Sequence properties

To show the sequence properties in the Property Panel, select the sequence in the Object Explorer as shown in Figure 1. The Property Panel displays the set of properties of the sequence, as illustrated in Figure 2.

Figure 1: Selection of the sequence in the Object Explorer.

Figure 2: Property Panel displaying sequence properties.

No. of slices

This property shows the number of slices in the sequence.

Distance b/slicess

This property defines the distance between consecutive slices in the sequence. This distance is the same for all slices and is specified in the unit of measure defined by the Unit of Measure property that is also available from the Property Panel. The unit of measure also appears abbreviated ( um in the example of Figure 2) next to the literal Distance b/slices in the Property Panel. To change this property, simply click on its current value to edit it. Insert the new value and press Enter.

Note: This property and the pixel size define the aspect ratio of the 3D models. Thus, incorrect values of any of these properties may result in deformed 3D reconstructions and incorrect 3D measures (volume and surface area).  

Note: Changing this property does not automatically change the 3D models, but all the affected objects are marked with the icon  meaning that the object needs to be updated.

Slice Width and Slice Height

These properties show the size of the slices in pixels, which delimits the work area of slice views (for registration and contour detection). BioVis3D selects default values for these properties when you create a sequence based on the images size, but, as you move the slices to align them, it may be necessary to extend this area (see Figure 3).  To change them, simply click on its current value to edit it. Insert the new value and press Enter. Alternatively, change the slice width and height by dragging the edges with the mouse similarly as resizing a window.


Figure 3: Effect of changing the Slice Width and Slice Height properties.

Note: The modification of these properties impacts all the slices of the sequence.  

Unit of Measure

BioVis3d uses this unit to present all the measures that it calculates such as contour perimeters, and object volumes. To change the unit of measure, select a new value from the combo box.

Figure 4: Selection of a unit of measure.

Note: Changing this property does not affect neither the 3D models nor the contours or slices.

Pixel Size

This property shows the size of the pixel used in the sequence as a pair of numbers that defines the size in the horizontal and vertical directions respectively. The sequence pixel size is used as the default value for new slices added to the sequence. If all images in the sequence have the same pixel size, they can all be modified in one single operation by editting the sequence pixel size.

To edit this property, make sure no slice is open, otherwise, a message asking for closing all slice views appears. Then click on the Calc button that appears once clicking on the value of the property (see Figure 5).


Figure 5: Changing the pixel size.

This opens a dialog box to change the pixel size shown in Figure 6.  

Figure 6: Sequence pixel size edition.

If the pixel size is known, select a unit of measure and set the vaues in the fields Pixel Size (X), and Pixel Size (Y). Otherwise, click Load from image to obtain the pixel size from an image that contains an object of known size. See Obtaining the pixel size from an image, for specific instructions.

When the dialog box is confirmed, BioVis3D automatically sets the pixel size of all images in the sequence to have the same value as the sequence pixel size.  

Note: There is no undo option for this operation.