CIBC:Seg3D:Documentation:UseCase:Ellisman
From SCIRun Documentation Wiki
This page describes a typical use case for the Ellisman collaboration.
The Ellisman project is to work with the folks at NCMIR to develop software that they can use to perform segmentations of 3D electron tomography scenes. There are many types of structures that they segment from very complex scenes. Their goal is to divine function from structure of details of cellular anatomy. Most of their segmentations are done using manual contouring. We hope to speed the process by giving them semiautomated techniques that they can also use.
A use case for segmentation of the cristae of the mitochondria is illustrated in the following video. There are many other use cases that may pertain to the Ellisman group, but this one is an easy way to start.
/usr/sci/cibc-data/Seg3D/Seg3D-NCMIR2.mov
also posted here.
The data from this video can be found in
/usr/sci/cibc-data/Seg3D/king_filt-full.nhdr
The video shows the following:
- Load and navigate the dataset
- Start the ThresholdSegmentationLevelSetImageFilter tool
- Create a new layer
- Draw some seed regions within the cristae in one slice
- Run the Threshold... filter
- Periodically generate an isosurface as the filter runs
As of release 1.7 Seg3D is transitioning to the wxWidgets toolkit for the basic GUI elements. This means that the menu bar and dialogs will now have a native look and feel rather than what is presented in the movie. Although this is the case the basic functionality presented remains the same.
