skeleton_plot
is a plotting tool for neuronal skeletons.
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 .
skeleton_plot
is designed to work with
SWC
and
MeshParty skeletons.
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:
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
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**
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']
Standardized swc files (www.neuromorpho.org) -
- 0 - undefined
- 1 - soma
- 2 - axon
- 3 - (basal) dendrite
- 4 - apical dendrite
- 5+ - custom