# vedo
**Repository Path**: leftwillow/vedo
## Basic Information
- **Project Name**: vedo
- **Description**: No description available
- **Primary Language**: Python
- **License**: CC0-1.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No
## Statistics
- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-04-25
- **Last Updated**: 2025-03-11
## Categories & Tags
**Categories**: Uncategorized
**Tags**: None
## README
[](https://www.codacy.com/manual/marcomusy/vedo?utm_source=github.com&utm_medium=referral&utm_content=marcomusy/vedo&utm_campaign=Badge_Grade)
[](https://pepy.tech/project/vedo)
[](https://en.wikipedia.org/wiki/MIT_License)
[](https://anaconda.org/conda-forge/vedo)
[](https://repology.org/project/vedo/versions)
[](https://doi.org/10.5281/zenodo.4609336)
[](https://circleci.com/gh/marcomusy/vedo)
`vedo` is a lightweight and powerful python module
for scientific analysis and **v**isualization of **3d** **o**bjects.
## ✨ Philosophy
Inspired by the [vpython](https://vpython.org/) *manifesto* "3D programming for ordinary mortals",
`vedo` makes it easy to work with three-dimensional meshes and volumes, creating displays and animations
in just a few lines of code, even for less experienced programmers.
`vedo` is based on [numpy](http://www.numpy.org/) and [VTK](https://www.vtk.org/),
with no other dependencies.
## 💾 Installation
```bash
pip install vedo
```
additional installation details (click to expand)
- As some of the features work better and faster on the older VTK version 8 you can install it via:
`pip install vtk==8.1.2`
- To install the latest _dev_ version of `vedo`:
`pip install -U git+https://github.com/marcomusy/vedo.git`
- To install from the conda-forge channel:
`conda install -c conda-forge vedo`
---------------------------------------------------------------------
📌 **Done?** Run any of the built-in examples. In a terminal, type e.g.:
**`vedo -r covid19`**
Visualize a file from web URL (or your dropbox!), type:
**`vedo https://vedo.embl.es/examples/data/panther.stl.gz`**
## 📙 Documentation
[The webpage of the library with documentation is available here](https://vedo.embl.es).
📌 **Need help?** Have any question, or wish to ask for a missing feature?
Do not hesitate to open a [**issue**](https://github.com/marcomusy/vedo/issues)
(or send an [email](mailto:marco.musy@embl.es)).
## 🎨 Features
The `vedo` library includes a [large set of working examples](https://github.com/marcomusy/vedo/tree/master/examples)
for a wide range of functionalities:
working with polygonal meshes and point clouds (click to expand)
- Import meshes from VTK format, STL, Wavefront OBJ, 3DS, Dolfin-XML, Neutral, GMSH, OFF, PCD (PointCloud),
- Export meshes as ASCII or binary to VTK, STL, OBJ, PLY ... formats.
- Analysis tools like Moving Least Squares, mesh morphing and more..
- Tools to visualize and edit meshes (cutting a mesh with another mesh, slicing, normalizing, moving vertex positions, etc..).
- Split mesh based on surface connectivity. Extract the largest connected area.
- Calculate areas, volumes, center of mass, average sizes etc.
- Calculate vertex and face normals, curvatures, feature edges. Fill mesh holes.
- Subdivide faces of a mesh, increasing the number of vertex points. Mesh simplification.
- Coloring and thresholding of meshes based on associated scalar or vectorial data.
- Point-surface operations: find nearest points, determine if a point lies inside or outside of a mesh.
- Create primitive shapes: spheres, arrows, cubes, torus, ellipsoids...
- Generate glyphs (associate a mesh to every vertex of a source mesh).
- Create animations easily by just setting the position of the displayed objects in the 3D scene. Add trailing lines and shadows to moving objects is supported.
- Straightforward support for multiple sync-ed or independent renderers in the same window.
- Registration (alignment) of meshes with different techniques.
- Mesh smoothing.
- Delaunay triangulation in 2D and 3D.
- Generate meshes by joining nearby lines in space.
- Find the closest path from one point to another, traveling along the edges of a mesh.
- Find the intersection of a mesh with lines, planes or other meshes.
- Interpolate scalar and vectorial fields with Radial Basis Functions and Thin Plate Splines.
- Add sliders and buttons to interact with the scene and the individual objects.
- Visualization of tensors.
- Analysis of Point Clouds:
- Moving Least Squares smoothing of 2D, 3D and 4D clouds
- Fit lines, planes, spheres and ellipsoids in space
- Identify outliers in a distribution of points
- Decimate a cloud to a uniform distribution.
working with volumetric data and tetrahedral meshes
- Import data from VTK format volumetric TIFF stacks, DICOM, SLC, MHD and more
- Import 2D images as PNG, JPEG, BMP
- Isosurfacing of volumes
- Composite and maximum projection volumetric rendering
- Generate volumetric signed-distance data from an input surface mesh
- Probe volumes with lines and planes
- Generate stream-lines and stream-tubes from vectorial fields
- Slice and crop volumes
- Support for other volumetric structures (structured and grid data)
plotting and histogramming in 2D and 3D
- Polygonal 3D text rendering with Latex-like syntax and unicode characters, with 14 different fonts.
- Fully customizable axis styles
- donut plots and pie charts
- Scatter plots in 2D and 3D
- Surface function plotting
- 1D customizable histograms
- 2D hexagonal histograms
- Polar plots, spherical plots and histogramming
- Draw latex-formatted formulas in the rendering window.
- Quiver, violin, whisker and stream-line plots
- Graphical markers analogous to matplotlib
integration with other libraries
- Integration with the [Qt5](https://www.qt.io/) framework.
- Support for [FEniCS/Dolfin](https://fenicsproject.org/) platform for visualization of PDE/FEM solutions.
- Interoperability with the [trimesh](https://trimsh.org/), [pyvista](https://github.com/pyvista/pyvista) and [pymeshlab](https://github.com/cnr-isti-vclab/PyMeshLab) libraries.
- Export 3D scenes and embed them into a [web page](https://vedo.embl.es/examples/fenics_elasticity.html).
- Embed 3D scenes in *jupyter* notebooks with [K3D](https://github.com/K3D-tools/K3D-jupyter) (can export an interactive 3D-snapshot page [here](https://vedo.embl.es/examples/geo_scene.html)).
## ⌨ Command Line Interface
Visualize a polygonal mesh from a terminal window simply with e.g.:
```bash
vedo my_mesh.obj
```
Volumetric files (_mhd, vti, slc, tiff, DICOM etc.._) can be visualized in different modes:
|Volume 3D slicing
`vedo --slicer embryo.slc`| Ray-casting
`vedo -g`| 2D slicing
`vedo --slicer2d`| Colorize voxels
`vedo --lego`|
|:--------|:-----|:--------|:-----|
| || | |
Type `vedo -h` for the complete list of options.
## 🐾 Examples
`vedo` currently includes 300+ working [examples](https://github.com/marcomusy/vedo/tree/master/examples) and [notebooks](https://github.com/marcomusy/vedo/tree/master/examples/notebooks).
| | | |
|:--------|:--------|:--------|
| [](https://github.com/marcomusy/vedo/tree/master/examples/advanced/cutWithMesh2.py) | [](https://github.com/marcomusy/vedo/tree/master/examples/simulations/grayscott.py)| [](https://github.com/marcomusy/vedo/tree/master/examples/simulations/tunnelling2.py) |
| *Easily work with volumes, tetrahedral and polygonal meshes.* | *Turing system of reaction-diffusion between two molecules.* | *Quantum-tunnelling of a particle in a box hitting a sinusoidal potential.* |
| [](https://github.com/marcomusy/vedo/blob/master/examples/other/trimesh) | [](https://vedo.embl.es/content/vedo/dolfin.html)| [](https://github.com/marcomusy/vedo/tree/master/examples/pyplot/whiskers.py) |
| *Interoperability with external libraries like [trimesh](https://trimsh.org/), [pymeshlab](https://github.com/cnr-isti-vclab/PyMeshLab), and [pyvista](https://github.com/pyvista/pyvista).* | *Support for the [FEniCS/Dolfin](https://fenicsproject.org/) library for PDE and finite element solutions.* | *Advanced 2D/3D histogramming and plotting capablities.* |
### Galleries
Check out the example galleries organized by subject here:
## 📜 References
**Scientific publications leveraging `vedo` (formerly known as `vtkplotter`):**
- X. Diego *et al.*:
*"Key features of Turing systems are determined purely by network topology"*,
[Physical Review X, 20 June 2018](https://journals.aps.org/prx/abstract/10.1103/PhysRevX.8.021071).
- M. Musy, K. Flaherty *et al.*:
*"A Quantitative Method for Staging Mouse Limb Embryos based on Limb Morphometry"*,
Development, 5 April 2018, [doi: 10.1242/dev.154856](http://dev.biologists.org/content/145/7/dev154856).
- G. Dalmasso *et al.*, *"Evolution in space and time of 3D volumetric images"*, in preparation.
- F. Claudi, A. L. Tyson, T. Branco, *"Brainrender. A python based software for visualisation of neuroanatomical and morphological data."*,
[DOI](https://doi.org/10.1101/2020.02.23.961748).
- J. S. Bennett, D. Sijacki, "Resolving shocks and filaments in galaxy formation
simulations: effects on gas properties and star formation in the circumgalactic medium",
Monthly Notices of the Royal Astronomical Society, Vol. 499, Issue 1, Nov. 2020, DOI.
- J.D.P. Deshapriya et al., *"Spectral analysis of craters on (101955) Bennu"*. (DOI: 10.1016/j.icarus.2020.114252)
**Have you found this software useful for your research? Star ✨ the project and cite it as:**
M. Musy et al.,
"vedo, a python module for scientific analysis and visualization of 3D objects and point clouds",
Zenodo, 2021, doi: 10.5281/zenodo.4609336.
[](https://www.embl.es)