CIBC:Seg3D

From SCIRun Documentation Wiki

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.

Developer information is available for the Seg3D 2 project.

The tutorial is a work in progress; a draft is currently available.

Building Seg3D 2

Contact the Seg3D mailing list to get help with build issues.

Downloading the binary installer for Windows and Mac OS X is strongly recommended unless you are customizing Seg3D 2.

Windows

Read this page before building on Windows.

Mac OS X

Read this page before building on OS X.

Linux

Linux users must build Seg3D from source.

The GCC C and C++ compilers, cmake, the Qt SDK (minumum version 4.6, 4.7 recommended) and the libpng library are all required.

Configure Seg3D in the bin directory using CMake, either through the command line utility cmake, or the curses based version ccmake, or the GUI version if installed. This CMake help page may be helpful. The default configuration should be fine for most users. A build script has been included to configure Seg3D2 using CMake and build using GNU make. If a compatible CMake version cannot be found, the script will attempt to download (using wget or curl) and build CMake.

Typical build steps are:


 tar xzvf Seg3D_2.1.3-code.tgz
 cd Seg3D_2.1.3-code
 ./build.sh --release
 cd bin
 ./Seg3D2

Get build script usage using the --help flag.

 ./build.sh --help

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 tmp.ses 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

Documentation

User Documentation

Basic Seg3D functionality - Keyboard, Mouse, Interface, and Filter documentation.
File formats - File formats supported by Seg3D.
Tutorial - A simple example of the use Seg3D.
Use case scenario for the Capecchi collaboration - This example shows a segmentation process for delineating mouse bones from CT data of the forelimb.
Use case scenario for the Ellisman collaboration - This example shows a segmentation process for delineating mitochondrial cristae from electron tomography data.
Quick Tutorial for Brooks/Kurugol users - This is a quick tutorial for the Dana Brooks/Sila Kurugol DEJ segmenters. Emphasizes use of polyline segmentation tool.
CIBC:Seg3D:Documentation:UseCase:Dougherty
Speedline tools - Overview of the Speedline tools.

Developer Documentation

Building - Building Seg3D from the latest source code.
Session file format - Description of the Seg3D session file format.
Design - Overview of the design of Seg3D
Adding a filter to Seg3D by Ramón Casero Cañas
- Example 1
- Example 2
Future Plans - Future plans for Seg3D
Development - Overview of the development processes.
[Skinner Canvas Overview] - Open Office Presentation
[Skinner Canvas Overview] - Power Point

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 seg3d@sci.utah.edu.

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@sci.utah.edu.

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.