Scientific visualization for Python

Analysis and visualization of 3D objects, point clouds and volumetric data.

vedo wraps the power of VTK and NumPy in a lightweight API for exploration, publication-quality rendering, animation insight, and interactive scientific workflows.

$ pip install vedo

Explore meshes, volumes, and scenes with a lightweight python toolkit.

vedo supports fast terminal-driven exploration and custom scientific visualization workflows.

Loading examples...

QUICK START

Install vedo and run the example gallery from your terminal.

Install once, then launch examples, inspect your own meshes, images, and volumes immediately.

$ pip install vedo

terminal

$ pip install vedo
$ vedo -r buildmesh
$ vedo data/panther.stl.gz

From dataset preview to custom analysis Python scripts.

Open a remote file directly

Visualize a mesh from a URL straight from your terminal.

vedo https://vedo.embl.es/.../panther.stl.gz

Load an interactive 3D scene

Point vedo to a saved scene and inspect it interactively.

vedo https://vedo.embl.es/examples/geo_scene.npz

Render your first object

Create and show a cone in a few lines of Python.

from vedo import Cone

c = Cone()
c.show(axes=1)

Build a lit mesh scene

Load a mesh, add custom lights, and compose a richer 3D view.

from vedo import *

man = Mesh("https://vedo.embl.es/examples/data/man.vtk")
man.c("white").lighting("glossy")

p1 = Point([1, 0, 1], c="yellow")
p2 = Point([-1, 0, 2], c="red")
l1 = Light(p1, c="yellow")
l2 = Light(p2, c="red")

show("Hello World", man, l1, l2, p1, p2, axes=True)

Create a volume from NumPy

Build a scalar field, turn it into a Volume, and extract a legosurface.

import numpy as np
from vedo import *

X, Y, Z = np.mgrid[:30, :30, :30]
field = ((X - 15)**2 + (Y - 15)**2 + (Z - 15)**2) / 225

vol = Volume(field)
lego = vol.legosurface(1, 2).cmap("afmhot_r").add_scalarbar()

show(lego, axes=True)

Resources

One place for docs, sample data, and auxiliary tools.

Docs

API documentation

Browse the generated docs and module reference from the main documentation entry point.

Open docs

Examples

Dataset catalog

Search the bundled files, preview thumbnails, and jump directly to the assets used in examples.

Browse datasets

Typography

Font previews

Inspect the shipped fonts, filter monospaced entries, and open larger preview snapshots.

View fonts

Learning

Tutorials

Go directly to the curated tutorials section instead of leaving the site for an older entry point.

Read tutorials

Stack

Built on

vedo stands on the shoulders of these libraries.

VTK NumPy SciPy Matplotlib

References

Scientific literature

vedo is used in a wide range of scientific contexts, from biology to engineering. Here are some examples of how it has been used in the wild.

Latest publications

2026

L. Aviñó-Esteban et al., "Limblab: pipeline for 3D analysis and visualisation of limb bud gene expression", BMC Bioinformatics 27(1): 6 (2026).
D. Krsikapa, I. Y. Kim, "Gradient-based optimization of component layout: addressing accessibility and mounting in assembly system design", Journal of Mechanical Design 148(3): 031702 (2026).

2025

A. Kharlamova et al., "Spatial CAPTCHA: Generatively Benchmarking Spatial Reasoning for Human-Machine Differentiation", arXiv preprint arXiv:2510.03863 (2025).
J. F. Fuhrmann et al., "Apical extracellular matrix regulates fold morphogenesis in the Drosophila wing disc", bioRxiv 2025-09 (2025).
B. Li et al., "Three-dimensional spatial transcriptomics at isotropic resolution enabled by generative deep learning", bioRxiv 2025-08 (2025).
T.-T. Hsu et al., "Shared Alteration of Whole-Brain Connectivity and Olfactory Deficits in Multiple Autism Mouse Models", bioRxiv 2025-02 (2025).
A. Arrabi et al., "C-arm guidance: A self-supervised approach to automated positioning during stroke thrombectomy", 2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI).
L. Aviñó-Esteban, H. Cardona-Blaya, J. Sharpe, "Spatio-temporal reconstruction of gene expression patterns in developing mice", Development 152: DEV204313 (2025), DOI.
B. Bortolon et al., "GRASPLAT: Enabling dexterous grasping through novel view synthesis", 2025 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS).
L. Carreira et al., "Targeted nano-energetic material exploration through active learning algorithm implementation", Energetic Materials Frontiers 6(1): 3-13 (2025).
M. Chirillo et al., "PyReconstruct: A fully open-source, collaborative successor to Reconstruct", Proceedings of the National Academy of Sciences 122(31): e2505822122 (2025).
B. Clayton et al., "A facile method to create continuum stochastic sheet-based cellular materials", Additive Manufacturing: 104917 (2025).
A. Gross et al., "STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses", Scientific Reports 15(1): 28599 (2025).
A. Gauvain et al., "HydroModPy: A Python toolbox for deploying catchment-scale shallow groundwater models" (2025).
K. N. Halwachs et al., "Effects of Stiffness and Degradability on Cardiac Fibroblast Contractility and Extracellular Matrix Secretion in Three-Dimensional Hydrogel Scaffolds", ACS Biomaterials Science & Engineering 11(11): 6521-6533 (2025).
R. Kliman et al., "Toward an Automated System for Nondestructive Estimation of Plant Biomass", Plant Direct 9(3): e70043 (2025).
J. Laussu et al., "Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell", PLOS Computational Biology 21(1): e1012681 (2025).
M. Mitelut et al., "Continuous monitoring and machine vision reveals that developing gerbils exhibit structured social behaviors prior to the emergence of autonomy", PLoS Biology 23(9): e3003348 (2025).
J.S. Posada et al., "morphoHeart: A quantitative tool for integrated 3D morphometric analyses of heart and ECM during embryonic development", PLOS Biology 23(1) (2025), DOI.
A. Prashanth, S. Hathwar, "Comparing the Effectiveness of Deep Learning Models Combined with Loss Functions in Cardiac Segmentation" (2025).
M. Levin Thomas et al., "Banner cloud formation at the Matterhorn: Measurements versus large-eddy simulations", Journal of the Atmospheric Sciences 82(8): 1661-1675 (2025).
H. Xu, "A Progressive Interactive Exploration Framework for Vector Field Data Guided by Storylines", 2025 18th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI).
S. M. Zahedi et al., "Comparative evaluation of neural networks and transfer learning for predicting mechanical properties of 3D-printed bone scaffolds", Macromolecular Materials and Engineering 310(10): e00073 (2025).

2024

C. Lei et al., "Automatic tooth arrangement with joint features of point and mesh representations via diffusion probabilistic models", Computer Aided Geometric Design 111: 102293 (2024), Code.
S. Li et al., "MogaNet: Multi-order Gated Aggregation Network", International Conference on Learning Representations (2024).
J. Cotterell et al., "Cell 3D Positioning by Optical encoding (C3PO) and its application to spatial transcriptomics", bioRxiv 2024.03.12.584578 (2024), DOI.
D. Galvez Alcantara, "Development of a finite element framework for biological applications" (2024).
M. Gazziro et al., "Fully Automated Ultra-Personalized 3D Printed Prosthetic Breasts", American Journal of Biomedical Science & Research 20: 128-132 (2024).
I. G. Gonçalves, J. M. García-Aznar, "Neurorosettes: a novel computational modelling framework to investigate the Homer-Wright rosette formation in neuroblastoma", Computational Particle Mechanics 11(2): 565-577 (2024).
E. Guiltinan et al., "pySimFrac: A Python library for synthetic fracture generation and analysis", Computers & Geosciences 191: 105665 (2024).
R. Haase et al., "Benchmarking large language models for bio-image analysis code generation", bioRxiv 2024-04 (2024).
Y. Jiang, S. L. Bugby, J. E. Lees, "PMST: A custom Python-based Monte Carlo Simulation Tool for research and system development in portable pinhole gamma cameras", Nuclear Instruments and Methods in Physics Research Section A 1061: 169161 (2024).
D. Li, F. Pucci, M. Rooman, "Prediction of paratope-epitope pairs using convolutional neural networks", International Journal of Molecular Sciences 25(10): 5434 (2024).
M. Marro, L. Moccozet, D. Vernez, "A numerical model for quantifying exposure to natural and artificial light in human health research", Computers in Biology and Medicine 171: 108119 (2024).
M. Deepa Maheshvare et al., "Kiphynet: an online network simulation tool connecting cellular kinetics and physiological transport", Metabolomics 20(5): 94 (2024).
S. Scholz et al., "Factors influencing pain medication and opioid use in patients with musculoskeletal injuries: a retrospective insurance claims database study", Scientific Reports 14(1): 1978 (2024).
J. Sultana, M. Naznin, T. R. Faisal, "SSDL - an automated semi-supervised deep learning approach for patient-specific 3D reconstruction of proximal femur from QCT images", Medical & Biological Engineering & Computing 62(5): 1409-1425 (2024).
S. Wang et al., "A 3D dental model dataset with pre/post-orthodontic treatment for automatic tooth alignment", Scientific Data 11(1): 1277 (2024).

2023

S. Baumer et al., "Robocasting of ceramic Fischer-Koch S scaffolds for bone tissue engineering", Journal of Functional Biomaterials 14(5): 251 (2023).
R. Blain et al., "A tridimensional atlas of the developing human head", Cell 186(26): 5910-5924 (2023).
B. Bogusławski et al., "Increasing brightness in multiphoton microscopy with a low-repetition-rate, wavelength-tunable femtosecond fiber laser", Optics Continuum 3(1): 22-35 (2023).
G. Gust et al., "3D Analytics: Opportunities and Guidelines for Information Systems Research", arXiv preprint arXiv:2308.08560 (2023).
T.-T. Hsu, C.-Y. Wang, Y.-P. Hsueh, "Tbr1 autism mouse model displays altered structural and functional amygdalar connectivity and abnormal whole-brain synchronization", bioRxiv 2023-07 (2023).
J. Laussu et al., "Deciphering interplay between biology and physics: finite element method-implemented vertex organoid model raises the challenge", bioRxiv 2023-05 (2023).
Y. Li et al., "Research on the evolutionary history of the morphological structure of cotton seeds: a new perspective based on high-resolution micro-CT technology", Frontiers in Plant Science 14: 1219476 (2023).
S. Monji-Azad et al., "SimTool: A toolset for soft body simulation using Flex and Unreal Engine", Software Impacts 17: 100521 (2023).
S. Triarjo et al., "Automatic 3D digital dental landmark based on point transformation weight", 2023 International Conference on Artificial Intelligence in Information and Communication (ICAIIC).
V. Zinchenko et al., "MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy", eLife 12: e80918 (2023).

2022

M. Blanc et al., "A dynamic and expandable digital 3D-atlas maker for monitoring the temporal changes in tissue growth during hindbrain morphogenesis", eLife 11: e78300 (2022).
G. Dalmasso et al., "4D reconstruction of murine developmental trajectories using spherical harmonics", Developmental Cell 57, 1-11 September 2022, DOI.
M. Deepa Maheshvare et al., "A Graph-Based Framework for Multiscale Modeling of Physiological Transport", Frontiers in Network Physiology 1: 802881 (2022), DOI.
M. Erber et al., "Geometry-based assurance of directional solidification for complex topology-optimized castings using the medial axis transform", Computer-Aided Design 152: 103394 (2022).
J. Hellar et al., "Manifold approximating graph interpolation of cardiac local activation time", IEEE Transactions on Biomedical Engineering 69(10): 3253-3264 (2022).
A. Jaeschke, H. Eckert, L. J. Bray, "Qiber3D - an open-source software package for the quantitative analysis of networks from 3D image stacks", GigaScience 11: giab091 (2022).
J. Klatzow, G. Dalmasso, N. Martínez-Abadías, J. Sharpe, V. Uhlmann, "µMatch: 3D shape correspondence for microscopy data", Frontiers in Computer Science (2022), DOI.
N. Lamb et al., "DeepJoin: Learning a Joint Occupancy, Signed Distance, and Normal Field Function for Shape Repair", ACM Transactions on Graphics 41(6) (2022), DOI.
J. E. Santos et al., "MPLBM-UT: Multiphase LBM library for permeable media analysis", SoftwareX 18: 101097 (2022).
D. J. E. Waibel et al., "Capturing Shape Information with Multi-scale Topological Loss Terms for 3D Reconstruction", Lecture Notes in Computer Science 13434 (2022), DOI.

2021

F. Claudi, A. L. Tyson, T. Branco, "Brainrender. A python based software for visualisation of neuroanatomical and morphological data.", eLife 10: e65751 (2021), DOI.
F. Claudi, T. Branco, "Differential geometry methods for constructing manifold-targeted recurrent neural networks", bioRxiv 2021.10.07.463479 (2021), DOI.
X. Lu et al., "3D electromagnetic modeling of graphitic faults in the Athabasca Basin using a finite-volume time-domain approach with unstructured grids", Geophysics (2021), DOI.
S. Ortiz-Laverde et al., "Proposal of an open-source computational toolbox for solving PDEs in the context of chemical reaction engineering using FEniCS and complementary components", Heliyon 7(1) (2021).
J. Paglia et al., "TRACER: a toolkit to register and visualize anatomical coordinates in the rat brain", bioRxiv 2021-10 (2021).
A. Pollack et al., "Stochastic inversion of gravity, magnetic, tracer, lithology, and fault data for geologically realistic structural models: Patua Geothermal Field case study", Geothermics 95 (2021), DOI.

2020

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 499(1) (2020), DOI.
J. D. P. Deshapriya et al., "Spectral analysis of craters on (101955) Bennu", Icarus (2020), DOI.

2018

X. Diego et al., "Key features of Turing systems are determined purely by network topology", Physical Review X 8, 021071 (2018), DOI.
M. Musy, K. Flaherty et al., "A Quantitative Method for Staging Mouse Limb Embryos based on Limb Morphometry", Development 145(7): dev154856 (2018), DOI.

Talks and presentations

G. Dalmasso, "Evolution in space and time of 3D volumetric images", talk at Image-based Modeling and Simulation of Morphogenesis.
G. Dalmasso, "A four-dimensional growing mouse limb bud reconstruction", talk at SEBD.
M. Musy, "vedo. A python module for scientific analysis and visualization of 3D data", seminar at MOIA (Microscopy Optics and Image Analysis), Heidelberg, November 2021.

Cite vedo

M. Musy et al., "vedo, a python module for scientific analysis and visualization of 3D objects and point clouds", Zenodo, 10.5281/zenodo.2561401.