Scientific Volume Imaging

The Huygens Ortho Slicer

This article is a tutorial on how to use the Huygens Ortho Slicer, available since Huygens 3.3.

Introduction

The orthogonal Slicer is designed to show the same point in 3D space from 3 orthogonal directions;

• axial or xy (top left);
• frontal or xz (bottom left);
• transverse or yz (bottom right).

If you move one of the slices, the others will follow to make sure that the center of each of the slices intersects in the same point in space. This behaviour makes the Ortho Slicer a useful tool to study small objects in 3D.

The crosshair cursor

The position of your mouse is projected as cross-hairs pointer on all slices. The value besides the center of the cross-hairs gives the distance of the mouse position to this projection. If this number is positive, it means that real pointer is more towards you (in front of your screen).

The 'View' menu

Use the view menu to show or hide image properties and guides. These are:

• Pointer coordinates. The position of the mouse pointer in microns or in voxel coordinates.
• Time. The time for the current slice in seconds or frame numbers.
• Intensity values. The intensity values for all channels on the current pointer location.
• Zoom. The zoom value in screen-pixels per micron. A magnification factor is displayed as well; using the pixel density for your monitor, this value gives an estimation for the absolute magnification.
• Wireframe box. Show or hide the wireframe box, which shows the data volume (red), the cutting plane (green), and the displayed slice (gray).
• Crosshairs. Show or hide the large crosshairs cursor.

Panning

Click and hold the right mouse button on the slice to move it around. Pressing 'c' centers the slice.


For further information you can look at the Orthogonal Slicer Tutorial