Stomach Annotation Tool

A simple tool to identify anatomical regions and markers of interest on predefined meshes that describe the geometry of the stomach.

Tool views

There are three major views within the tool. The Source Mesh View displays the 3D geometry of the target mesh. The 'Anatomical Regions' Tab View, enables digitization and visualization of stomach regions. The 'Anatomical Points' Tab View, enables digitization and visualization of point based anatomical markers.

Source Mesh View

The graphical elements displayed on the view are linked to the 'Anatomical Regions' and 'Anatomical Points' views. The linkage is not dynamic and the user is required update the view using 'Update Texture' and 'Update Source' buttons.

User can zoom, rotate and translate the mesh. Double clicking on the view will reset the view to the initial view configuration.

Anatomical Regions View

Anatomical Regions view enables the user to digitize and mark anatomical regions on the stomach. The view provides a cross-section of the stomach. The stomach is assumed to be symmetric along the esophagus-duodenum axis. A sample region marking is shown below .. image:: RegionMapping.png Regions can be defined by clicking on the scene (Left mouse button), a polygon is created in the order in which the points are clicked. Points can be moved by left clicking and holding the mouse on the point and moving the mouse. Points can be removed by right mouse button click on the point.

Points cannot be created on an existing region, however, they can be created nearby and moved inside a region. Each region can be associated with a name and color. This can be modified by double clicking on the region item in the Anatomical Region Lists view. Double clicking will popup a colorbar and enable the user to select a color. After the bar is closed, the list name can be edited. Ideally this should be a well defined anatomical name. An FMA code is recommended.

Controls

New regions can be created by clicking on the 'Create new region' icon. Current region can be deleted by clicking on the 'Remove current region icon'.

The ordering of the region list is important. Regions should overlap sufficiently so that their projection on to the source mesh ensures complete coverage. The texturing is created by applying the region polygon to clip the source mesh. The order of application of the clipping determines the final regions, therefore, the order of the regions in the list is important. The order can be changed using the 'Move up' and 'Move down' buttons.

Regions can be displayed or hidden by checking and unchecking the associated list item.

Creating and Saving projects

New projects can be created using File->New Project. This will create a dialog in which the user needs to specify project related metadata and a folder where the project contents can be stored. The user can choose either 'Symmetric' or 'Human' mesh as the source mesh. The symmetric mesh is an artificially reconstructed but represents a the stomach geometry. The 'Human' mesh is based on human mesh geometry.

Project's can be saved using File->Save Project. Previously saved projects can be saved using File->Open Project. The user should select a file named <Project Name>.ann from the project folder. Project's can be saved to a new folder using File->Save As.

Current project details.

Metadata and marker file related data for a project can be determined using the Edit->Project Details. User can change Author and Comments sections.

Version Control

The tool does not provide for direct version control. It is left to the user either by saving the marker files with different names or associating the project folder to a version control mechanism. Ideally, the project folder should be linked to a github repository and version controlled using git. It is recommended that the project folder be associated with a PMR workspace. This allows for version control and sharing with provenance.