Skeleton Plot

skeleton_plot is a plotting tool for neuronal skeletons.

Installation

skeleton_plot can be installed from PyPI using pip:

pip install skeleton-plot

You can also install a local clone (e.g. if you want to install in editable mode):

git clone https://github.com/AllenInstitute/skeleton_plot.git
cd skeleton_plot
pip install -e .

Input data

skeleton_plot is designed to work with SWC and MeshParty skeletons.

Usage

Usage of skeleton_plot is described in more detail in the demo notebook, using example neurons that can be pulled from the public-facing MICrONS dataset.

A few examples (and how to make this plot) are also described below:

If you have an object with vertices and edges, or vertices and edges:

use skeleton_plot.plot_tools.plot_verts. This is how the leftmost skeleton plot above was plotted:

skeleton_plot.plot_tools.plot_verts(vertices, edges,  ax = ax[0], 
    invert_y=True, line_width = 2.2, color = 'maroon', plot_soma = True)

note: more arguments are available to be used with this function such as color and radius maps

If you have an meshparty skeleton that you want to plot:

use skeleton_plot.plot_tools.plot_skel. This is how the skeleton plot above in the middle was generated:

skeleton_plot.plot_tools.plot_skel(sk,  ax = ax[1], pull_radius = True, 
    pull_compartment_colors = True, invert_y=True, plot_soma = True, 
    line_width = 3, color = 'darkslategray') 

note: in order to use pull_radius argument, store the radius information in sk.vertex_properties['radius'] via

sk.vertex_properties['radius'] = **series with radius of each node of same length as sk.vertices**

If you have a meshparty meshwork:

use skeleton_plot.plot_tools.plot_mw_skel. This is how the skeleton plot on the right was generated:

skeleton_plot.plot_tools.plot_mw_skel(mw, ax = ax[2], pull_radius = True,
    invert_y=True, line_width = 5, plot_soma = True,
    pull_compartment_colors = True, plot_presyn = True,
    plot_postsyn = True)

note: in order to use pull_radius argument, you should have:

• the appropriate root/soma location stored in mw.skeleton.root
• basal dendrite labels stored in mw.anno[basal_table]
• apical labels stored in mw.anno[apical_table]
• axon labels stored in mw.anno[axon_table]

you may also want to plot synapses, in which case they must be stored in

• mw.anno.pre_syn['pre_pt_position']
• mw.anno.post_syn['post_pt_position']

Compartment label conventions

Standardized swc files (www.neuromorpho.org) -

• 0 - undefined
• 1 - soma
• 2 - axon
• 3 - (basal) dendrite
• 4 - apical dendrite
• 5+ - custom