CIBC:Seg3D:Documentation:UseCase:Capecchi

From SCIRun Documentation Wiki

This page describes a typical use case for the Capecchi collaboration.

The Capecchi project requires 3D segmentations of bones of the mouse forelimb from volumetric CT data. The goal is to do length and shape analysis of the segmentations and compare our results with measurements from the Capecchi lab that were generated by physical examination of skeletal preparations. We have several undergrads who are paid on an hourly basis to do the segmentations and would like to switch to using Seg3D. We are segmenting all phalanges and metacarpals for each of the 5 digits of the right forelimb. In addition, we need to produce segmentations of the right radius for each mouse to normalize for size/length.

A use case for the paw bones is illustrated in the video:

/usr/sci/cibc-data/Seg3D/Seg3D-Mouse1.mov

also posted here.

The data from this video can be found in

/usr/sci/cibc-data/Seg3D/AA-Paw.mhd

In the video, we do some navigation of the dataset followed by an edge-preserving smoothing of the data (GradientAnisotropicDiffusionImageFilter). This smoothing step takes several minutes, which have been edited out of the video. An initial segmentation of all forelimb bones is then performed using the ConfidenceConnectedImageFilter. Finally, the video shows a little bit of the process of defining individual bones manually using the painting interface. The user begins to move slice-by-slice and delineate individual bones, using the initial segmentation as a mask.

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.