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 1.9.3 is available.
The Seg3D 1.9 series features a reworking of the tool and filter GUI. It also uses unsigned character based labels with more efficient memory packing, many IO improvements, a more general label mask implementation, and many bug fixes.
Seg3D 1.9.3 is the third in the 1.9 bugfix series. In addition Seg3D now features undo capability for tools and filters. There is a new layer information tool to give some statistics about the current layer such as size and number of labels marked. The polyline tool features an erase button and a few new logical operator volume filters have been added.
New features in 1.9.3
- 61 Undo
- 165 Add Layer Information Tool
- 292 Polyline tool erase
- 293 More logical operator filters
- 302 Add new hotkeys
Major bugs fixed in 1.9.3
- 235 Save always uses default filename
- 287 Fix layer hotkey handling
- 288 Threshold tool and slices out of sync
- 289 Cannot read some images
- 290 Fast tool deadlock on linux
- 291 Remember seed points
- 294 Mask Data results in grey masked area.
- 295 Label cropping is broken
- 296 Confidence connected filter multiplier should be float
- 297 Remove redundant ITK Threshold Filter
- 298 Dilate->Erode doesn't do anything
- 299 Logical operations on mismatched label sizes causes crash
- 300 Slow layer drawing on windows laptops
- 301 Polyline tool speckling
Downloads
- Release 1.9.3 - June 24, 2008
- Seg3D1.9.3-win32.exe Windows Installer
- Release 1.9.3 - June 10, 2008
- Seg3D-1.9.3-win32-installer.exe Windows Installer
- Seg3D-1.9.3-Intel.dmg OSX Intel
- Seg3D-1.9.3-Linux-x86_64.tar.gz Linux 64 bit Intel executable
- seg3d-1.9-4.x86_64.rpm 64 bit SUSE/Redhat Linux
- seg3d_1.9-3ubuntu0_amd64.deb 64 bit Ubuntu/Debian Linux
- Seg3D-1.9.3-Linux-x86.tar.gz Linux 32 bit Intel executable
- seg3d-1.9-4.i386.rpm 32 bit SUSE/Redhat Linux
- seg3d_1.9-3ubuntu0_i386.deb 32 bit Ubuntu/Debian Linux
- Example datasets
- AA-Paw.nrrd The mouse paw dataset used to test the Capecchi use case scenario.
Documentation
- Basic Seg3D functionality - Keyboard, Mouse, Interface, and Filter documentation.
- Tutorial - A simple example of the use Seg3D.
- Building - Building Seg3D from the latest source code.
- Design - Overview of the design of Seg3D
- Future Plans - Future plans for 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.
- [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 Michael Callahan.
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 Michael Callahan.
Seg3D Mailing List and More Information
Please join the Seg3D email list for news and more information.
