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Download Seg3D Here

Seg3D Overview

Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute. Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit. Users can explore and label image volumes using volume rendering and orthogonal slice view windows.


Seg3D 2

Download the new, improved version of Seg3D! Binary versions are available for Windows and OS X.

Much of the tool and filter information on this wiki applies to the new Seg3D2 release, although we are working on updating this wiki and the tutorial document.

Tools and Filters Documentation

Documentation for all the tools and filters available in Seg3D 2 are indexed on this page. Documentation for each tool and filter is also available inside Seg3D by pressing the ? button at the top of the tool or filter user interface window.

New OS Support

OS X 10.8+

The Seg3D2 installer is not currently signed. The unsigned installer can be run on OS X 10.8 and newer by control-clicking (or right-clicking if 2 button mouse support is enabled) on the installer package and selecting open.

Developer Information

Current developer documentation is available on GitHub. Historical development documentation is available also.


Dowload the tutorial and basic functionality manual.

Seg3D 1.x Sessions

Here is a brief set of instructions on migrating Seg3D 1.x sessions to Seg3D 2.

Build Instructions

See the GitHub build instructions.

We need feedback!

Seg3D is in active development and we like feedback on any bugs or new feature requests. Please create a wiki account and contribute so we can make Seg3D a successful application.

Feature Requests and Bugs

A list of feature requests currently under consideration can be found on the features discussion page.

Please add all bugs to the SCI GForge portal (SCI developers and collaborators with SCI accounts), or mail them to

New releases should come approximately once every three months. Because Seg3D is under active development the plan is to release binaries with new features and bug fixes quite often. Please update your version Seg3D often and keep us notified of any feature requests or bugs encountered. Any comments, suggestions, or bug reports can be sent to

Seg3D Mailing List and More Information

Please join the Seg3D email list for news and more information. A complete list of NCRR CIBC project mailing lists is also available.

Seg3D 1.x

The Seg3D 1.12 release was released in September 2009. It contains a few new features and several bug fixes.

New features in 1.12.0

  • Now compatible with 64-bit Windows
  • Unified build with CMake
  • New autosave feature. Defaults will autosave the session to in your home directory every 15 minutes.
  • Autosave time interval and directory location are configurable via Edit->Preferences
  • New hotkey for polyline tool. Pressing backspace (delete for OS X) will delete the last point in the polyline.

Bug fixes in 1.12.0

  • If a Mask Label is set, filling in a region defined by the polyline tool will only fill in the region overlapping the mask.

This behavior for the polyline tool now matches the behavior for the paintbrush tool.

Older Releases

Building Seg3D from source

Seg3D 1.x Documentation

User Documentation

Developer Documentation