Object properties

To show the properties of an object in the Property Panel, select the object in the Object Explorer. The Property Panel displays the properties of the object as shown in Figure 1.

   

Figure 1: Object “Brain” is selected in the Object Explorer and the Property Panel displays its properties.

Name

To change the name of the selected object, click on its current value in the Property Panel to edit it. Insert the new value and press Enter. Alternatively, rename an object directly in the Object Explorer. Select the object in the Object Explorer and then left click on it to edit the name (notice this is not the same as double clicking). 

Color

The Color property of an object determines the color used for its 3D reconstruction and the color used for drawing all its contours in every slice (dot sets have their own independent color property). To change the color of the selected object, press the button labeled “…” that appears when clicking on the property as shown in Figure 2.

 

Figure 2: Color property of an object.  

This opens a standard color selection dialog box, similar to that presented in Figure 3.

 

Figure 3: Standard color selection dialog box.

Smoothing

This property specifies the level of smoothness desired for the surface of the 3D reconstruction of the object. To change this property, select a new value from the combo box (see Figure 4). 

Figure 4: List of smoothing values.

The predefined smoothing values range from None to Extremely High. Select the option Custom, as shown in Figure 4, to fine tune smoothing parameters.   

Note: Changing this property does not automatically change the 3D model, but the affected object is marked with the icon  meaning that it needs to be updated.  

Figure 5 shows two 3D reconstructions of the same object setting the Smoothing property to None and Low. Be aware that, although a smooth surface may be desired, an excessively high value of the Smoothing property may result in undesired object deformations in some cases. Figure 6 shows a reconstruction of the same object setting the Smoothing property to Extremely High. Notice that the object has been shrunk and its surface has been completely flatten. Show all contours of the object, as depicted in Figure 7, to check a 3D reconstruction against the contours that define it.

Figure 5: Smoothing 3D reconstructions.

Figure 6: Effect of setting the Smoothing property to an excessively high value.

Figure 7: Showing object contours to check a 3D reconstruction.

Small Overlapping  Correction

In cases where consecutive sections of an object yield small overlapping regions, the default 3D reconstruction method may produce the kind of artifact shown in Figure 8. Some contours are shown in Figure 8 together with the 3D reconstruction of an object, to easily visualize the overlapping area across slices.

 

Figure 8: Default 3D reconstruction of an object with small overlapping regions across slices.

Notice that the 3D reconstruction of the object connects consecutive sections through a small area causing alternating  shrinkage and expansion of the volume, which may not be natural for objects that are known to progress smoothly across sections. 

When the property Small Overlapping Correction is set to true, BioVis3D aligns the centroids of each section of the object before generating its 3D reconstruction. This will generally enlarge the overlapping area between consecutive slices, and will therefore avoid the artifacts shown in Figure 8. Figure 9 shows the same object, this time setting the property Small Overlapping Correction to true.

Figure 9: A 3D reconstruction setting the property Small Overlapping Correction to true.

Volume

This property shows the selected object volume measured in the unit specified by the Unit of Measure property of the sequence. The value is computed automatically each time the 3D model of the object is updated. Click the Calc button that appears when clicking on the property (see Figure 10.)

Figure 10: The button Calc forces the computation of the object volume.

Surface Area

This property shows the area of the selected object 3D reconstruction surface, measured in the unit specified by the Unit of Measure sequence property. The value is computed automatically each time the 3D model of the object is updated. You can also click the Calc button that appears when clicking on the property.

Area in Slice

This property is shown in the Property Panel only when a slice view is open and active. It gives the area of the selected object intersected with the open slice, measured in the unit specified by the Unit of Measure sequence property. Its value is determined by the contours detected in the slice, hence, a 3D reconstruction of the object is not necessary for obtaining it. To compute its value click the Calc button that appears when clicking on the property.