neurom.view.view.tree3d

neurom.view.view.tree3d(tr, new_fig=True, new_axes=True, subplot=False, **kwargs)

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:
  • tr – Tree neurom.Tree object
  • linewidth – float Defines the linewidth of the tree, if diameter is set to False. Default value is 1.2.
  • alpha – float Defines throughe transparency of the tree. 0.0 transparent through 1.0 opaque. Default value is 0.8.
  • treecolor – str or None Defines the color of the tree. If None the default values will be used, depending on the type of tree: Basal dendrite: “red” Axon : “blue” Apical dendrite: “purple” Undefined tree: “black” Default value is None.
  • new_fig – boolean Defines if the tree will be plotted in the current figure (False) or in a new figure (True) Default value is True.
  • subplot – matplotlib subplot value or False If False the default subplot 111 will be used. For any other value a matplotlib subplot will be generated. Default value is False.
  • diameter – boolean If True the diameter, scaled with diameter_scale factor, will define the width of the tree lines. If False use linewidth to select the width of the tree lines. Default value is True.
  • diameter_scale – float Defines the scale factor that will be multiplied with the diameter to define the width of the tree line. Default value is 1.
  • white_space – float Defines the white space around the boundary box of the morphology. Default value is 1.
Returns:

A 3D matplotlib figure with a tree view.