Overview 3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: a rich set of geometric objects for improved visual differentiation between annotations markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologies a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT. We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region. The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. Both modules are accompanied by training materials and documentation to ensure usability.

Mark Up List Selection List with the following options Create New Mark Up List List Names of existing Mark Up Lists Rename (pop up window) Delete Copy (pop up window) Mark Up Help Properties Mark Up Module Color Annotation Type Selection List: * BiDimensional * Point * Seed Widgets (see Fiducial list) * Box Widgets * Spline Widgets Selection List with the following options Create New Mark Up List existing Mark Up in Lists Rename Delete Copy Selection List: * Off * Caption * Balloon Pop Up window looking like this Tag Text Entry – tag is later used for queries and searches in XNAT Measurements A check box for displaying measurements provided by the markers in the annotation box, such as width in BiDimensional measurements Defining Glyph for seed widgets and Text

Annotation Annotation List Help Create Annotation Mark Up List Selection List with the following options Create New Annotation List List Names of existing Annotation Lists Rename (pop up window) Delete Copy (pop up window) List with annotations - Allow deletion of entries - Change order - linking of several annotations List of existing Mark Up Lists Mark Up Annotation Properties List of Mark Ups in List Oncology List of Oncology Terms (Link to Query Atlas) Text Free Text field Measurements Numeric Entry Field