The Landmark Control
Many operations in BioImage Suite require the use of landmark points. These include generating "Talairach Transformations" in neuroimaging as well as seeding of levelset-type segmentation algorithms etc. All landmark editing/storage etc. in BioImage Suite is handled by the Landmark Control. This is a multifunctional control that has capabilities for both landmark editing as well as curve tracing/extraction.

Invoking and Interaction with the Viewers

Figure 1. A viewer with the Features Menu.

When supported, the landmark control lives under the "Features" menu as shown in the figure. There may be up to three option boxes in the top of this menu marked: If "Shift/Click to Landmark" is enabled (default), then to manipulate a landmark the user must hold the "Shift" key down and click with the left mouse button. This enables the use of the left mouse button alone for navigating in the images as usual. If desired, this option may be turned off, in which case navigation via the left mouse button is disabled and all left mouse button events are captured by the landmark control. (An exception to this is in some applications when the Electrode Editor is present; this is really a very specialized version of the landmark control and replaces its functionality). BioImage Suite also enables tracing on volume rendering or polygonal surfaces. These options are enabled using the "Enable Volume Trace" or "Enable Geometry Trace" menu selections. Enabling one of these disables the other. Volume tracing works by shooting a ray from the location of the virtual image camera and places a landmark at the first "non-zero" voxel in the image. It is most suitable for outlining cortical sulci from skulled-stripped brain images.

The Landmark Control

Figure 2. The Landmark Control.

The Landmark Control is a complex tool for acquiring, storing, and manipulating "point-sets" which are simply collections of ordered points -- the control can keep 9 different point sets in memory. Figure 2 on the right shows a snapshot of the control, which is divided visually into four parts, namely: (i) the menu bar, (ii) the "point set properties" frame, (iii) the list of current points in the currently selected pointset and (iv) the "global properties" frame. All operations (either point acquisition or from the Landmark Control menu) are applied to the current pointset as selected using the option menu marked as (D) in Figure 2 (see also expanded version in Figure 3).

Handling Mouse Input

Figure 3. Expanded views of the option menus A-D of the Landmark Control, as defined in Figure 2 above.

Mouse operations (typically shift/click with the left button) are interpreted depending on the current mode, which is selected using the left option menu in the "General Properties" frame (this is marked as (C) in Figure 2 and shown expanded in Figure 3). There are 5 different options:

PointSet Properties

In the pointset properties frame (see Figure 2) there are three items which control how a point-set is displayed.

The mode option menu ((A) in figure 2 and shown also in figure 3), lets you choose the display format for the set of points:
  • Landmarks (i.e. individual points)
  • Open or Closed Curve - A curve is drawn which connects the points in order and, if closed, connects the last and first points.
  • Bounding box simply draws the bounding box enclosing all points in 3D (this is useful for generating Talairach transformations).
The point size menu ((B) in figure 2) controls the size of the points in mm, ((B) in figure 2).

On the far right, a checkbox determines whether the points are displayed or not.

At the bottom of the pointset properties frame, a status textbox displays information about the current pointset, namely its name and the number of points in the set.

The List of Current Points simply lists the coordinates of all points in the current point set in mm.

Figure 4. The Landmark Control Setup Tool. Landmark names can be added by typing them in the text box next to the update button and pressing the Add button.

The Landmark Control Menu

The "File" Menu

The File Menu contains options for loading and saving the pointsets. Pointsets can be loaded/saved to file in the default .land format. In addition they can be exported to standard vtk surface format (.vtk), as well as image objectmaps (where the voxel closed to each landmark is colored in).

The "Edit" Menu

This contains self-explanatory options for copy/paste operations etc. The "Edit Point" option brings up a dialog box which enables direct manipulation of point coordinates by typing them into textboxes.

The "Color" Menu

There are two options here: Landmark color, which enables setting the color of all the landmarks and Highlight color, which can be used to set the color of the "current" point -- most commonly the last point.

The "Setup" Menu

It is often desirable to guide the user to click a set of landmarks in a presribed order. The Setup Tool has facilities to acoomplish this. Pressing the Edit Setup File option under the setup menu brings up the Label Editor. This can be used to edit/create a set of labels. The setup prescription can be loaded/saved using the Load Setup File/Save Setup File options under the Setup menu. One preset mode is the Talairach Mode -- an example of using this can be found in the Coordinates page.

The "PointSet" Menu

This is the equivalent of the "Edit" menu for whole point sets. "Copy" and "Paste" copy or paste the current landmark to/from the clipboard. "Paste 2D" enables pasting only the x and y coordinates. Create Circle creates a circle in the XY plane.

The "Curve" Menu

This contains operations for manipulating the pointset as a curve. Options include area and length computation, use of the curve to define a region of interest to perform ROI analysis on the underlying image and options for smoothing and resampling the curve.

The "Operations" Menu

There are two options here. (i) Angle returns the angle between the last two points and the x-axis. This is often useful in reslicing an image. (ii) Extract performs a local iso-contour extraction from the original image.

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