Slicing in Volocity

Sometimes the XY plane in which a sample was imaged isn’t ideal for presentation. With the slice view in Volocity it is possible to reslice the data and in doing so change its orientation. Before trying the slicing feature it is important that the X, Y and Z calibrations are correct. If in doubt please check the properties. For details on how to do this please consult page 116 of the Volocity User’s guide. If you are using Volocity 3.1 or higher you can access this through the Volocity ‘Help’ menu.

Let’s take a look at how to slice a Volume. Double click on the Volume to open it then click on the slice tab.

Here you will see the current slice together with the Volume boundary as highlighted in red. The slider on the right hand side controls the depth of the slice. The input fields at the bottom of the Slice view show the degrees of rotation about the X, Y and Z axes.

The XY, XZ and YZ buttons can be used to apply preset slice orientations.

If you already know the degrees of orientation you require you can simply type the values into the X, Y and Z fields to produce the desired result. However you will probably find it easier to use the slice tools to change the slice’s orientation. Before we go into this further it is probably a good idea to show the preview this will show you what the current slice will look like based on the settings that are being applied.

You may already be familiar with the toolbar from using the HR renderer. The Slice view has buttons to rotate, zoom, move and fly around the volume.

There are two additional buttons to change the orientation of the slice.

The first button rotates the current slice

Here the volume remains stationary but the slice orientation in all three axes can be changed by clicking and dragging.

Alternatively you can use the second button, which rotates the volume about the current slice.

Here the slice remains stationary and the volume is moved.

On choosing a slice orientation the slice can be moved through the volume by using the depth slider. A tool tip will show the depth through the volume in microns.

The Navigation palette can be used with the Slice view in very much the same way as it is used with the Image view. To view the palette;

The Navigation palette has playback controls, these would be appropriate if you were dealing with an image sequence containing a 4D dataset. There are also further options to adjust channel brightness and cloak the channel/s if required.

For further information on the navigation palette please consult page 90 of the Volocity User’s guide.

To slice the Volume go to the Slice menu and select either;

Slice (Reslice) Image or Slice Sequence.

OR

Slice (Reslice) Image to folder or Slice Sequence to Folder.

As I am dealing with a volume the menu options I have available are shown below.

Slice (Reslice) Image or Slice Sequence, will produce a new Volume or Image sequence using the new orientation.

Slice (Reslice) Image to Folder or Slice Sequence to Folder, will produce a series of images from the Volume or Image sequence using the new orientation.

When the option Slice (Reslice) Image or Slice Sequence is used the new volume is interpolated using tri-cosine interpolation so each axis has the same calibration as the axis with the highest resolution in the original data. The calibration is changed, the size of the dataset will not change, neither will calibrated measurements. However non-calibrated measurements, i.e. voxel counts will not be the same as in the original data.

In the Slice menu there are also further options;

  • Capture Snapshot produces a 2D image of what is displayed in the Slice view.
  • Show/Hide Floor, Scale, Orientation, change the display of the slice view.
  • Scale and Slice View Options, change the color of the background and grid thus allowing you to better display your data.

I used the Slice Image to make a new volume at the orientation I chose. Below I have opened it in the XYZ view in Volocity, take a look at how the orientation has been changed.

That’s all for this month, see you next time!