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Seg3D is a [[CIBC:Documentation:Seg3D:License | 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.

[[Image:Seg3D-torso2-small.png]]

==Latest Release==
'''Seg3D 1.12.0 soon to be available.'''

The Seg3D 1.12 release will be 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.



<big>'''[http://www.sci.utah.edu/download/seg3d/ Download Seg3D Here]'''</big>

[[CIBC:Seg3D:Downloads | Older Releases]]

[[CIBC:Seg3D:Documentation:Building | Building Seg3D from source]]

==Documentation==
'''User Documentation'''

* [[CIBC:Documentation:Seg3D | Basic Seg3D functionality]] - Keyboard, Mouse, Interface, and Filter documentation.
* [[CIBC:Seg3D:Documentation:FileFormats | File formats]] - File formats supported by Seg3D.
* [[CIBC:Documentation:Seg3DTutorial | Tutorial ]] - A simple example of the use Seg3D.
* [[CIBC:Seg3DUseCaseCapecchi | Use case scenario for the Capecchi collaboration ]] - This example shows a segmentation process for delineating mouse bones from CT data of the forelimb.
* [[CIBC:Seg3DUseCaseEllisman | Use case scenario for the Ellisman collaboration ]] - This example shows a segmentation process for delineating mitochondrial cristae from electron tomography data.
* [[CIBC:Seg3D:Documentation:UseCase:Brooks | 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_Speedlines | Speedline tools]] - Overview of the Speedline tools.

'''Developer Documentation'''

* [[CIBC:Seg3D:Documentation:Building | Building]] - Building Seg3D from the latest source code.
* [[CIBC:Seg3D:Documentation:SessionFormat | Session file format]] - Description of the Seg3D session file format.
* [[CIBC:Documentation:Seg3DDesign | Design ]] - Overview of the design of Seg3D
* [[CIBC:Seg3D:Documentation:Future | Future Plans ]] - Future plans for Seg3D
* [[CIBC:Seg3D_Develop | Development]] - Overview of the development processes.
* [[http://software.sci.utah.edu/devbuilds/seg3d/SkinnerCanvas.odp Skinner Canvas Overview]] - Open Office Presentation
* [[http://software.sci.utah.edu/devbuilds/seg3d/SkinnerCanvas.ppt 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 [[CIBC:Documentation:Seg3D:FeatureRequests|features discussion page]].

Please add all bugs to the [http://bugzilla.sci.utah.edu/bugzilla/buglist.cgi?bug_status=__open__&product=Seg3D Seg3D Bugzilla], or mail them to [mailto://seg3d@sci.utah.edu seg3d@sci.utah.edu].
To obtain a Bugzilla account, please send email to the Seg3D email list.

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 [mailto://seg3d@sci.utah.edu seg3d@sci.utah.edu].


'''Seg3D Mailing List and More Information'''

Please join the [http://www.sci.utah.edu/lists Seg3D email list] for news and more information.
A [http://www.sci.utah.edu/lists complete list] of NCRR CIBC project mailing lists is also available.