AMI GUI Design V1.1 by Kilian Pohl

1. AMI GUI Design V1.1by Kilian Pohl • Reflects changes in AMI MRML Structure • Includes feedback from AMI Workshop in Dec 09

2. 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.

3. Annotation Application Module Help Application 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) • List with Annotation Types • - Allow deletion of entries • Change order (Types will be displayed in this order in the Annotate module) • Create new Entries • Change Name Properties Continues next page

4. Selection List: * Off * Caption * Balloon Annotation Application Module – Property Frame Text Entry – tag is later used for queries and searches in XNAT Properties Tag Pop Up window looking like this Widget Selection List: * BiDimensional * Point * Seed Widgets (see Fiducial list) * Box Widgets * Spline Widgets Color Annotation Annot. Type Measurements Selection List: * Free Text * Dictionary – define dictionary entries 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

5. Annotate Module Help Select an Application (‘Basic’ is set by default) Define Application Application Lists the annotation types associated with the application – were defined by the application module Type of Annotations Function impacts all annotations in list: visible, change order, delete, property (eg changes font across entries) • List of annotations of current volume/ scene • Buttons: visible, scene, delete - scene: resets view to when annotation was set - only changes viewer not entire MRML scene • Tabs: Name , Value, Abbreviated Annotation - single mouse click: set annotation in active state - double mouse click: modifying value of tab - cursor over entry: a pop up appears with all annotation entries - use hidden tab to list/edit annotation style List Annotate Manipulate View • Change volume props, viewer layout, mouse behavior • mouse behavior= zoom, edit, pan, window/level. • - edit= just enough clicks for widget (single click), or keep adding (double click) Save Results • Save Scene, Save Annotation, Snapshot, Report • Taking a snapshot triggers a pop up window showing the snapshot and a place to save it

6. Things we need in Slicer • Change mouse behavior – add window/level with mouse • New buttons • Snapshot of 2D and 3D scene • Direct manipulation approach to reformat & in plane rotation • Better 2D 3D correspondence • Slice indicators (from other views ) in slice planes • Change cursor based on mouse node