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https://github.com/JacobBumgarner/VesselVio
An open-source application for the analysis and visualization of segmented vasculature datasets
https://github.com/JacobBumgarner/VesselVio
analysis open-source visualization
Last synced: 3 months ago
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An open-source application for the analysis and visualization of segmented vasculature datasets
- Host: GitHub
- URL: https://github.com/JacobBumgarner/VesselVio
- Owner: JacobBumgarner
- License: gpl-3.0
- Created: 2021-05-07T14:03:42.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-18T19:02:17.000Z (6 months ago)
- Last Synced: 2024-06-21T12:26:36.449Z (5 months ago)
- Topics: analysis, open-source, visualization
- Language: Python
- Homepage: https://jacobbumgarner.github.io/VesselVio/
- Size: 77.4 MB
- Stars: 92
- Watchers: 2
- Forks: 21
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-starred - JacobBumgarner/VesselVio - An open-source application for the analysis and visualization of segmented vasculature datasets (open-source)
README
# VesselVio
[](https://doi.org/10.1016/j.crmeth.2022.100189) [](https://zenodo.org/badge/latestdoi/365252628) [](https://communityinviter.com/apps/vesselvio/join-vesselvio-on-slack)
VesselVio is an open-source application designed for the analysis and visualization of segmented vasculature datasets.
There are several ways to use VesselVio:
- [Download the app](https://jacobbumgarner.github.io/VesselVio/Downloads.html) for Windows and MacOS.
- Run the app from your terminal by using the VesselVio.py file (single-line executable)
- Follow the Windows & MacOS build instructions [here](https://jacobbumgarner.github.io/VesselVio/Build.html)
- Modify the analysis pipeline and add custom analyses using the VVTerminal.py file
VesselVio is compatible with several different types of segmented vasculature datasets, including:
- Segmented vascular volumes from any imaging source (e.g., LSFM, µCT)
- Annotated volumes, including:
- Whole-brain vasculature datasets with Allen Brain Institute ID-based annotations
- Manually labelled datasets with a program such as [ITK-Snap](http://www.itksnap.org/pmwiki/pmwiki.php)
- RGB-based annotations, such as those created with [QuickNII](https://www.nitrc.org/projects/quicknii)
- Pre-constructed graphs (both edge- and vertex- based graphs)
- 2D and 3D datasets
- Isotropic and Anisotropic datasets
## Analysis
VesselVio reconstructs vascular networks to extract whole-network and individual segment features. Several examples of feature outputs can be seen below.
## Visualization
Visualization with VesselVio is made possible with [PyVista](https://github.com/pyvista/pyvista), an intuitive and high-level VTK package. Thanks to PyVista, users can easily visualize and examine their vasculature datasets with numerous options to create for accompanying figure images.
Mouse Retinal Vasculature | Human Brain
:--: | :--:
|
## Segmentation Tips
If you are looking for help with segmenting your vasculature, there are numerous packages available for this process[1](https://github.com/ChristophKirst/ClearMap2)[2](https://github.com/vessap/vessap)[3](https://github.com/giesekow/deepvesselnet).
## Contributing
Contributions to VesselVio are absolutely welcome! The [guide](https://github.com/JacobBumgarner/VesselVio/blob/main/CONTRIBUTING.md) to contributing should be read and followed. Briefly, [Issues](https://github.com/JacobBumgarner/VesselVio/issues) should be used for bug reports and feature requests. [Discussions](https://github.com/JacobBumgarner/VesselVio/discussions) and [Slack](https://communityinviter.com/apps/vesselvio/join-vesselvio-on-slack) should be used for general support or tutorial requests. Pull-requests should follow the guidelines described in the contributing document. Thank you!
## Other
Any suggestions, improvements, or comments should be directed to [Jacob Bumgarner](mailto:[email protected]).
Feel free to join us on [Slack](https://communityinviter.com/apps/vesselvio/join-vesselvio-on-slack) for general communication or troubleshooting purposes!
## Citing VesselVio
If you use VesselVio in your research, please cite our publication in [Cell Reports Methods](https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(22)00044-3).
>Bumgarner JR, and Nelson RJ. (2022). Open-source analysis and visualization of segmented vasculature datasets with VesselVio. Cell Rep Methods 2, 100189. https://doi.org/10.1016/j.crmeth.2022.100189
BibTex:
```
@article{bumgarner2022vesselvio,
title = {Open-source analysis and visualization of segmented vasculature datasets with VesselVio},
journal = {Cell Reports Methods},
volume = {2},
number = {4},
pages = {100189},
year = {2022},
issn = {2667-2375},
doi = {https://doi.org/10.1016/j.crmeth.2022.100189},
url = {https://www.sciencedirect.com/science/article/pii/S2667237522000443},
author = {Jacob R. Bumgarner and Randy J. Nelson},
}
```