plot

  • tree (neurom.core.Section or neurom.core.Neurite) – plotted tree

  • plane (str) – Any pair of ‘xyz’

  • diameter_scale (float) – Scale factor multiplied with segment diameters before plotting

  • linewidth (float) – all segments are plotted with this width, but only if diameter_scale=None

  • color (str or None) – Color of plotted values, None corresponds to default choice

  • alpha (float) – Transparency of plotted values

  • realistic_diameters (bool) – scale linewidths with axis data coordinates

Note

If the tree contains one single point the plot will be empty since no segments can be constructed.

neurom.view.plot_tree3d(ax, tree, diameter_scale=1.0, linewidth=1.2, color=None, alpha=0.8)[source]

Generates a figure of the tree in 3d.

If the tree contains one single point the plot will be empty since no segments can be constructed.

Parameters
  • ax (matplotlib axes) – on what to plot

  • tree (neurom.core.Section or neurom.core.Neurite) – plotted tree

  • diameter_scale (float) – Scale factor multiplied with segment diameters before plotting

  • linewidth (float) – all segments are plotted with this width, but only if diameter_scale=None

  • color (str or None) – Color of plotted values, None corresponds to default choice

  • alpha (float) – Transparency of plotted values