Navigating in 3D and Slice Views

We describe how to navigate in 3D scenes and slice views generated by 3D Slicer.

Slice Views

The slice views should now display the intensity information in greyscale, and the CLUMPFIND "labels" (i.e., object positions) as colored contours. The views show (in sequence from left to right, encoded "HorizontalAxis-VerticalAxis") RA-Velocity, Velocity-DEC, and RA-DEC diagrams. The slice positions can be moved by sliding the controls above each window.

In case slices do not change when sliding the controls, please check that the slice orientations (field 'Or') are set to either 'Axial', 'Sagittal', or 'Coronal'. Also, make sure that the FITS data was converted to NRRD using the "-a1000" option of fits2itk.

Greyscale maps can be selected for each slice view separately. Set the background ('Bg') and foreground ('Fg') fields accordingly. You may switch between foreground and background using the slider next to the view selector in the menu window.

The 3D Scene

The 3D scene should not contain any data at this point. Data can only be displayed as surfaces, which still need to be created for the example data. You can, however, overlay the slice views onto the 3D scene. Toggle the 'V' buttons next to the slice views to do so.

The viewing angle can be changed by dragging the mouse in the viewer window while holding the left mouse button. Zooming and sideways movements are possible when holding the right and the middle button, respectively, while dragging. The view selector in the menu window can be used for finer control of the view window.

The initial view can be restored by choosing the "A" perspective. This perspective corresponds to the usual projection of astronomical objects, with north up and east to the left. Velocity increases towards the back of the volume. All perspectives except "A" and "P" correspond to position-velocity diagrams.

The perspective names (e.g., "A", "L", "S") presently refer to medial terms. Later Slicer versions will have a view selector not only taylored to needs in medicine.

The actual orientation of data in the slice views and the 3D scene depend on the ordering of the data in the FITS file. The displayed data orientation will deviate from the one explained above, in case a FITS file does not comply with the data orientation requested by the FITS reader (i.e., data ordered RA-DEC-Velocity, decreasing RA with increasing RA index, increasing DEC with increasing DEC index, increasing velocity with increasing velocity index). Please use the "-r" and "-v" options of fits2itk, as well as the IDL scripts offered together with fits2itk in this case.

Now proceed to colorscale adjustment.