3D software

Listed here are software that are especially useful for the analysis of 3D data. Note: many of the entries are just cross references (links shown in this font) to software listed elsewhere on this site.

geomorph A morphometrics package in R for the collection and analysis of landmark-based geometric morphometric data. It is available on the CRAN package website. Thanks to Dean Adams. 11/1/2012
TIVMI Requires a (free) license, and allows for the treatment of DICOM files, 3D HMH reconstruction, segmentation, along with numerous operations described in the manual TIVMI also includes a facial approximation module, AFA3D, still on development.

This software can be used to collect landmarks on 3D and automatize geometric operations. The recently added "Path 3D" plug-in allows for the positioning of series of points on outline that can be resampled to be equidistant. The segmentation module is the latest one, and is similar to what Amira (Avizo) proposes.

The software TIVMI (Treatment and Increased Vision for Medical Imaging), is developed by the University of Bordeaux (B. Dutailly, UMR 5199 PACEA), and is freely downloadable.

3D-ID Geometric Morphometric Classification of Crania for Forensic Scientists. 3D-ID is a dedicated, but flexible, Java program providing geometric morphometric tools to aid in the assessment of the sex and/or ancestral affiliation of unknown cranial remains. By Dennis E.Slice and Ann Ross. 1/19/2010
  Article from 2008 giving overview of 3D procedures.  

Free open source software for analysis and visualization of multidimensional biomedical images. Website. Theoretically BioImageXD will run on nearly any platform/hardware with an OpenGL graphics card, but for comfortable use with large images you really need gigabytes of RAM, a modern processor running at 1.5 or more GHz, and 256 or more MB of memory on your graphics card.

Landmark editor

Landmark was developed by the scientists at the Institute for Data Analysis and Visualization (IDAV) and the University of California, Davis. Working together with collaborators at the American Museum of Natural History, the team was able to build an easy to use tool for 3D landmark editing and placement on geometric surfaces typically obtained via laser range scans.). Version 3.6. Documentation, and software as well as an example of its application to "evolutionary morphing.". Note: this software is no longer being maintained by David Wiley.


Checkpoint is an integrated software package for geometric morphometrics that allows you to collect thousands of landmark and semi-landmark points in 3D. It loads both surface meshes and volumetric DICOM scans to be used for shape analysis, shape modeling, and imaged supplemented diagnostics. Website at Stratovan.

Edgewarp3 Thin-plane splines and related methods for 3D data. Linux and Mac OSX. Reads CT and other medical images in Dicom format and produces a grayscale volume which can be navigated and landmarked by the usual Edgewarp tools. By Bill Green and Fred L. Bookstein. 2/24/2005
3D Imaging Workstation The MGI Workstation operates on 3D Image data derived from a variety of sources of section scan data or from Laser surface scans. Developed for Maxillo-facial surgery, this has found many applications in orthopaedic and other surgery. The user can use a variety of cutting, repositioning and joining procedures on the 3D data, which will have been acquired from CT, MRI or even 3D ultrasound. Surface views of the manipulated image can be viewed from any direction; sectional images can be reconstructed along any plane, allowing full assessment of the spatial image structure modified by the user. By Robin Richards, Medical Physics, MEDICAL IMAGING GROUP, University College London and the UCL Hospital. 2006
VTK VTK software is free and was built for CT scans. Can use its Marching Cubes algorithm to produce 3-D surfaces and then export it in a format for INTEGRATE. 2/22/2005
DSDIGIT A program to collect 2 and 3-dimensional coordinates of points using a digitizer. By Dennis Slice. 11/5/1994
Morpheus et al.

Cross-platform package for morphometric data analysis. Versions for AIX, DOS/WIN, LINUX, and SGI. Provides a comprehensive, cross-platform environment for the acquisition, processing, and analysis of morphometric data. By Dennis E. Slice.

Morphologika2 Morphologika is a program that is now freely available for the analysis of 3d coordinate data. It offers GPA and PCA of tangent space coordinates and allows ready visualisation of results.Follow the link at the left to download the software. For more information contact Paul O'higgins. Version 2.5. 12/8/2007
IMP The Integrated Morphometrics Package for Windows contains programs that can be used on 3D data. Developed by David Sheets and described in the primer by Zelditch et al. (2004). 7/7/04
MorphoStudio Commercial 2D & 3D software they describe as a "software suite for dentists, orthodontists, oral and maxillofacial, craniofacial, plastic and cosmetic surgeons, and other specialists... , who need advanced geometric-morphometrics tools." Includes GPA, finite element analysis, thin-plate spline, measurement analysis, and statistical tests. MorphoStudio incorporates a dense correspondence algorithm so that a mean object can be derived from a sample, ready for further analyses e.g. PCA etc Version 2.0 (for 2D data) and 3.0 (that can load 3D surface scans as wrl files) are available. 4/19/2005

General 3D visualization software

Software are listed here that provide some general tools for visualizing 3D shapes.

Geomagic Studio

Comprehensive software to collect point data from all major 3D scanners, creates meshes, export data to 3D CAD, fits surfaces to mesh data, and other operations.


Clean up 3D scan data and to create NURBS surfaces.

Rapidform XOS

Convert 3D Scans to Complete Meshes & NURBS Surface Models with your 3D Scanner and Rapidform XOS.


3D visualization software. A free trial is available.


Volume analysis and visualization. Free from NIH.


Medical Imaging Processing Group at the University of Pensylvania. Includes three free programs (3DVIEWNIX, SNARK93, and EVAL3DPET).


David Clunie's Medical Image Format Site. Many links to information about image formats (other sties, books, etc.)..


If you work with medical imaging files, this site can help you. Looking for a free DICOM viewer, DICOM converter, or PACS client? You'll find them here. idoimaging.com tracks free medical imaging applications and resources: conversion programs, image display and analysis, surface and volume rendering, PACS clients and servers. Many programs are classified by a speciality to allow you to find similar programs by imaging modality, medical specialization, or similar. Half of all the programs listed here work with DICOM files, but there are over 25 file formats covered.

All the programs included are free and intended for distribution; there are no "demo" versions of commercial applications. If you are involved in programming, many of the programs are open-source, and provide APIs and SDKs for radiology programmers.

Meshlab MeshLab is an open source, portable, and extendible system for the processing and editing of unstructured 3D triangular meshes. The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes. 5/18/07
RGL A 3D visualization device system for R. Uses using OpenGL as the rendering backend. The rgl package is a visualization device system for R, using OpenGL as the rendering backend. An rgl device at its core is a real-time 3D engine written in C++. It provides an interactive viewpoint navigation facility (mouse + wheel support) and an R programming interface. 2/24/05
3D Slicer The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical data. An online User Guide is available.  

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