PyVista
PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK) - Published in JOSS (2019)
PVGeo
PVGeo: an open-source Python package for geoscientific visualization in VTK and ParaView - Published in JOSS (2019)
PyPEEC
PyPEEC: A 3D Quasi-Magnetostatic Solver using an FFT-Accelerated PEEC Method with Voxelization - Published in JOSS (2025)
Manif
Manif: A micro Lie theory library for state estimation in robotics applications - Published in JOSS (2020)
abspy
abspy: A Python package for 3D adaptive binary space partitioning and modeling - Published in JOSS (2025)
Scyland3D
Scyland3D: Processing 3D landmarks - Published in JOSS (2020)
bleiglas
bleiglas: An R package for interpolation and visualisation of spatiotemporal data with 3D tessellation - Published in JOSS (2021)
connected-components-3d
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)
lamem
LaMEM (Lithosphere and Mantle Evolution Model) - a 3D parallel code to simulate geodynamic and geomechanical processes
monailabel
MONAI Label is an intelligent open source image labeling and learning tool.
fsbrain
R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.
slmsuite
Python package for high-performance spatial light modulator (SLM) control and holography. Supports features from aberration-corrected 3D point clouds to automated Fourier-domain calibrations.
nat
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
polygnn
PolyGNN: Polyhedron-based graph neural network for 3D building reconstruction from point clouds [ISPRS 2024]
globalmatch
GlobalMatch: Registration of forest terrestrial point clouds by global matching of relative stem positions [ISPRS 2023]
easyfea
EasyFEA is a user-friendly Python library that simplifies finite element analysis.
edt
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
https://github.com/wolph/numpy-stl
Simple library to make working with STL files (and 3D objects in general) fast and easy.
tetgen
A Python interface to the C++ TetGen library to generate tetrahedral meshes of any 3D polyhedral domains
spatialmath-matlab
Create, manipulate and convert representations of position and orientation in 2D or 3D using Python
@stdlib/array-base-ternary3d
Apply a ternary callback to elements in three three-dimensional nested input arrays and assign results to elements in a three-dimensional nested output array.
@stdlib/array-base-broadcasted-binary3d
Apply a binary callback to elements in broadcasted input arrays and assign results to elements in a three-dimensional nested output array.
@stdlib/array-base-broadcasted-unary3d
Apply a unary callback to elements in a broadcasted nested input array and assign results to elements in a three-dimensional nested output array.
@stdlib/array-base-quinary3d
Apply a quinary callback to elements in five three-dimensional nested input arrays and assign results to elements in a three-dimensional nested output array.
https://github.com/google-research/sofima
Scalable Optical Flow-based Image Montaging and Alignment
icellr
Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
vrn
:man: Code for "Large Pose 3D Face Reconstruction from a Single Image via Direct Volumetric CNN Regression"
pymicro
A Python package to work with material microstructures and 3d data sets
https://github.com/ami-iit/blend-my-bot
Import your robot in blender and animate it!
river-runner
Uses USGS/MERIT Basin data to visualize the path of a rain droplet to its endpoint.
3d-forest
Visualization, processing and analysis of Lidar point clouds, mainly focused on forest environment. New version of 3D Forest. Process files with terabytes of data. Edit new point attributes. Simple addition of new features by plugins.
https://github.com/alexriss/chemfilesviewer.jl
Julia library to visualize molecules and other chemical structures
https://github.com/astorfi/3d-convolutional-speaker-recognition
:speaker: Deep Learning & 3D Convolutional Neural Networks for Speaker Verification
https://github.com/google-research/visu3d
3d without friction (Torch, TF, Jax, Numpy)
https://github.com/drprojects/point_geometric_features
Python wrapper around C++ utilities for computing neighbors and local geometric features of a point cloud
https://github.com/blockresearchgroup/compas_3gs
3D graphic statics add-on for the COMPAS framework
renderformer
Official Code Release for [SIGGRAPH 2025] RenderFormer: Transformer-based Neural Rendering of Triangle Meshes with Global Illumination
wavemap
Fast, efficient and accurate multi-resolution, multi-sensor 3D occupancy mapping
https://github.com/chenzhaiyu/awesome-planar-reconstruction
A curated list on piecewise-planar reconstruction
array-base-broadcasted-ternary3d
Apply a ternary callback to elements in three broadcasted input arrays and assign results to elements in a three-dimensional nested output array.
https://github.com/adaptivemotorcontrollab/cellseg3d
A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks
array-base-unary3d-by
Apply a unary function to each element retrieved from a three-dimensional nested input array according to a callback function and assign results to elements in a three-dimensional nested output array.
@stdlib/array-base-binary3d
Apply a binary callback to elements in three-dimensional nested input arrays and assign results to elements in a three-dimensional nested output array.
cls-cad
Automated CAD assembly generation based on Combinatory Logic Synthesis.
nightmare_of_polycubes
(Very) challenging 3D shapes for polycube-based hex-meshing
opengl-pyramid-tutorial
OpenGL Pyramid and other shapes and colored lights tutorial
@stdlib/array-base-mskunary3d
Apply a unary callback to elements in a three-dimensional nested input array according to elements in a three-dimensional nested mask array and assign results to elements in a three-dimensional nested output array.
https://github.com/brainlesion/panoptica
panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps
@stdlib/array-base-unary3d
Apply a unary callback to elements in a three-dimensional nested input array and assign results to elements in a three-dimensional nested output array.
https://github.com/abrg-models/morphologica
C++ header-only graphing and data visualization with Modern OpenGL
@stdlib/array-base-quaternary3d
Apply a quaternary callback to elements in four three-dimensional nested input arrays and assign results to elements in a three-dimensional nested output array.
points2poly
Reconstructing compact building models from point clouds using deep implicit fields [ISPRS 2022]
sciview
sciview is a tool for visualization and interaction with ND image and mesh data
wakis
3D electromagnetic time-domain solver, specialized in wake potential and beam-coupling impedance computation for particle accelerators
superpoint_transformer
Official PyTorch implementation of Superpoint Transformer introduced in [ICCV'23] "Efficient 3D Semantic Segmentation with Superpoint Transformer" and SuperCluster introduced in [3DV'24 Oral] "Scalable 3D Panoptic Segmentation As Superpoint Graph Clustering"
3d-viz-score-cam
Visualizing 3D ResNet for Medical Image Classification With Score-CAM
array-base-mskbinary3d
Apply a binary callback to elements in two three-dimensional nested input arrays according to elements in a three-dimensional nested mask array and assign results to elements in a three-dimensional nested output array.
physicell
PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!
superterrainplus
SuperTerrain+: A real-time procedural 3D infinite terrain engine with geographical features and photorealistic rendering.
phenomenal
Phenomenal: An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping
gcs-shape
gcs is a Python library for creating generalized cylindrical shells (GCS).
awesome-robotics-3d
A curated list of 3D Vision papers relating to Robotics domain in the era of large models i.e. LLMs/VLMs, inspired by awesome-computer-vision, including papers, codes, and related websites
3dcp.fyi
A Comprehensive, Chronologically Sorted Literature Database on the State of the Art in Additive Manufacturing with Cementitious Materials. Links to Open-Access Fulltexts are provided. Updated Quarterly-ish.