CIBC:Seg3D
From SCIRun Documentation Wiki
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.
Latest Release
Seg3D 1.10.0 is available.
The Seg3D 1.10 series primarily features a new cleaner session file format. It also contains a set of new speedline tool and bug fixes for large and small volume spacings. There is also the usual plethora of smaller bug fixes.
New features in 1.10.0
- 238 Use archive for session files
- 314 New Speedline Tool
- 315 Add Blur to Intensity Correction Filter
Major bugs fixed in 1.10.0
- 316 Change to Connected Component Filter
- 317 Fix Save Volume for labels
- 318 Screen space seed picking
- 319 Seed points broken at large/small scales
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.
- 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
- 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.
A list of feature requests currently under consideration can be found on the features discussion page.
Please add all bugs to the Seg3D Bugzilla, or mail them to Allen Sanderson.
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 Allen Sanderson.
Seg3D Mailing List and More Information
Please join the Seg3D email list for news and more information.
