https://github.com/alleninstitute/skeleton_plot
tools for plotting swc and meshparty skeletons
Science Score: 36.0%
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○Scientific vocabulary similarity
Low similarity (10.5%) to scientific vocabulary
Keywords from Contributors
Repository
tools for plotting swc and meshparty skeletons
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- Language: Jupyter Notebook
- Default Branch: main
- Size: 12.4 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 4
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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 pullradius argument, you should have:
- the appropriate root/soma location stored in mw.skeleton.root
- basal dendrite labels stored in ``mw.anno[basaltable]
- apical labels stored inmw.anno[apicaltable]
- axon labels stored inmw.anno[axontable]``
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
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Issue comment event: 1
- Push event: 1
- Pull request event: 1
Last Year
- Issues event: 1
- Watch event: 1
- Issue comment event: 1
- Push event: 1
- Pull request event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| emjoyce | e****5@g****m | 48 |
| bdpedigo | b****o@g****m | 5 |
| emjoyce | = | 5 |
| Keith Wiley | k****y@a****g | 2 |
| Forrest Collman | f****n@g****m | 1 |
| bethanny.danskin | b****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 3
- Total pull requests: 7
- Average time to close issues: about 1 month
- Average time to close pull requests: about 2 months
- Total issue authors: 2
- Total pull request authors: 4
- Average comments per issue: 0.67
- Average comments per pull request: 0.14
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 7 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- fcollman (2)
- bdpedigo (1)
Pull Request Authors
- kebwi (2)
- bpdanskin (2)
- ceesem (2)
- bdpedigo (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 172 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
pypi.org: skeleton-plot
package for plotting skeletons
- Homepage: https://github.com/AllenInstitute/skeleton_plot
- Documentation: https://skeleton-plot.readthedocs.io/
-
Latest release: 0.1.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- matplotlib *
- meshparty *
- seaborn *