The Visualization Pane is composed of four sub-panes: the volume pane on top, and the sagittal, coronal, and axial slice panes on the bottom. Initially, the volume pane displays a three dimensional representation of the data as orthogonal slices.

Controls in the slice panes allow selection of any slice. Changes in the slice panes are reflected in the volume pane (when it is displaying orthogonal slices). Slices are selected using slider controls or mouse actions. Figure 2.5 shows the sagittal slice pane, its slider, and cross-hairs controls.

Initially, the slice plane is placed at the center of the volume, which, for the tooth dataset, corresponds to the 51^st slice along the sagittal axis. Move the sagittal slice plane slider to the right until it reads 68. The 68th sagittal slice is now displayed in both the slice and volume panes, as shown in Figure 2.6.

Cross-hairs correspond to planes orthogonal to the slice beneath the cross-hairs. Press Button2 (middle mouse button) and drag the cross hairs to select new slices in orthogonal planes.

Table 2.1, “Slice Pane Controls” lists mouse actions and keyboard keys that select slices or alter display of slices.

Figure 2.5. A Slice Pane and its Controls

Figure 2.6. Slice plane slider moved to 68th sagittal slice

The colors displayed in the slice panes are greyscale and represent the underlying density data values: highest density corresponds to white, lowest density are colored black, and in between areas are colored shades of grey.

It is possible to change the color range used. A color range that goes from blue to red, or one that uses rainbow colors can be used. To change the color range, click the Visualization Settings pane's Planes tab. Then select a color range by clicking one of the Color Planes By radio buttons—see Figure 2.7, item 10.

Figure 2.7. Options for controlling planes

Figure 2.8. Rainbow colormap

Choose the Rainbow colormap and notice the difference in the resulting images displayed in the slice plane as shown in Figure 2.8.

With the rainbow colormap it is easier to see small variations in the data, for example the variation in the center of the tooth root from blue to green. Using the greyscale colormap the whole center appears the same shade of grey.

With the greyscale colormap it is easier to tell what the underlying data values are. With the greyscale colormap you know that a dark grey region is substantially different than a white region. Using a rainbow colormap they show up as green and red, and it is not as obvious that green and red represent substantially different data values. It is also not as obvious that red represents a high data value, and the blue represents a low data value.

Window width and level controls are used to emphasize data values displayed in the Visualization pane. Window width is the range of values relative to the ranges center value, or level. The default window width is the entire dataset. The default level is the center value of the entire dataset. With the default window and level, all values in the dataset are visible in the viewer. Certain features of the dataset, bone for example, may be emphasized by changing window width and level values.

One way to change the window width and level is by using Window/Level slider controls located in the Visualization Settings pane's Planes tab. Figure 2.7 shows these controls. Two sliders are used to set the window width and level. It is also possible to type values by clicking on the text entry boxes displayed next to the slider controls.

The mouse can also be used to change the width and level. Press Button1 and drag up and down inside of a slice pane to change the level. Press Button1 and drag the mouse from side to side to change the window width.

The tooth dataset's values range from 0 to 1300. The dataset's default level is 650 and default width is 1300. To view only the enamel, set the window width to 77 and the window level to 942.

Figure 2.9. Window Width and Level Sliders

BioImage provides a simple paintbrush tool for coloring the Volume. First click on the Volume Rendering Tab, shown in Figure 2.11 and then click the Add Paint Layer button shown in Figure 2.11 item 10. Note a new item named "Paint" is added to the list of color layers in Figure 2.12.

Figure 2.12. Paint Layer

The paint color defaults to a random color so that each new paint layer has a unique color. Click on the "Color" rectangle in Figure 2.11 item 11 to bring up the color picker.

Using the color picker, set the color to blue by moving the red and green scrolls to the left, the blue scroll to the right, and the alpha scroll to the center, as show in Figure 2.13. Then click OK to close the color picker.

Figure 2.13. Paint Color Picker

Scroll through the remaining layers and disable them by toggling their "On" buttons, as show in Figure 2.14, so that only the recently added paint layer is active. These layers are covered in the Transfer Function section.

Figure 2.14. Only the paint layer is active

Using your left mouse button, color the area inside of the top of the tooth as displayed inside of the sagittal viewer. You should now see the blue color applied to the volume as shown in Figure 2.15.

Figure 2.15. Paint applied to enamel

Now add another paint layer, and set its color to red. Again, using the left mouse button color the area inside of the root display in the sagittal viewer. You should now see the root colored in red and the top of the tooth colored in blue.

BioImage allows editing of a transfer function. A transfer function assigns color (and other properties) to three dimensional data to help the user comprehend the data visually. Figure 2.16 shows BioImage's interface for editing transfer functions.

To edit the transfer function, press Edit Transfer Function, located in the Visualization Settings pane's Volume Rendering Tab, see Figure 2.11 item 3. The new paint layer appears in the list of current editing widgets. To remove any layer, click the red X delete button next to the paint layer to remove it from the available widgets. You may also turn it on or off using the On toggle. After removing the paint layer, the transfer function editor should look as it does in Figure 2.16.

Figure 2.16. The Transfer Function Editor

The transfer function editor displays a histogram of data values as shown in Figure 2.17.

The histogram's horizontal axis corresponds to the dataset's range of values. For the tooth dataset the measure quantity is density. For the tooth dataset, density values range from 0-1300.

The histogram's vertical axis measures gradient magnitude. Areas of high gradient magnitude correspond to material borders in the dataset. Areas of low gradient magnitude correspond to different materials in the dataset.

Figure 2.17. Histogram of values in dataset

Other transfer function editor controls are used to toggle a transfer function on/off, change its color, or assign it a name. Transfer function sets can be saved to disk and later reloaded.

In the tooth histogram in Figure 2.17 four distinct materials are visible, denoted by areas of high concentration near the bottom of the histogram.

Turn off the current widgets by clicking the corresponding On checkboxes. The tooth's root is visualized by adding a rectangle over the first material area, as shown in Figure 2.18. To do this, click the Add Rectangle button in the Editor UI.

Figure 2.18. Transfer function highlighting the tooth's root

Now move the rectangle, in turn, to the other material regions to discover the air surrounding the tooth Figure 2.19, the tooth dentin Figure 2.20, and tooth enamel Figure 2.21.

Figure 2.19. The air around the tooth displayed in the viewer

Figure 2.20. Tooth dentin

Figure 2.21. Tooth enamel

The arcs in the histogram Figure 2.17 represent borders between different materials in the tooth dataset.

To visualize the dentin-enamel border, add a triangle and position it on the arc connecting the dentin and enamel, —see Figure 2.22.

Figure 2.22. Dentin, enamel border

The Processing Pane guides the user through processing their data for visualization. It has two top-level menus: File and Help. The File menu items Save Session... and Load Session... allow the user to stop and resume BioImage sessions. After loading a saved session with Load Session..., resume processing and visualization by clicking Update. The Restore Panes File option (or Control-R) will bring any detached Panes that have been hidden or closed to the front of the screen. The Help menu item Show Tooltips toggles tooltips. "Hovering" the mouse pointer over a control displays a tooltip describing a control.

Under the Processing Pane menus are the filter buttons. These buttons allow the user to add steps to a dynamic pipeline. See “Dynamic Filters” below for more information regarding adding filters to the pipeline.

Directly below the filter buttons, is a scrolled window containing the History of steps in the user's dynamic pipeline. A BioImage pipeline will always contain a Load section as the first step in the pipeline. See Chapter 5, Data Input for more information regarding loading data. Any filters added by the user will appear in the pipeline with their unique UI.

Dynamic Filters

Not every user's pre-processing steps will be the same nor in the same order. One user may want to crop first then resample while another may prefer to resample first and crop later. BioImage does not impose an order to the processing steps. The user can add and delete steps to form the desired pipeline. This pipeline is represented in the History section of the Processing Pane.

The history will always start with a Load Data step and corresponding user interface. All subsequent filters will appear under the Load Data UI.

Anatomy of a Filter UI

Each filter UI contains four main components as shown in in Figure 4.1: the visibility icon to collapse or expand the filter UI, the filter label, insert bar, and close button. In addition to these four things, each filter contains a unique interface representing its particular parameters.

The visibility icon is located in the top left of each filter UI and is labeled 1 in Figure 4.1. This icon controls whether the entire filter UI is displayed and in full view or just the label and close button. By clicking this icon, the user can hide or show the filter UI.

To the right of the visibility icon is a label which will remain visible whether the UI is in full view or hidden. It is labeled 2 in Figure 4.1. The label defaults to be the string "Filter - Unknown". By right clicking on the label, the user can edit the label to be something more meaningful. This is especially useful when a pipeline contains many instances of the same type of filter.

The red close button, labeled 3 in Figure 4.1 will delete the filter from the pipeline. See the section Deleting Filters for more information.

The insert bar is used for inserting new filters between existing filters and is discussed more in the Adding and Inserting Filters section. It is shown by the label 4 in Figure 4.1

Figure 4.1. Each filter UI contains four main components: the visibility icon, label insert bar, and close button.

Adding and Inserting Filters

There are two ways to add a new filter to the pipeline. The first approach is to click the button for the corresponding filter. These buttons are located directly above the history section as shown in Figure 4.2. When clicking one of these buttons, the filter will always be added to the end of the pipeline.

Figure 4.2. Filter butttons available in BioImage.

The second approach to adding filters to the pipeline allows the user to insert a filter between two existing filters. One of these filters may also be the Load Data step. To insert a filter, the user must click the blue bar which separates the two filters, causing a menu of available filters to appear. Selecting one of these filters will add the appropriate filter in the specified location into the pipeline.

Deleting Filters

The red close button is located in the top right corner. Clicking this button will delete the filter from the pipeline and remove the UI from the history. All settings for that filter will be lost. Since there must always be data to process, the Load Data UI does not have the close button.

Currently Viewed Data - The Eye

The radiobuttons to the left of the insert bars indicate the currenlty viewed data or the eye. Changing the eye allows the user to view input and output data to a filter. For example, if the radiobutton below a crop filter is selected, the cropped image will be shown in the Visualization Pane. If the radiobutton above a crop filter is selected, the un-cropped dataset will be shown. As filters are added or inserted, the eye will update to be the set to the output of the new filter. It is especially helpful when editing Crop value to have the eye selected for the Crop filter being edited.

Anytime a filter parameter has changed, the user must click the green Update button located towards the bottom of the Processing Pane to see the results. The Update button is only enabled when a change has been made which requires re-execution.

The bottom of the Processing Pane contains a Progress Indicator, a text description indicating the current state of the application, and suggests the next processing step. The Progress Indicator indicates an error if an error occurs. Clicking on the Progress Indicator displays an error log.

The upper window is the 3D volume pane. The volume pane can display slice planes of the axial, sagittal and coronal planes oriented relative to each other in 3-space, maximum intensity projections, and a view a full 3D volume rendering of the data. The volume pane is manipulated using the mouse. Please see the SCIRun Userguide for more information on navigating inside of the volume pane's Viewer Window. Section 6.3 of the SCIRun Userguide: "Mouse Control in the Viewer Window".

The remaining slice panes display 2D images of the individual slice planes as well as maximum intensity projections (MIP). The lower right pane controls the axial plane, the lower center pane controls the coronal plane, and the lower left pane controls the sagittal plane. The sagittal plane and its controls can be seen in Figure 2.5.

Each slice pane contains a mode UI located in the bottom of the pane, which contains the modes Slice mode, Slab mode, and MIP mode. This mode UI can be hidden or expanded by clicking the bar on the bottom. To change the mode, click the corresponding radiobutton. The slider configuration below the radiobuttons will change.

Slice mode uses a single slider to specify which slice along the axis to view. The user can change the slice in four ways: move the slice slider, enter a value in the entry box to the right of the slider and hit the Enter key, use the mouse scroll wheel to view the previous/next slice, or use the < and > keys to scroll through slices.

For Slab mode, a range widget will appear below the radiobuttons that allow the user to specify a minimum and maximum slice value. The resulting image will be a maximum intensity projection of just the slab of slices specified with the range widget. Users can click on the minimum or maximum sliders to change their values or click on the red bar between the two sliders. When dragging the red bar, the range width will remain the same and the minimum and maximum sliders will move in sync.

Clicking the MIP mode removes the sliders and shows the maximum intensity projection of all of the slices. This would be equivalent to using the Slab mode and setting the minimum and maximum to zero and the maximum slice respectively.

The Planes tab as illustrated in Figure 2.7 contains all of the controls regarding the slice, slab and MIP planes. Depending on the mode selected in each of the slice panes, the corresponding slice, slab, or MIP will be shown in the volume pane. To turn these objects on or off in the volume pane, click the corresponding Plane Toggle (labeled 2). In addition to the views from the slice panes, MIP views may be shown at the borders of the volume. To turn these on or off, use the MIP Toggles (labeled 3).

The "window width" and "level" controls can be used to emphasize data values in all four viewer windows. The default "level" (or center value) is the center value of the dataset, and the "range" (range of displayed values) is the whole dataset. With the default window and level, all values in the dataset are visible in the viewer. Changing the "window width" and "level" may allow us to view certain features of the dataset. Users can change the window width and level in three ways: use the slider shown in label 4 of Figure 2.7, type in a numerical value for the window with and level in the entry boxes next to the sliders and hit the Enter key, or using the mouse buttons in the slice panes. Left cicking and dragging the mouse up and down inside of the slice pane changes the level. Left clicking and dragging the mouse side to side inside of the slice pane changes the window width.

By default, the window width and level controls for the Planes tab are linked to the window width and level controls in the Volume Rendering tab. For more information regarding the controls on the Volume Rendering tab, see “Volume Rendering Tab”.

The Background Threshold slider (labeled 5) corresponds to the range of data values and indicates a threshold of values to be displayed in all of the viewing panes. Dragging the slider will essentially clip out any points in the volume less than or equal to the threshold.

The Font Controls (labeled 6) control the text in the 2D slice panes. Turn the text on/off using the Show 2D Window Text toggle and ajust the text size using the corresponding slider. Users can also change the text color using the color selection widget in the Font Controls frame.

The Show Guidelines checkbox allows the user to toggle the slice panes guidelines on or off. When on, guidelines will appear in the current 2D slice pane.

The Filter 2D Textures checkbox forces BioImage to linearally interpolate the textures for a smoother appearance when zooming in. With this option off, when the user zooms in on a slice either the volume or slice panes then each pixel is represented as a little square, with it on, each pixel is linearally interpolated for a smoother appearance.

The Anatomical Coordinates checkbox (labeled 9) changes between using anatomical labels such as superior, anterior, etc. with a standard X, Y, Z coordinate system.

The Color Planes By frame allows the user to change the planes colormaps to use other ranges of colors. Select the radiobutton for the desired colormap and the planes should be re-colored immediately.

The Volume Rendering tab contains all of the controls pertaining to the 3D volume rendering. To turn the volume rendering on or off in the volume pane, click the Show Volume Rendering checkbox.

The Mode allows the selection of standard (Over Operator), or maximum intensity projection (MIP) rendering styles.

The Sampling frame controls the rendering quality. Increasing the value of the Final Rate improves rendering quality. The Interactive Sampling Rate controls the number of samples while translating, rotating, or zomming into the volume and when decreased allows for faster interaction.

The full control pane normally found at the bottom of the SCIRun ViewWindow, has been replaced with the most frequently used subset of those controls, and is located on the 3D Options tab. For example, to visualize data, press the AutoView button to move the rendered geometry into the middle of the volume pane, or press Ctrl-V while the mouse is in the pane.