analySIS®

Slice and Voxel

The
Viewer
telePresence
Add-in
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Slice and VoxelViewer SliceViewer and VoxelViewer 4

SliceViewer 6

Moving the model and planes ................................................... 8

The SliceViewer button bar .....................................................10
Context menu in SliceViewer ..................................................14
Convert the SliceViewer window into an image ......................18

VoxelViewer 20

An example .............................................................................21
The VoxelViewer button bar ....................................................22
Settings for 3D Display ............................................................29
Context menu in VoxelViewer .................................................43
The Create Animation dialog box ............................................44

Create Image Stack 48

Preparing the Images 49

SliceandVoxelViewer0805E
 SliceViewer and VoxelViewer • What is the "Slice and VoxelViewer"?

SliceViewer and VoxelViewer

What is the "Slice and VoxelViewer"?

Introduction
The Slice Viewer and Voxel Viewer add-in enables the comfortable viewing
of image stacks. You can navigate through an image stack and view it spa-
tially.
Image Stacks An image stack is made up of a series of 2D images. Each image is a cross
section of an object on another Z position. An image stack cuts an object into
slices. All images in an image stack are of the same type.
Format Image stacks are in multidimensional TIF format. It is important to know that
working with image stacks (including the loading of image stacks) requires
a lot of computing. The processing speed depends on the file size, as well
as the capacity of your computer.
Requirements All the images in an image stack must be calibrated and should also be
aligned.
Image stack icons in the Image stacks consisting of gray-value images
image buffer box

Image stacks consisting of RGB images

SliceViewer The SliceViewer calculates and draws 2 slices orthogonal to the image
plane in the image stack. The image stack is shown here as a series of slices
lying upon each other.
The illustration shows the
image stack as a series of
images which are located
consecutively on the Z
plane. One of them is
colored in the illustration.
SliceViewer also calculates
and draws an X and Y plane
4

in addition to the Z plane. All

3 planes can be moved in-
dependently enabling you to
view the inner structure of
the image stack.
 Installing the add-in

Voxel A voxel, the most basic volume element, is created when a thickness is as-
signed to a pixel; each pixel has an area resulting from calibration. This
thickness is equivalent to the Z distance between 2 acquired images. The
intensity in a voxel is constant.

The expansion of the image point concept to its three-dimensional pendant: the voxel (abbreviation of volume element)

VoxelViewer VoxelViewer enables a direct volume visualization of image stacks.

Important note VoxelViewer requires a special software license.

Short tool presentation Both tools consist of a window for viewing loaded 2D image stacks (Slice-
Viewer window / VoxelViewer window).
"3D" in your image The SliceViewer and Voxel Viewer commands are located in the 3D-Images
analysis program button bar.
Please note that the 3D image functionality is independent from the Oper >
3D-Surface, which perhaps is also contained in your image analysis pro-
gram. When using the 3D surface, a three-dimensional model is created
with the help of a height map. The heights are encoded in a gray-value
image, whereby the heights are proportional to the intensity values of the
image points. Contrary to the methods in SliceViewer and in VoxelViewer,
the functionality of the 3D-Surface is based on a process of surface recon-
struction.

Installing the add-in

Should the current configurations of your image analysis program not offer
you the 3D-Images button bar, you must execute the following steps in order
to activate the add-in:
How to... 1) Use the Special > Add-In Manager... command.
2) In the Available Add-Ins list, select the check box in front of the Slice

5
and VoxelViewer entry.
3) Click the Close button.
4) Close the program and restart it.
 After this add-in has been installed, the 3D-Images button bar is
available.
 The Oper menu has an additional 3D-Images sub-menu after the
add-in has been installed.
 SliceViewer and VoxelViewer • SliceViewer

The 3D-Images button bar

in the default configuration
(left) and with the extra
license for the VoxelViewer
(right).

SliceViewer
Application / The SliceViewer enables the visualization of image stacks and the naviga-
Performance Range tion through image stacks via the help of 2D slices.
3 planes (XY), (XZ), and (YZ), support the depiction of the three-dimensional
space, so that you can move along the Z axis and perpendicularly to it.
These 3 planes can be selected arbitrarily. The (XY) plane is the image
plane in the image stack. Planes (XY) and (YZ) serve as a cross section of
the image stack.
The (XY) plane, also termed
Z-Slice, is the image plane
in the image stack. Planes
(XY) and (YZ) are cross sec-
tions of the image stack.
6

There are 4 distinct views that are based on these planes: the X-Slice, the
Y-Slice, the Z-Slice and the so called "fence view" which is a three-dimen-
sional view of the X-, Y-, and Z-Slices. A fifth view - the Tile View - shows an
overview of all four basic views. Use the fence view in the Tile View as
"Navigator" in order to optimally orientate the object and to be able to directly
follow the slices in the remaining views. With the help of a menu, you can
quickly determine the active view mode.
The Fence View and Tile View enable you to position the fence view object
in any orientation in space; zoom in or out.
SliceViewer window The image stacks (i.e. image plane and cross sections) are displayed in an
extra window - the SliceViewer window.
Adjust window You can adapt the size of the window by
• maximizing the window so that it covers the entire document area;
 SliceViewer

• or altering the size of the window however you like. If you enlarge or
decrease the size of the window, the shown object (e.g., the slices
shown) are automatically enlarged or decreased in size accordingly.
You close the active window by clicking the cross icon at the upper right of
the title bar, or via the [Ctrl+F4] key stroke.
Numerous windows are Several SliceViewer and VoxelViewer windows can be simultaneously
supported. opened within your image analysis program.
Numerous SliceViewer windows can be created per image stack. Use this
possibility to compare numerous views of the same image stack.
Each window remains open as long as you do not explicitly close it.
The image which was The SliceViewer window always shows the image stack which was in the ac-
active during opening is tive image buffer when the Oper > 3D-Images > SliceViewer... command
shown. was initiated. This means: SliceViewer is not updated if you activate another
image buffer.
The entire functionality of SliceViewer is accessible via a button bar and a
context menu.
SliceViewer button bar You will find SliceViewer´s most important functions in the button bar.
Please note that some of the SliceViewer functions (e.g., Switch viewing
mode) are only accessible via the SliceViewer button bar. Even the Slice-
Viewer online help is accessible via a button located in the SliceViewer but-
ton bar.
Starting SliceViewer 1) Activate the image buffer which contains the image stack which you
want to visualize.
2) If necessary, execute the preparations for the visualization in Slice-
Viewer (siehe Preparing the Images auf Seite 49).
3) Click the SliceViewer button located in the 3D-Images button bar.
• Alternatively use the Oper > 3D-Images > SliceViewer... command.
 The SliceViewer window opens.

7
 SliceViewer and VoxelViewer • Moving the model and planes

The SliceViewer window shows the image stack located in the active image buffer when SliceViewer is opened. In this
example, Fence View is the selected view mode. The (XY) plane which is the image stack's image plane is also called
Z-Slice. 2 planes which are orthogonal to each other as well as to the Z plane are displayed perspectively. The current
plane positions are shown in the lower left hand corner of the SliceViewer window.

Moving the model and planes

8

Note The fence view object or the slices which are shown in the SliceViewer win-
dow are called "model".

Magnify the SliceViewer window to optimally display the model. To create

more room, select the Fence View so that the fence view object is displayed.
The other views are hidden. You can additionally magnify the fence view ob-
ject within the SliceViewer window.

Related topics
Rotate model 9
Zoom model 10
 Moving the model and planes

Select displayed slices

The main characteristic of SliceViewer is that you can move 3 planes of the
model arbitrarily, independent of the view mode you are using.
Working with the Using the left mouse button, click the model.
mouse  The 3 planes meet at the clicked point.
 The coordinates of these points are automatically updated in the X,
Y, and Z fields.
Key stroke You can use the following keys to move the position of the individual slice
planes. The coordinates are automatically updated in the X, Y, and Z fields.
Key What happens
Arrow up Y becomes larger
Arrow down Y becomes smaller
Arrow left X becomes larger
Arrow right X becomes smaller
Image up Z becomes larger
Image down Z becomes smaller

Rotate model
You can rotate models only in the "fence view" (in the Tile View mode and
in the Fence View mode as well).
Working with the
mouse
1) Switch to the fence view. To do so, click the Switch viewing mode but-
ton and select the Fence View mode from the menu.

2) Click the Rotate With Mouse button located in the SliceViewer button
bar.
 The pointer in the SliceViewer window changes its appearance.
3) In the fence view, click on the fence view object or on any location near
it with the left mouse button and keep it depressed.
4) While keeping the mouse button depressed, move the mouse in the de-
sired tilt direction. The farther you click away from the center of the im-

9
age, the faster the movement.
 The fence view object rotates in the respective direction.
Note Should the Animate mouse function be activated additionally (see Animate
mouse on page 17), the rotation of the fence view object continues as long
as you keep the left mouse button depressed.
 SliceViewer and VoxelViewer • The SliceViewer button bar

Key stroke The fence view object can be rotated or tilted with the following key strokes.
Key stroke What happens
[Ctrl] + Arrow up Tilt "up"
[Ctrl] + Arrow down Tilt "down"
[Ctrl] + Arrow left Rotation clockwise
[Ctrl] + Arrow right Rotation clockwise
Note regarding Please note: the key strokes work independent of whether the Rotate With
the key strokes Mouse mode is active or inactive. Thus the key strokes can be used to quick-
ly jump back and forth between navigation and rotation.

Zoom model
Working with the Zooming is only possible with the mouse.
mouse
1) Click the Zoom With Mouse button.
 The pointer in the SliceViewer window changes into a magnifier.
2) Leftclick on any position in the fence view.
3) Keep the left mouse button depressed and move the mouse down-
wards.
 The fence view object increases in size.
4) Release the left mouse button.
5) Leftclick on any position in the fence view.
6) Keep the left mouse button depressed and move the mouse upwards.
 The fence view object decreases in size.
7) Release the mouse button.
Note Should the Animate Mouse (see Animate mouse on page 17) be additionally
activated,the magnification of the current fence view object proceeds as
long as you keep the left mouse button depressed.

The SliceViewer button bar

You will find the button bar at the top of the SliceViewer window. The button
bar is anchored to the SliceViewer window and cannot be moved. It cannot
10

be hidden. It contains the following buttons.

 The SliceViewer button bar

Switch viewing mode

Click the arrow next to the Switch viewing mode button to open a menu with
all of the viewing modes. Select the viewing mode in which the image stack
is to be shown.
Please note: instead of clicking on the arrow next to the button, click directly
on the button to go back and forth between 2 views, e.g., between the Z-
Slice and Tile View.
For example: if Show Z-Slice view mode is checked, you can switch back
and forth between the Z-Slice and Fence View view modes by simply click-
ing the Switch viewing mode button.
Tile View Tile view shows the four possible views in the SliceViewer window.

11

You determine the view mode with the Switch viewing mode button. In the Tile View mode, all four views occupy the
SliceViewer window. Since you can track the inner structure of the image stack directly in all four partial views, this
mode helps you with orientation before switching to a one-sided view.
All 3 slices are spatially compiled in Fence View. Rotating, moving of planes, and zooming are supported in Fence
View.

Show Z-Slice An image of the image stack is shown in the Z-Slice. Use the Z field located
in the SliceViewer button bar to show various images of the stack.
Show X-Slice, Y-Slice The X-Slice respectively, Y-Slice view also shows a single image. In con-
trast to the Z-Slice, the X-Slice and Y-Slice are, however, calculated images.
Use the X or Y fields to select the various X or Y positions.
 SliceViewer and VoxelViewer • The SliceViewer button bar

Please note that the X/Y ratio of these images is dependent on the distance
between the individual Z planes. X or Y planes are shown in the SliceViewer
in a way so that the proportions of the image stack can be reproduced accu-
rately.
The illustration shows how
various Z distances effect
the view of an X-Slice or Y-
Slice in the SliceViewer. The
smaller distance in the left
example leads to a narrow,
elongated image. If the
distance is larger (right), the
X/Y ratio of the X-Slice or Y-
Slice changes respectively.

Fence View The fence view shows a 3D view of your image stack. This view shows all 3
planes displayed spatially. You can rotate and zoom the fence view object
in the fence view. This also is true if the fence view has been selected as a
single view, as well as for the fence view within the tile view.

Display Coordinate Axes

Click the Display Coordinate Axes button to show or hide the coordinate sys-
tem.You will recognize the X, Y, and Z coordinate axes based on their color.
The X axis is red, the Y axis green, and the Z axis blue.

Switch Light On
12

Activate the Switch Light On button so that the image stack will be illuminat-
ed by an imaginary light source. The program uses the artificial light rays il-
luminating the 3 planes to calculate the shading. Use this command in the
fence view to highlight the transitions between the planes.

Related topics
Rotate model 9
Zoom model 10
 The SliceViewer button bar

The illustration shows the effects of the Switch Light On command on a schematic image stack. The command simu-
lates a light source shining onto the image plane. A fictitious shading is the result. Without shading (left), the transitions
between the orthogonal planes are not visible. With the selected command (right), it is possible to recognize the
straight intersection line of 2 orthogonal planes as well as the spacial relations due to the different shading effects.

Rotate With Mouse

Click the Rotate With Mouse button to rotate the image stack in any direction
desired in the fence view (see Rotate model on page 9).

Zoom With Mouse

You can zoom in or zoom out the fence view object in the fence view with
the activated Zoom With Mouse button (see Zoom model on page 10).

Move To Home Position

Click the Move To Home Position button to reset the image stack to the start-
ing values in the SliceViewer window.
The home position can be defined with the Set Home Position command
from the context menu. You can open the context menu by clicking the right
mouse button on the image which you would like to set as the beginning
scene.

X, Y, and Z Fields
The X, Y and Z fields provide the current position of the intersection point

13
where the 3 planes (X-Slice, Y-Slice, and Z-Slice) intersect. These fields can
be edited freely. In other words, with the help of these fields, you can define
the position of this point and as a consequence the position of the 3 planes.
To do this, enter new values in the appropriate fields or click the arrow but-
tons to the right.
Here you can see the coor-
dinates of the intersection
point. You can also enter
new intersection point coor-
dinates directly into the X, Y
and Z fields.
 SliceViewer and VoxelViewer • Context menu in SliceViewer

Context menu in SliceViewer

Rightclick on one of the
possible views in the Slice-
Viewer window to open a
context menu. Depending
on the selected view, not all
of the commands are
available.

Copy
Use the Copy command to copy the active view of the SliceViewer window
to the clipboard.
Via the clipboard, you can export this view to another application program
such as MS-Word.
You can also insert the contents of the clipboard into a vacant image buffer
of your image analysis program. Thus, you get an identical RGB image
which you can save.
Availability The Copy context menu command is always available in the SliceViewer
window. This means that all the possible views (X-Slice, Y-Slice, Z-Slice and
Tile View) can all be saved to the clipboard. Please note that the values for
X, Y, and Z in the bottom left of the SliceViewer window are copied as well.

Create Image From View

Use the Create Image From View... command to create an identical RGB
image from the active view. The image is virtually a snapshot of the Slice-
Viewer and can be used for presentations and for documentation. Please
note that this image is not calibrated.
Availability The Create Image From View... command is always available in the Slice-
Viewer window. This means that you can use it in all view modes: Fence
View, Tile View, X-Slice, Y-Slice, and Z-Slice.
Since the labelling (e.g., X for X-Slice as well as the position along this axis)
14

is displayed as well, this image is especially good for presentations.

How to create an image 1) Select the appropriate view.
from the fence view 2) Determine the destination image buffer.
3) Click the right mouse button in the SliceViewer window.
 The context menu opens.
4) Use the Create Image From View... command.
 The Create Image From View dialog box opens.
5) In the Image size group, enter the image size of the image to be creat-
ed in pixels.
Select the Ratio Viewer entry so that the 3D view is reduced or en-
larged based on the preset width and that the X/Y ratio of the 3D view
is retained.

Related topics
Convert the SliceViewer window into an image 18
 Context menu in SliceViewer

6) You set the image format in the View group.

Select the 3D-View in RGB entry to create a color image from the view
shown in the SliceViewer window.
7) In the group Output Location you determine whether the created image
is to be copied into the image buffer, clipboard, or as a file.
Select the Image Buffer entry so that the image is saved into the desti-
nation image buffer.
8) Click the Create button.
 A new color image is created from the existing view located in the
SliceViewer window. The resulting image is written to the destina-
tion image buffer.
 The Create Image From View dialog box remains open, so that you
can create additional images (e.g., the remaining views) from the
same image stack, when necessary.
You enter the desired size,
image format, and target of
the output image in the Out-
put tab located in the Create
Image From View dialog
box.

Create Image From Slice

15
Use the Create Image From Slice command to create a calibrated image
from the existing 2D views (X-Slice, Y-Slice or Z-Slice). Using this command
you can also create images which are not part of the image stack. This is the
case when working with the X slices and Y slices.
The XY calibration of the resulting image is dependent on the stack's Z dis-
tances. The resulting image of an X-Slice or Y-Slice is usually not calibrated
the same way because the Z distance is usually larger than the pixel size of
the source image.
Since the resulting image is calculated without interpolation, it does not nec-
essarily look like the view in the SliceViewer window. The image can appear
distorted.
The image type and bit depth of the created image are adopted from the
source images (gray-value or color image / 8 bit or 16 bit).
 SliceViewer and VoxelViewer • Context menu in SliceViewer

Availability The context menu command Create Image From Slice is only available for
the fence views (X-Slice, Y-Slice, and Z-Slice).
How to create an image You have visualized an interesting slice (e.g., X-Slice) in your image stack.
from a slice You want it to be converted to a gray-value image.
1) Switch to the Show X-Slice view.
2) Determine the destination image buffer.
3) Click the right mouse button in the SliceViewer window.
 The context menu opens.
4) Use the Create Image From Slice command.
 A new gray-value image is created from the selected slice.
 The created image will be written into the destination image buffer.
Retaining the The resulting image is calculated without interpolation. The calibration data
calibration data is adopted. You can execute measurements in the resulting image, even if
the image appears distorted.
Drag&Drop Operation Please note that you can also create an image of the displayed slice via
Drag&Drop (see Drag&Drop on page 19).
On the right is an illustration
of an image stack with its
calibration data shown. You
have 2 possibilities to calcu-
late an X-Slice from a stack:
1. Use the Create Image
From Slice command from
the SliceViewer context
menu. The raw data is re-
tained. The image has been
calibrated differently in the X
and Y directions. Drag the
slice from the SliceViewer
into an image stack. The X
and Y calibration is identical
in the resulting image and
the proportions remain.

Reslice
16

Use the Reslice command to alter the slice direction. Instead of using the
preset slice direction (Z direction), you can have the image stack created as
a series of X-Slices or Y-Slices.
Availability The context menu command Reslice is only available for the Show X-Slice,
Show Y-Slice and Show Z-Slice views. The use of the command on the Z-
Slice remains with no effects, since the image stack is a series of Z slices by
default.
 Context menu in SliceViewer

How to alter the slice direction

1) Select the slice along which the image stack is to be sliced. For exam-
ple, select the X-Slice, so that the image stack will be calculated orthog-
onally to the coordinate axis X. To do so, select the appropriate slice
mode, e.g., Show X-Slice.
2) Determine the destination image buffer.
3) Click the right mouse button to open the context menu and then select
the Reslice command.
 A new image stack is created and saved to the destination image
buffer.
 The new image stack is calculated orthogonally to the X axis.
 The new image stack contains the name of the original image stack
with an addition which informs you about the slice direction (e.g.,
_DirX).
4) Access SliceViewer once again.
 The created image stack can be viewed in a new SliceViewer win-
dow.

Animate mouse
Use the Animate mouse command to alter the mouse's behavior when
rotating and zooming.
Should the Animate mouse context menu command not have been
activated, the following will happen:
If the Rotate With Mouse button has been activated, the pointer appears as
a circular double arrowhead as soon as you move across the fence view.
This means that the image stack can be rotated or tilted in single steps.
1) To do so, leftclick the Fence View and keep the mouse button de-
pressed.
2) While keeping the mouse button depressed, move the mouse in the de-
sired tilt direction.
 The fence view object rotates in the corresponding direction as long
as you keep pulling with the mouse.
If the Zoom With Mouse button has been activated, the pointer appears as

17
a magnifier as soon as you move across the fence view. This means that the
image stack can be zoomed in or zoomed out in single steps.
1) To do so, leftclick on any position in the SliceViewer.
2) Keep the left mouse button depressed and move the mouse down-
wards.
 The image stack is zoomed in step by step.
3) Keep the left mouse button depressed and move the mouse upwards.
 The image stack is zoomed out step by step.
 SliceViewer and VoxelViewer • Convert the SliceViewer window into an image

Should the Animate mouse context menu command have been activated,
the following will happen:
If the Rotate With Mouse button has been activated, the pointer appears as
a circular double arrowhead as soon as you move across the fence view.
This means that the image stack can be continually rotated or tilted.
1) To do so, click on a neighboring position on the fence view in the direc-
tion which the fence view object is supposed to rotate. For example,
click up in the SliceViewer window, so that the fence view object rotates
in the upward direction.
 The fence view object will rotate in this direction continuously as
long as you keep the mouse button depressed. If you release the
mouse button, the rotation will discontinue.
If the Zoom With Mouse button has been activated, the pointer appears as
a magnifier as soon as you move across the fence view. This means that the
image stack can be zoomed in or zoomed out continuously.
1) To do so, use the left mouse button to click on a position in the slice
view below the fence view object and keep the mouse button de-
pressed.
 The fence view object will be magnified continuously as long as you
keep the left mouse button depressed or if the display of the fence
view object reaches its maximum zoom.
2) Using the mouse, leftclick on a position in the slice view above the
fence view object and keep the mouse button depressed.
 The fence view object will be zoomed out continuously as long as
you keep the left mouse button depressed or if the display of the
fence view object reaches its minimum zoom.
Note Deactivate the Animate mouse command, if you want to move the mouse in
small controlled intervals.

Set Home Position

Use the Set Home Position context menu command to set a scene in the
SliceViewer window. This scene will be called the "home position". The
"home position" covers the size and position of the image stack and the 3
slice planes in the SliceViewer window.
18

Use the Set Home Position command to "put aside" an interesting scene.
You can then continue working in the SliceViewer window and, when
necessary, quickly return to the interesting scene with the Set Home Posi-
tion button. You will find the button in the SliceViewer button bar.

Convert the SliceViewer window into an image

The SliceViewer offers numerous possibilities to export the views shown in
the SliceViewer window (the fence view object, or the shown slice) as an im-
age. Use the following possibilities to use the displayed SliceViewer view as
an image in your image analysis program or to use it in another application
program.
 Convert the SliceViewer window into an image

Copying via clipboard The Edit > Copy command or the corresponding key stroke [Ctrl + C] en-
ables you to quickly copy the shown SliceViewer view to the clipboard. You
can then insert it either into another application program or into an available
image buffer of your image analysis program.
Resulting image • You always create an RGB image via the clipboard.
properties • The headings of the SliceViewer view and the position of the slices will
be used as image names. The image name "Test_x100_y100_z50" is
therefore a SliceViewer view of the "Test" stack with the position
X=100, Y=100 and Z=50.
• The image size corresponds to the size of the SliceViewer window.
Image From View The Create Image From View... command from the SliceViewer context
menu enables you to create an image of the shown view in any view mode.
This command gives you more setting possibilities than the Edit > Copy
command. You can, for example, select the format of the resulting image
(see Create Image From View on page 14).
Both of the following methods enable you to create calibrated images from
the X or Y slices. Before creating the images, switch to the X-Slice or Y-Slice
view. To do so, click the Switch viewing mode button and select, for exam-
ple, the Show X-Slice mode from the menu.
Drag&Drop If you drag&drop the slice shown in the SliceViewer window onto an image
buffer, you will create a calibrated image which looks identical to the one dis-
played in the SliceViewer.
Resulting image • A 16 bit image stack is reduced to 8 bits.
properties • The headings of the SliceViewer view and the position of the slices will
be used as image names. The image name "Test_Y=100" is an X slice
from the "Test" stack in the Y position 100.
• When pulling a view via drag&drop out of the SliceViewer onto an im-
age buffer, the program interpolates the data between the original im-
age data. The object's proportions are portrayed correctly.
How to drag an image from SliceViewer onto an image buffer
1) In the SliceViewer window, leftclick the slice you want converted to an
image.
2) Keeping the left mouse button depressed, move the mouse directly
onto any one of the image buffers.

19
Image From Slice If you use the Create Image From Slice command from the SliceViewer con-
text menu, you create a calibrated image of the slice shown in the SliceView-
er window.
Resulting image • The raw data of this image remain intact. In other words, it is created
properties without any interpolation. The resulting image can therefore appear a
bit distorted in comparison to the SliceViewer view. To ensure that the
image is correctly calibrated, the X and Y calibration are usually differ-
ent. Measurements deliver correct measurement results in these
images (see Create Image From Slice on page 15).
 SliceViewer and VoxelViewer • VoxelViewer

VoxelViewer
Terms
VoxelViewer VoxelViewer displays the image stack as a 3D image. For this purpose, vox-
els are reconstructed from the stack's images. This visualization technology
is based on a ray-tracing method.
Voxel Voxel is a made-up word and stands for volume element. A voxel is the
smallest part of a three-dimensional image. It is the result of a pixel to which
a height is assigned. This height is equivalent to the Z distance between 2
acquired images of the image stack. The intensity in a voxel is constant.
The expansion of the image
point concept to its three-
dimensional pendant: the
voxel (abbreviation of
volume element)

Every single voxel of a 3D image has a color. Only the outer surface of the
3D image will be shown. However, to avoid displaying the 3D image as sim-
ply a massive block, VoxelViewer offers various projection methods; you
can also use Raycasting methods to extract a 3D object from the 3D image.
VoxelViewer window The VoxelViewer window is where you can view the loaded image stack as
a 3D image.
You close the active window by clicking the cross icon at the upper right, or
via the [Ctrl+F4] key stroke.
Numerous windows are Several SliceViewer and VoxelViewer windows can be simultaneously
supported. opened within your image analysis program.
Each window remains open as long as you do not explicitly close it. The
document area can become very confusing if too many windows have been
20

opened.
VoxelViewer button bar You will find VoxelViewer´s most important functions in the button bar.
Please note that some of the VoxelViewer functions (especially the Voxel-
Viewer Settings) are only accessible via the VoxelViewer button bar. Even
the VoxelViewer online help is accessible via a button located in the Voxel-
Viewer button bar.
Starting VoxelViewer 1) Activate the image buffer which contains the image stack which you
want to visualize.3
2) If necessary, execute the preparations for the visualization in Voxel-
Viewer.(siehe Preparing the Images auf Seite 49)
3) Click the VoxelViewer button located in the 3D-Images button bar.
• Alternatively use the Oper > 3D-Images > VoxelViewer... command.
 The VoxelViewer window opens.
 An example

An example
Working with the VoxelViewer should be demonstrated in an example.

Starting VoxelViewer
1) Load the image stack which you want to view in VoxelViewer.
2) Use the Oper > 3D-Images > VoxelViewer... command or click the Vox-
elViewer button located in the 3D-Images button bar.
 The VoxelViewer window opens and shows the current image
stack. The setting for the visualization are adopted from settings
used during the previous start of VoxelViewer.

Setting properties
3) Click the VoxelViewer Settings button located in the VoxelViewer but-
ton bar.
 The VoxelViewer Settings dialog box opens. Now you can deter-
mine the properties.
4) In the Filter tab, select the Voxel-Binning check box to combine neigh-
boring voxels.
 In doing so, the amount of data to be processed is reduced.
5) Select the Maximum Size option.
 During Voxel binning, all of the images of an image stack are auto-
matically reduced to the smallest dimension of the (X, Y, or Z) im-
age stack, without distorting the image stack.
6) In the Smooth data group, select the Gaussian blur check box. Enter
the value "1" voxel in the Radius field.
 In doing so, image artifacts and disturbances are removed.
 High contrast transitions are then blurred.
7) In the Edge enhancement group, select the Gradient magnitude filter
check box.
 The object's view becomes sharper and more detailed.
8) Switch to the Display tab.
9) In the Step width field located in the Accuracy group, you determine
which image point is to be used for viewing the object.

21
Select a larger step width if the surface appears smooth.
Select a smaller step width if important details do not appear on the sur-
face.
Enter the value 2 pixels as a step width.
Observe how the mesh size of the grid becomes coarser/finer while
you increase/decrease step width.
• Please note: with smaller step widths, the 3D image can no longer be
moved quickly, since more points have to be calculated.
10) In the Sampling rate field located in the Accuracy group, determine in
which distances the volumes are to be scanned by the visual rays. En-
ter the value 0,5 voxel.
Maximize or minimize the sampling rate and observe how the detail
depth of the displayed surface changes.
 SliceViewer and VoxelViewer • The VoxelViewer button bar

Selecting a projection
11) Click the Mean Intensity Projection button located in the VoxelViewer's
button bar.
 In VoxelViewer, the object is shown in the selected projection.
When working with the Mean Intensity Projection, the mean inten-
sity along the visual rays will be determined and displayed.

The VoxelViewer window shows the image stack which is located in the active image buffer when VoxelViewer is
opened. In the illustrated example, the object has been depicted with help of the Blending Projection. When clicking
the Settings button located in the VoxelViewer button bar, you open the VoxelViewer Settings dialog box to select pa-
22

rameters which are relevant for the projection method. Alter the parameters until an optimal result has been reached.

The VoxelViewer button bar

You will find the button bar at the top of the VoxelViewer window. The button
bar is anchored to the VoxelViewer window and cannot be moved. It cannot
be hidden. It contains the following buttons.
 The VoxelViewer button bar

Settings
Click the Settings button to open the VoxelViewer Settings dialog box.

Projections
A projection is the illustration of a 3D image in a two-dimensional plane. For
instance, when working with the Maximum Intensity Projection, the voxels
with the brightest intensity (i.e., maximum gray value) are determined and
displayed.
Maximum Intensity Projection
When working with the Maximum Intensity Projection, the voxels with the
highest intensity (brightest voxels) are determined and used for display. This
projection accentuates the structures with higher intensity. Normally, this
projection method is appropriate for objects with inclusions.
Please note, that this projection does not inevitably provide a reliable three-
dimensional appearance of the object.
Minimum Intensity Projection
The voxels with the lowest intensity (i.e. the darkest voxels) are determined

23
and used for the visualization. This projection highlights the structures which
have a lower intensity and is especially useful for brightfield acquisitions.
Please note, that this projection does not inevitably provide a reliable three-
dimensional appearance of the object.

Related topics
Settings for 3D Display 29
 SliceViewer and VoxelViewer • The VoxelViewer button bar

This object was displayed in

VoxelViewer in the Minimum
Intensity Projection. This
projection does not enable
one to see what is in the
"foreground" and "back-
ground". To be able to
differentiate this, you can ro-
tate the 3D object with the
Create Animation com-
mand. You can find the
command in the
VoxelViewer's context
menu.

Mean Intensity Projection

The mean value of the voxels along the projection axis is calculated. Only
the voxels with an intensity higher than 0 contribute. The profile is spread in
order to cover the entire dynamic area. This projection accentuates the ar-
eas of mean intensity.
Please note, that the projection does not inevitably provide a reliable three-
dimensional appearance of the object.
Isosurface Projection
A voxel, whose intensity is less than or equal to (respectively, greater than
or equal to) the fixed isovalue, is searched along the visual ray. This voxel
is interpreted as a part of the surface which is to be displayed. The Isosur-
face Projection looks for a closed three-dimensional surface in the image
stack. This surface or isosurface consists of voxels with equal intensity.
The Isosurface Projection directly provides a proper spatial impression.
The illustration shows the
same object as in the prior il-
lustration, however this time
24

displayed using a different

projection method: the Isos-
urface Projection. This pro-
jection method enables you
to create lifelike 3D image.
 The VoxelViewer button bar

Blending Projection
The Blending Projection enables you to make layers transparent, thus mak-
ing the colored inner structures of the 3D image model visible. The Blending
Projection directly provides a spatial impression.
Comparison of the five projection methods
As a summary, the five VoxelViewer projections are compared on a simple
example 3D image. The selected 3D image consists of 3 simple nested geo-
metric forms. The 3 forms have various gray values (intensity 0, 160, and
255). The cube has the highest value, the pyramid the middle value, and the
sphere the lowest value.
Composite of the example
3D image used. The curve
shows the gray-value
histogram.

When using the Maximum Intensity Projection only the cube's voxels are
shown, since they all have the highest intensity.
When using the Minimum Intensity Projection all of the voxels with the low-
est intensity are used for the display in VoxelViewer. The entire sphere and
only the sphere consists of such voxels. Only the sphere is shown.
When using the Mean Intensity Projection the shown image intensities are
calculated from the mean value of all the voxel intensities located along the
projection axis.
 The lifelike impression enables you to identify the Isosurface Pro-
jection. 172 is the Isovalue which was selected for showing the ex-

25
ample object. Since the intensity of the cube (255) and the
pyramid (160) are above the selected threshold, the cube and
pyramid cannot be displayed completely. The Isovalue can be se-
lected, so that only the sphere, for example, is shown completely.
The same Isovalue was used with the Blending Projection as
above for the Isosurface Projection. The opacity was set to 100 %
between the intensity value 0 and 174, and to 0 between intensity
values 174 and 255. In doing so, the cube and the pyramid (with
intensity values smaller than, respectively much smaller than) are
displayed completely, respectively partially transparent). The
cube (with intensity values above 174) appears non-transparent.
Non-transparency and transparency are represented by colors
which can be manually set.
 SliceViewer and VoxelViewer • The VoxelViewer button bar

An overview of the five pro-

jection methods in an exam-
ple of a schematic 3D im-
age. It consists of a cube, a
pyramid and a sphere. The
latter fits in the pyramid. The
pyramid, in turn, fits in the
cube.
The cube consists of voxel
all possessing an intensity
of 255, the pyramid consists
of voxels of medium intensi-
ty, and the sphere consists
of voxels with lower intensi-
ty.
In the left column, from top
to bottom: Maximum Intensi-
ty Projection, Minimum In-
tensity Projection and Mean
Intensity Projection.
In the right column: Isosur-
face Projection (top and
middle), Blending Projection
(below).
26

Display Coordinate Axes

Activate the Display Coordinate Axes button to show and fade out the X, Y,
and Z coordinate axes. The origin of the coordinate system is marked by a
yellow point.

Switch Light On
You activate the Switch Light On button in the Blending Projection, so that
3D volumes are illuminated from an imaginary light source irradiating from
the Z plane. This way, you alter the overall impression of the 3D volume.
 The VoxelViewer button bar

Central Perspective
Activate the Central Perspective button to determine the type of perspective.
The type of perspective determines the two-dimensional depiction of three-
dimensional objects. You can switch to and fro between the central perspec-
tive and the parallel perspective. The central perspective is active when the
button has been activated. The 3D image is shown in the parallel perspec-
tive when the button has not been activated.
For every object point, a perpendicular to the projection plane is drawn when
using the parallel perspective. Each object point is then mapped at the in-
tersection of the normals with the projection plane. In doing so, parallel lines
are shown on parallel lines. The depiction is not perspectively distorted.
The central perspective reconstructs how someone would view a 3D ob-
ject. The three-dimensional object is projected onto the projection plane
from a central point - which is the observer's eye. The central perspective
delivers a more realistic image.
The illustration shows the
effects of the Central Per-
spective command on a
cuboid (left: parallel per-
spective, right: central per-
spective).

Rotate With Mouse

Click the Rotate With Mouse button to rotate the 3D image as you like. You
rotate the model exactly like you would in SliceViewer (see Rotate model on
page 9).
You can also rotate or tilt it in any direction with the following key stroke.
Key stroke What happens
[Ctrl] + Arrow up Tilt "up"

27
[Ctrl] + Arrow down Tilt "down"
[Ctrl] + Arrow left Rotation clockwise
[Ctrl] + Arrow right Rotation clockwise

Zoom With Mouse

Click the Zoom With Mouse button to maximize or minimize the representa-
tion of the 3D image in the VoxelViewer window. You zoom the model ex-
actly like you would in SliceViewer (see Zoom model on page 10).
 SliceViewer and VoxelViewer • The VoxelViewer button bar

Move To Home Position

Click the Move To Home Position button to reset the object to the starting
values in the VoxelViewer window.
The home position can be defined with the Set Home Position command
from the context menu. You can open the context menu by clicking the right
mouse button on the image you would like to determine as the beginning
scene.

Create Animation...
Click the Create Animation button to define an automatic rotation of the ob-
ject and to save it as a short film, for example.
The command opens the Create Animation dialog box, where you can de-
fine the rotation and the characteristics of the animation.
You can save the animation in one of the following file formats: AVI, Multiple
TIFF-file or animated GIF. You can visualize it later with an appropriate ap-
plication program.
This command is also available as a context menu command.

Measure
VoxelViewer offers 3 measurement functions. Using this functionality, you
can quickly locate positions in volumes and measure segments. All the re-
sults are issued in a measurement sheet.
The unit for the measurement result of the XY calibration is adopted as a unit
for the measurement results.
How to... 1) Enlarge the VoxelViewer window so you can define measurement
points as precisely as possible. Leave some space along the lower
edge of the Graphical User Interface (GUI) to be able to see the mea-
surement sheet during measurement.
2) Click the Measure button in the VoxelViewer button bar to open a
menu.
Measure distances You want to measure an arbitrary distance in VoxelViewer.
3) Select the Measure Distances command located in the Measure menu.
 The pointer moves into the VoxelViewer window.
28

4) Position the pointer to the starting-point of the distance to be measured

and depress the left mouse button.
 A colored point appears in the VoxelViewer window.
 The coordinates of this point (X1, Y1 and Z1) are written to the mea-
surement sheet.
5) Position the pointer onto the end point of the distance to be measured.
To do so, you may need to alter the object's position in the VoxelViewer
window with the appropriate key stroke, i.e, with the help of one of the
4 arrow keys together with the [Ctrl] key. Click the left mouse button to
set the end point.
 The end point and the distance to be measured are drawn in the
VoxelViewer window.
Related topics
The Create Animation dialog box 44
 Settings for 3D Display

 The position of the endpoints (X2, Y2 and Z2) and the measured
distance between the end point and start point are written to the
measurement sheet.
6) Repeat the last 2 steps for all distances to be measured.
 The additional distances to measure appear in different colors in
the VoxelViewer window.
 The individual coordinates of the start and end points and the mea-
sured distances are added to the measurement table.
7) End the distance measurement by clicking the right mouse button.
Click on Yes to confirm the query.
Parameter Meaning
Name Image Name
Distance Measured distance between the 2 points
2 2 2
( X 1 – X 2 ) + ( Y1 – Y 2 ) + ( Z 1 – Z 2 )

X, X1, X2, X3... X coordinate of the point with the corresponding indication
Y, Y1, Y2, Y3... Y coordinate of the point with the corresponding indication
Z, Z1, Z2, Z3... Z coordinate of the point with the corresponding indication
Distance X
2
(X – X )
1 2

Distance Y 2
( Y1 – Y 2 )

Distance Z
2
(Z – Z )
1 2

Indication 1 always marks the first point set in a measurement, 2 the second,
and so on.
Link with Measure You can either show or hide the measurement values in the 3D image. To
Sheet do so, click the Measure button and select the Link with Measure Sheet
command from the menu. The check in front of the command shows wheth-
er or not the measurement values are displayed.
You can also use the Link with Measure Sheet command to load measure-

29
ment values from an already existing results sheet and once again display
it in the 3D image.
The measurement value from the active sheet are always displayed. If nu-
merous measurement sheets have been loaded, first activate the sheet and
then select the Link with Measure Sheet command.

Settings for 3D Display

Terms
Opacity The opacity stands for the "Non-transparency" of the voxels. Intensities with
opacity 0 are transparent and are not displayed in the projection. Intensities
with opacity 1 are considered as not transparent.
 SliceViewer and VoxelViewer • Settings for 3D Display

Raycasting The Raycasting procedure consists of scanning the area row by row with vi-
sual rays. The opacity is determined at the intersection point of the ray with
the object's surface.
Method The VoxelViewer Settings dialog box is opened after accessing the Settings
button bar command. It contains the Filter, Display, Isosurface and Blending
tabs. Click the different tabs to alter the settings in VoxelViewer. The set-
tings regarding how voxels are represented in the VoxelViewer are deter-
mined in the Filter and Display tabs. The 2 last tabs are reserved for
administering the Isosurface Projection and Blending Projection.
Visual rays are shot into the 3D image in equidistant intervals. The volume
is scanned along the visual ray in regular intervals. At these points, the data
is interpolated in small volume units.
Gradients are calculated at each interval point using differentiation filters.
The opacity is accounted for. The probability that there is a surface located
on this point is deduced from the local gradient vectors. (The orientation of
a possible surface in the corresponding cube is determined as well). For ex-
ample: A larger gray value difference between neighboring scanning points
indicates the transition from a transparent to a non-transparent medium.
Consequently, a surface in the corresponding cube is plotted.
The algorithm then uses a local illuminating model to calculate the light
falling on the object. It is assumed that all of the voxels are illuminated from
a light source of equal intensity. This method enables the calculation for
each voxel of the intensity of the light reflected to the viewer.
This procedure provides in a high level of image quality. It does, however,
require a lot of computing.

The VoxelViewer Settings dialog box

To open the VoxelViewer Settings dialog box, click the Settings button locat-
ed in the VoxelViewer button bar. The dialog box contains the Filter, Display,
Isosurface and Blending tabs. The features for displaying the voxels are de-
termined in the Filter and Display tabs. The 2 last tabs are reserved for ad-
ministering the Isosurface Projection and Blending Projection tabs.
You can use all of the other VoxelViewer functions while the VoxelViewer
Settings dialog box is open.
• The rotate and zoom functions remain active. This enables you to ob-
30

serve the object from different views and/or in different sizes.

• You can change the projection and measure the object.
• The context menu is also available. Therefore, you can, for example,
export an image of the 3D model any time.
Click the icon with the cross in the upper right to close the VoxelViewer Set-
tings dialog box.
Reset button Click the Reset button to revert to the source image in the VoxelViewer win-
dow (i.e., to deactivate set parameters).
Apply button Click the Apply button to calculate the active projection using the current set-
tings. The projection is calculated and displayed in the VoxelViewer window.
 The filter tab

The filter tab

In the Filter tab, define a filter routine to reduce the volume, data smoothing,
and edge enhancement.
Voxel Binning Voxel binning is a procedure by which voxels are combined.
The Filter tab enables you to
determine the settings for
data processing (e.g., bin-
ning).

Volume reduction
Voxel Binning When using Voxel Binning, voxels are combined to increase the reading
speed and to improve the signal-to-noise ratio.
Maximum size Select the Maximum size option so that the data size, when necessary, can
automatically be adapted to the set size. When this size has been reached

31
the option remains without effect.
Step width Select the Step width option to interactively define the size of the filter matrix
using the X, Y, and Z fields. If you select a very large size, the filter has an
affect on voluminous structures.
Fields X, Y, and Z In the X, Y, and Z fields, enter the size of the voxels to be combined in all 3
directions for the Step width option.
 SliceViewer and VoxelViewer • Settings for 3D Display

Smooth data
Gaussian blur When smoothing images, the noise is eliminated from the image. Use the
Smooth data group together with the Volume reduction group. As a result,
the contrast is attenuated.
Radius Enter the size of the Gaussian blur in voxels into the Radius field.

The illustration shows an example of an Isosurface Projection and how the various smoothings effect the same 3D
image. The smoothing of the data is available in all five projection methods.

Edge enhancement
The object edges are enhanced to increase image sharpness whereby the
gradient magnitude filter removes noise and disturbing effects.
Gradient magnitude Select the Gradient magnitude filter check box to highlight edges and bor-
filter ders in images, for example, with many clear transitions. In doing so, the
original data is calculated anew.
As with all the functions of this tab, this check box is available for all projec-
tion methods. In the Blending tab you will find the Edge enhancement check
box which exclusively effects the Blending projection.
32
 The Display tab

The Display tab

The Display tab enables you
to alter the display in Voxel-
Viewer.

Colors group
If you like, you can alter the background color by selecting an arbitrary color
from the Background palette.
In the Colors group click on the button with the arrow to open a list with all
the available colors. Click there the color for the VoxelViewer window back-
ground.

Accuracy group

33
Step width In the Step width field, you determine the distance between the points to be
displayed. The step width which is best for your image depends on the im-
age. You should reduce the step width if your image contains many details.
Should your image contain homogenous regions, however, it is better to in-
crease the step width.
Sampling rate The Sampling rate field is where you can determine the distance (along the
visual ray) at which the volume data is to be scanned. The smaller the dis-
tance the more accurate the display of the object. A larger distance reduces
the processing amount required of your computer.
 SliceViewer and VoxelViewer • Settings for 3D Display

The illustration shows the

visual rays which go out
from the viewer and are shot
into the 3D image. The sam-
pling rate is the distance be-
tween the voxels on which
the data are scanned by the
algorithm.

The Isosurface tab

On the Isosurface tab, you define the settings of the Isosurface Projection.
Isosurface Projection When working with the Isosurface Projection, only those voxels are dis-
played which have an intensity of - depending on the background - respec-
tively less than or equal to or more than or equal to the fixed isovalue.
Background The background is the space which surrounds the 3D image. The back-
ground is especially important for the Isosurface Projection. If the back-
ground is bright, larger intensity values will be looked for; if the background
is dark, smaller intensity values will be looked for.
The Isosurface tab enables
you to prepare the Isosur-
face Projection.
34
 The Isosurface tab

The illustration shows an ex-

ample 3D image with vari-
ous isovalues. The outer
cube has the highest inten-
sity. In this image, the back-
ground has been set to
"Bright". Voxels with an in-
tensity less than or equal to
the isovalue are searched
for. The isovalue has been
set to the following intensi-
ties: 0 (upper left), 166 (up-
per right), 180 (lower left)
and 247 (lower right).

Working with the Isosurface tab

From the schematic 3D image example you only want to display spheres.
Note about fast Select the Automatic redraw check box on this tab, so that the projection is
graphic cards automatically recalculated after each new setting, instead of clicking the Ap-
ply button - resulting in the continual update of the display in the VoxelView-
er window.
How to... Defining the background
1) Select the entry entitled Bright from the Background picklist, so that the
values greater than or equal to the Isovalue are ignored and the rest
are taken into consideration.

35
 The Isosurface Projection is automatically recalculated and shown
in the VoxelViewer window.
Set the isovalue
2) Make sure that the histogram located in the dialog box is spread on the
entire intensity area. This can be done by entering the value 0 into the
Threshold low field and the value 255 (respectively, the highest possi-
ble value) into the Threshold high field.
3) Set the intensity value for the Isosurface Projection in the Isovalue field.
Enter a plausible value into the Isovalue field.
4) Confirm your entry by depressing the [Enter] key.
 The position of the green line is updated in the histogram.
 The Isosurface Projection button is automatically activated in the
VoxelViewer button bar.
 SliceViewer and VoxelViewer • Settings for 3D Display

 The Isosurface Projection is automatically recalculated and shown

in the VoxelViewer window.
5) Check to see whether the VoxelViewer has detected and displayed the
desired shell (layer of your 3D image).
If you are not satisfied, try an other Isovalue. (For fine adjustments, you
can additionally use the arrow to the right of the Isovalue field.)
• Alternatively, you can also move the green vertical with the mouse in
the histogram. This line illustrates the current threshold of the isovalue.
6) To do so, move the pointer onto the green line in the histogram.
 The intensity value from the active mouse position is shown in the
upper right corner.
 As soon as the pointer approaches the green line, it turns into a
double arrowhead.
7) Hold down the left mouse button and pull the line to the desired value.
 The intensity value is updated in the Isovalue field.
 The Isosurface Projection button is automatically activated in the
VoxelViewer button bar.
 The Isosurface Projection is automatically recalculated and shown
in the VoxelViewer window.
36

Using these settings (Isovalue = 163), you only see the sphere.
 The Isosurface tab

8) Repeat the last steps until only the desired surface (shell) is displayed
in the VoxelViewer window.
Define the color of the Isosurface Projection
9) Select a light, clear green color from the Isocolor list.
 The selected color of the Isosurface Projection is automatically
adopted and shown in the VoxelViewer window.

Description of the Isosurface tab

Isovalue The Isovalue field gives you the opportunity to set the intensity value of the
voxels which are to be displayed by future projections. When working with
the Isosurface Projection method, only the voxels with this intensity value or
smaller values are displayed in the VoxelViewer window, if the entry Bright
has been selected from the Background list. Only the voxels with this inten-
sity value or greater are displayed, if the entry Dark has been selected.
The isovalue can also be interactively set in the histogram by moving the
threshold line. Move the pointer onto the threshold line. The mouse pointer
will change into a double arrowhead. Hold down the left mouse button and
pull the threshold to the desired value.
Histogram, Threshold The diagram of the dialog box shows the intensity distribution. Here, the
low and Threshold high amount of the voxels against the gray values is plotted. Peaks indicate gray
values which occur frequently. Using the slide control to the left of the histo-
gram, you can alter the histogram's Y scale. The X scale is defined by the
Threshold low and Threshold high fields.
Background Select from the 3 entries:
• Dark: The voxels with the intensity value smaller than or equal to the
isovalue are searched for if the background has been set to Dark.
• Bright: The voxels with the intensity value greater than or equal to the
isovalue are searched for if the background has been set to Bright.
• Unknown: The program automatically determines whether or not the
background is to be interpreted as dark or bright.
Isocolor The Isocolor field enables you to select the color in which the 3D image is to
be displayed. Click the arrow to open a list with all the available colors. From
the list, select the desired color.
Automatic redraw Select the Automatic redraw check box, so that you do not have to click the

37
Apply button after making changes in the Isosurface tab.
Note This use of this function is especially recommended with quick graphics
cards.

Transparent Select the Transparent check box to make the 3D image transparent. The
opacity curve is shown. By default, the opacity curve lies horizontally in the
middle of the histogram (Opacity=50% for all intensity values).
The opacity curve should be newly defined so that it fits your object. This en-
ables you to make certain intensity areas transparent and allows you to look
into the object.
You redefine the opacity curve by altering its slope or modifying its course.
Modifying the opacity In the histogram, place the pointer on one of the curve's end point. (In the
curve histogram, the pointer changes into a double arrowhead.) The end points
are marked by a blue square. To move these end points up or down, click
the left mouse button and keep it depressed while moving the mouse.
 SliceViewer and VoxelViewer • Settings for 3D Display

You can alter the course of the opacity curve however you like: For this pur-
pose, add and move base points. When moving the points, the curve is au-
tomatically adapted in such a way, so that the curve always runs through the
set points. In the histogram, place the pointer onto the desired intensity
value (not necessarily on the curve) and click the left mouse button. The in-
tensity value of the position of the pointer can be seen at anytime in the right
corner of the tab. Modify the course of the opacity curve by moving the set
control points by keeping the mouse button depressed. To delete this point,
click on it while keeping the left mouse button and [Shift] key simultaneously
depressed. The point is removed and the curve is automatically adapted.

The Blending tab

The Blending tab is only relevant for the Blending Projection method.
Opacity The opacity marks the "Non-transparency" of the voxels. Intensities with
opacity 0 transparent and are not displayed in the projection. Intensities with
opacity 1 are considered as not transparent. The opacity curve enables you
to precisely fade out intensity areas.
Blending Projection The volume is crossed from front to back. The visual ray is traced. Color val-
ue and opacity from the 3D volume are read in certain distances and com-
bined.
The Blending tab is used for
allocating LUT and opacity
curves when working with
the Blending Projection.
38
 The Blending tab

Working with the Blending tab

Note: Select the Automatic redraw check box on this tab, so that the projection is
Automatic automatically recalculated after each new setting, instead of unnecessarily
redraw having to click the Apply button - which results in the corresponding
continual update of the display in the VoxelViewer window.
How to... Define the opacity for lower intensities
1) Set the opacity to 0% for lower intensities.
 To do so, use the mouse to pull the left control point of the opacity
curve to the bottom.
2) Add 2 control points to the opacity curve. To do so, click on 2 points of
your choice on the opacity curve.
Select a LUT
3) Click the Load Palette button.
 The Load Palette dialog box opens.
4) Select the Rainbow2.LUT palette and click the Open button.
 The selected palette is shown as a colored bar below the opacity
curve on the Blending tab located in the VoxelViewer Settings dia-
log box.
Define the slope of the opacity curve
5) From the 2 new control points in the blue area, pull the left one to the
bottom.
6) From the 2 new control points, pull the right one all the way to the top.
7) Pull the outer right control point located in the red area to the top.
 The opacity for lower intensities is equal to 0 and the intensity in
areas of interest quickly increases to 1.

39
 SliceViewer and VoxelViewer • Settings for 3D Display

Perform the projection

8) Click the Apply button to perform the Blending Projection using these
settings.
 The projection is recalculated and the results are shown in the Vox-
40

elViewer window.
Additional alterations to the opacity curve
9) Additional alterations to the opacity curve can be done until you are sat-
isfied with the display. Interactively alter the opacity curve by moving
the existing control points and/or adding new ones.
10) Click the Apply button again to appraise the Blending Projection in the
VoxelViewer window.

Description of the Blending tab

Histogram, Threshold The diagram of the dialog box shows the intensity distribution. Here, the
low and Threshold high amount of voxels against the gray values is plotted. Peaks indicate gray val-
ues which occur frequently. Using the slide control to the left of the histo-
gram, you can alter the histogram's Y scale. The X scale is defined by the
Threshold low and Threshold high fields.
 The Blending tab

The opacity curve is shown as a red curve. You can alter its course however
you like.
Load Palette Click the Load Palette button to load a new LUT. By clicking the Preview but-
ton, the selected palette can be displayed or hidden in the Load Palette di-
alog box.
To the right of the Load Palette button located in the Blending tab, you will
see the colored bar of the current LUT.
File... Click the File... button in order to save or load the opacity curves. The file
saves the opacity curve including the corresponding LUT. Save the opacity
curves if you want to use the same one on numerous 2D image stacks.
This is how you define opacity curves which you can use on other 2D
image stacks
1) Load an image stack and display it in the VoxelViewer.

2) Click the Settings button in VoxelViewer.

 The VoxelViewer Settings dialog box opens.
3) Activate the Blending tab.
4) Load the desired LUT by selecting it in the Load Palette dialog box.
To access the Load Palette dialog box, click the Load Palette button to
the left of the colored bar.
5) Interactively define the opacity curve in the histogram.
Saving an opacity curve 6) Click the File... button.
7) Enter the name of the opacity curve in the File field located in the Save/
Load opacity curve & LUT dialog box.
8) Click the Save button.
9) Close the VoxelViewer Settings dialog box.
Using a defined opacity 10) Load an additional image stack on which you would like to use the
curve opacity curve.
11) Load an opacity curve.
12) Click the Apply button located in the VoxelViewer Settings dialog box.
 The Blending Projection is recalculated and shown in the Voxel-
Viewer window.
Note You can change each LUT however you like. To do so, use the Oper > Edit

41
LUT... command.

Editing colors You can also alter the palette being used directly in the Blending tab. To do
so, click on the color bar. The Select Color of Space dialog box opens. Se-
lect the desired color. Close the Select Color of Space dialog box by clicking
OK to adopt the selected color in the LUT being used.
Edge enhancement Select the Enhance edges check box to increase the sharpness of the edg-
es in the Blending Projection so that structures appear clearer. The original
data, however, remains.
 SliceViewer and VoxelViewer • Settings for 3D Display
42

Effects of the Enhance edges check box on an example

Select the Automatic redraw check box, so that you do not have to click the
Apply button after making changes in the Blending tab.
Note This use of this function is especially recommended with quick graphics
cards.
 Context menu in VoxelViewer

Context menu in VoxelViewer

In the VoxelViewer window,
click the right mouse button
to open a context menu.

Copy
Use the Copy command to copy the active view of the VoxelViewer window
to the Windows clipboard.
Via the clipboard, you can export this view to another application program
such as MS-Word.
You can also insert the contents of the clipboard into a vacant image buffer
of your image analysis program. This way, you get a uniformly appearing
RGB image which you can save.

Create Animation...
Use the Create Animation... command to define an automatic rotation of the
object. The command opens the Create Animation dialog box, by which you
define the rotation and its output format.

Create Image From View

Use the Create Image From View... command to create an identical RGB
image from the current view in the VoxelViewer window.
Creating an image from the VoxelViewer window.
1) Determine the destination image buffer.
2) Click the right mouse button in the VoxelViewer window.
 The context menu opens.
3) Use the Create Image From View... command.
 The Create Image From View dialog box opens.
43
4) In the Image size group, enter the image size of the image to be creat-
ed in pixels.
Select the Ratio Viewer entry so that the 3D view is reduced or en-
larged based on the preset width and that the X/Y ratio of the 3D view
is retained.
5) You set the image format in the Appearance group.
Select the 3D-View in RGB entry to create a color image from the view
shown in the VoxelViewer window.
6) In the group Output Location you determine whether the created image
is to be copied into the image buffer, clipboard, or as a file.
Select the Image Buffer entry so that the image is saved into the desti-
nation image buffer.

Related topics
The Create Animation dialog box 44
 SliceViewer and VoxelViewer • The Create Animation dialog box

7) Click the Create button.

 A new color image is created from the current view of the Voxel-
Viewer window. The resulting image is written to the destination im-
age buffer.
The Create Image From View dialog box remains open to allow you to create
additional images from the same object, whereby you can vary the settings
or, for example, apply another projection method.

Animate mouse
Use the Animate mouse command to alter the mouse's behavior when ro-
tating and zooming.
The command behaves like in SliceViewer (siehe Animate mouse auf Seite
17).

Set Home Position

Use the Set Home Position context menu command to freeze a scene in the
VoxelViewer window. This scene will be called the "home position". The size
and position of the 3D image in the VoxelViewer window make up the "home
position".
Use the Set Home Position command to "put aside" an interesting scene.
You can then continue working in the VoxelViewer window and, when nec-
essary, quickly return to the interesting scene with the Set Home Position
(siehe Move To Home Position auf Seite 28)command.

The Create Animation dialog box

Available The Create Animation dialog box opens when the Create Animation... com-
mand is accessed. The command is located in the VoxelViewer button bar
and in the context menu.
Animation An animation is a small film which shows a certain rotation of the object. The
animation consists of numerous acquisitions. Each acquisition shows the
object in a different position in the VoxelViewer window.
An animation is automatically generated and saved as a file (e.g., AVI for-
mat) as soon as you click on the Create... button located in the Create Ani-
44

mation dialog box.

You can then play these files with tools used for playing videos (e.g., Win-
dows Media Player). Because it is a file, the animation is always accessible,
without having to redo the laborious reconstruction of the scene in Voxel-
Viewer. Use an animation to create professional-looking presentations.
You can define the amount of acquisitions, i.e., the distance between 2 con-
secutive acquisitions. The amount of processing required by your computer
increases considerably with the amount of acquisitions.
 The Create Animation dialog box

Working with the Create Animation dialog box

Example The Isosurface Projection delivers an object which already has a three-
dimensional appearance. You would like to view the object from all direc-
tions. You can, for example, let it rotate on its X axis.
1) Click the Isosurface Projection button located in the button bar of the
VoxelViewer window.
 Voxels with an intensity equal to the Isovalue are used for display-
ing the object.
2) Click the Settings button to open the VoxelViewer Settings dialog box.
3) You determine the Isovalue in the Isosurface tab.

Defining an animation
4) Click the Create Animation button.
 The Create Animation dialog box opens. The Rotation tab is dis-
played.
5) In the Mode group, select the Full Rotation entry from the list and select
the Open file check box.
6) In the Angle group, enter the value 5 degrees into the Increment field.
 Successive acquisitions will be made in 5° intervals.
7) In the Axis group select the Object Z-axis entry from the Rotation axis
list.
 The object rotates on its Z axis, regardless of its position in Voxel-
Viewer.
8) Go to the Output tab.
9) In the Size group select the Ratio of Viewer entry.
 The 3D view is reduced (respectively increased) to the size of the
set width, keeping its X/Y ratio unchanged.
10) Select the 3D-View in RGB entry from the Appearance group.
11) The animation will consist of color images.

Creating the animation

12) Return to the Rotation tab.

45
13) Click the Create... button.
 The Save as dialog box, which is used for saving files, opens.
14) In the Save as dialog box, give the animation a name and select the
AVI-Video-File (AVI) format.
 The animation is saved in this format.
15) Select the Keep color format entry from the Color Space list.
16) Click the Save button located in the Save as dialog box.
 The file is saved. The status bar of your image analysis program in-
forms you about the progress of this procedure.
 The animation is played in the image window of your image analy-
sis program. The rotation involves 360°. The individual images are
shown successively.
 Microsoft Windows Player then starts the AVI animation automati-
cally.
 SliceViewer and VoxelViewer • The Create Animation dialog box

 Microsoft Windows Player enables you to visually issue the anima-

tion as often as you like.

Description of the Create Animation dialog box

The Create Animation dia-
log box contains 2 tabs: Ro-
tation and Output.

Rotation tab
Mode The Mode group enables you to determine whether or not you want to carry
out a centric rotation or a complete rotation.
Select the Centric Rotation entry so that a three-dimensional appearance is
achieved for any projection of the active intensity distribution (e.g., maxi-
mum intensity in the case of the Maximum Intensity Projection).
Select the Rewind check box so that the object, after the completed rotation,
returns to the original position.
Select the Full Rotation entry so that a three-dimensional object is rotated
360° during the Isosurface Projection and Blending Projection.
Select the Open file so that the program used for playing automatically starts
46

after the animation has been created and saved.

 The Create Animation dialog box

The file format determines which application program is to be used and/or

automatically started for playing the animation.
Format
(animation) Open file Open File
check box not selected check box selected
AVI You manually open the anima- Microsoft Windows Player
tion from Windows Explorer starts and automatically plays
with Microsoft Windows the animation.
Player.
Multiple TIFF- You load the image stack into The animation is played in the
File your image analysis program. VoxelViewer window. A new
Show the Image Stack button image stack is created from
bar and click the Animate the animation and is written to
Stack button. the destination image buffer.
The images of the image stack
are the successive images of
the animation.
Animated GIF You manually open the anima- The animation is played in the
tion from Windows Explorer VoxelViewer window. After-
with Windows Picture and Fax wards, Microsoft Photo Editor
Viewer. The animation is is automatically started and
played. the first image of the animation
is shown.

Angle Increment As far as centric rotation is concerned, enter the angle range where the im-
ages are distributed into the Angle field. Enter the angle between the indi-
vidual images in degrees into the Increment field.
For a complete rotation, enter the angle between the various images of the
360° rotation into the Increment field. For example, if you enter the value 5
into the Increment field, an animation consisting of 72 acquisitions is the re-
sult.
The smaller the increment, the more images which describe the rotation.
Axis In the Axis group, determine the axis for the rotation.
Select between the entries Horizontal, Vertical, Arbitrary, or Object Z-axis.
Select Horizontal entry if the object is to rotate around a fictive horizontal
which would lie in the middle of the monitor.
Select Vertical entry if the object is to rotate around a fictive vertical which
would lie in the middle of the monitor.

47
Select Arbitrary entry if the object is to rotate on an axis. Define the angle of
the axis with respect to the horizontal in the Orientation field.
Select the Object Z-axis entry if the object is to rotate on its Z axis (Z axis of
the image stack).
 SliceViewer and VoxelViewer • Create Image Stack

Output tab
You enter the desired size
and image format of the out-
put image stack in the Out-
put tab located in the Create
Animation dialog box.

Size Enter the size (in pixels) of the acquired images which are to make up the
new image stack in the Size group.
View Determine the image type of the individual images in the View group.
• 3D-View in RGB: A color image is generated from the view in Voxel-
Viewer.
• Red-Green stereo: A stereo image pair is created from the view. The
human brain calculates spacial information from the different images
which are created on the retinas of both eyes, thus enabling you to see
spatially. The differences between the images on the right and left ret-
inas are a result of the variation of perspective of both eyes.
Button Click the Reset button to reset the entries in the Output tab to the default val-
ues.

Create Image Stack

48

Depending on the expansion version and configuration, your image analysis

program possess several routines to automatically create image stacks,
e.g., the ride module. The following section will describe how you can create
image stacks from already existing images.
Creating an image stack.
1) Click in the image window's button bar using the right mouse button.
 A list with all the available button bars appears.
2) Select the Image Stack button bar from the list and drag the button bar
to an appropriate position, e.g., below the Standard button bar.
The Image Stack button bar

3) Load images of the same type which are to make up the image stack.
 Preparing the Images

4) Select them in the image buffer box.

5) Click the Make Stack button located in the Image Stack button bar.

 A new image stack is created and written to the destination image

buffer. It is given the name of the first image with the file name ex-
tension [1].

Preparing the Images

The following steps might be necessary before working with the SliceViewer
and VoxelViewer, e.g., when working with images which were not acquired
with your image analysis program.

Reducing Data
To reduce the data, you can use the Oper > 3D-Images > Resize... and/or
Oper > Image geometry > Crop commands.
Note The reduction of data is not compulsory, but is recommended when dealing
with large amounts of data (i.e., high-resolution images) in order to reduce
the computing time and storage capacity.
Adapting the image stack size.
Select a representative 1) Show the Image Stack button bar.
image To do so, rightclick the image window's button bar and select the Image
Stack entry.
2) Click the Play button from the Image Stack button bar.
 The Animate Image Stack button bar opens.
The Animate Image Stack
button bar.

 The animation automatically starts, whereby all of the images of the

49
image stack are shown successively in the image window.
 The progress bar of the Animate Image Stack button bar shows the
progress of this procedure.
3) Discontinue the animation with the Stop button located in the Animate
Image Stack button bar as soon as an appropriate image is shown. An
appropriate image shows the object in its maximum dimensions and
will be used representatively for the entire image stack.
 The animation is stopped.
 The Animate Image Stack button bar is closed.
Adapt image size 4) Activate the 3D-Images button bar, if it has not already been activated.
5) Click the Resize button located in the 3D-Images button bar to alter the
image size of the entire image stack. Alternatively, you can also select
the Oper > 3D-Images > Resize... command.
 The Resize dialog box will be opened.
 SliceViewer and VoxelViewer • Preparing the Images

6) Select the Zoom axes homogeneously entry from the Ratio list.
 This setting enables you to zoom the images of the image stack in
X, Y, and Z direction evenly, i.e., the image stacks ratio remains un-
changed.
7) Enter the value 0.5 into the Factor field located in the X column and
confirm with Enter.
 The value in the Factor field located in columns Y and Z changes to
0.5.
 The values in the Size field located in columns X, Y and Z reduce
themselves by half.
8) Click the Execute button to execute the set alterations.
 Your image analysis program creates a new, smaller image stack
with the extension [1] in the destination image buffer.
In the Resize dialog box you
can zoom the active image
stack in all 3 directions. Via
a sensible factor selection
and with the Zoom axes ho-
mogeneously settings you
can considerably reduce the
required calculation time
and storage capacity with no
alteration on the stack ratio.

9) Use the Oper > Image geometry > Crop command.

10) Adjust the frame so that the low-data image sections are ignored and
the interesting areas are enclosed. You might have to move the frame
in order to properly position it. Use the mouse to do so.
11) Confirm the frame by clicking the right mouse button.
 A new image stack with the extension [2] is created in the destina-
tion image buffer. It only contains the areas from each image of the
stack which is located within the frame.

Image Calibration
Before working with the SliceViewer and VoxelViewer, you must make sure
50

that the image stack has been calibrated with the same units for X, Y, and Z.
1) Use the Image > Calibrate Image... command.
 The Calibrate Image dialog box opens.
2) Select the Z Calibration tab. In the Calibration of the Z-range group you
determine the Z-Offset (the position of the first image of the stack rela-
tive to plane Z=0) and the Z-Spacing (the distance between 2
consecutive stack images). The Z-Spacing should not have the value
0.
3) Click the Unit... button to set the unit of the Z axis.
 The Set Unit dialog box will be opened.
Here you can select a unit of measurement for the commonly used
physical quantities.
 SliceViewer and VoxelViewer expects a length calibration.
 Preparing the Images

4) Enter a unit of measurement (e.g., mm) for the Z axis, by selecting the
base unit (e.g., m for meter) and the scale (e.g., m for milli) from 2 lists.
 After clicking OK, you return to the Z Calibration tab.
 The specified unit is shown in the Z-Offset and Z-Spacing fields lo-
cated in the Calibration of the Z-range group.
5) Click the OK button to finish the Z calibration.
Warning You must select the same unit for X, Y and Z calibration. For example, select
the unit mm, if the unit shown in the XY Calibration tab is mm / P.

Requirements Please note that a sensible display in SliceViewer and VoxelViewer is only
then possible if the Z-Spacing and the X and Y scaling have the same pro-
portions.
You must select the same
unit for X, Y, and Z, in order
to guarantee a sensible dis-
play of the image stack in
SliceViewer and VoxelView-
er. The illustration shows
the Z-Offset (the distance
between the Z=0 plane and
the first image of the image
stack) and the Z-Spacing
(the distance between 2
consecutive images).

Please note If you have saved the image stack in TIF format, the calibration data is ad-
ministered as part of the image stack and is saved with it.

Use the Images > Calibrate

Image > Z Calibration tab to
define the Z-Offset (i.e., Z
origin) and the Z-Spacing
(distance between planes).
When clicking the Unit...

51
button, the Set Unit dialog
box appears, where you de-
termine a unit for the Z axis.
 SliceViewer and VoxelViewer • Preparing the Images

Smooth Image
A smoothing routine can be used to erase strong intensity jumps. The filtra-
tion proceeds three-dimensionally.
1) Click the Smooth button located in the 3D-Images button bar. Alterna-
tively, you can also select the Oper > 3D-Images > Smooth... com-
mand.
 The Smooth 3D-Image dialog box will be opened.
2) Enter the value 2 into the Radius field and confirm by clicking the Exe-
cute button.
 The Smooth 3D-Image dialog box will be closed.
 A new image stack is created in the destination image buffer.
The Radius value in the
Smooth 3D-Image dialog
box is the mean width of the
Gaussian distribution used
for smoothing.
52
 Index

Symbols Context menu

VoxelViewer 41
(XY) plane (SliceViewer) 9 Convert
(XZ) plane and (YZ) plane (SliceViewer) 9 View as an image (SliceViewer) 16
Coordinate Axes
Display 10, 24
Numerics Copy 41
Create
3D image (VoxelViewer) Animation (VoxelViewer) 26, 41, 42
Definition 18 Image From View 12, 41
Rotate 25 Image Stack 46
Zoom 25 Cross section 2, 9
3D representation
SliceViewer 10
VoxelViewer 25, 27 D
3D-View in RGB 12, 46
Display
Coordinate Axes 10, 24
A Distances (VoxelViewer)
Measure 26
Add-In Drag&Drop (SliceViewer) 17
Install 3
Start 5, 18
Animate F
Image Stack (button bar) 47
Mouse 15, 42 Fence view (SliceViewer) 4
Animated GIF-File 45 Fence view object (SliceViewer)
Animation Definition 6
Create (VoxelViewer) 26, 41, 42 Rotate 7
AVI-Video-File 45 Zoom 8
Format
Animation (VoxelViewer) 45
B Image Stack 2

Binning 29
Blending (VoxelViewer) 23 G
53
Blending Projection 23
Button bar GIF 45
3D-Images 4
Animate Image Stack 47
Image Stack 46 H
SliceViewer 8
Home position
VoxelViewer 20
Move to 11, 26
Set 16, 42
C
Calibrate I
Image Stack 48
Image
Central Perspective (VoxelViewer) 25
Calibrate 48
Clipboard (SliceViewer) 17
Copy 12, 41
Context Menu
From View 12, 41
SliceViewer 12
 Index

Image types 2 O
Smooth 50
Image Stack Opacity
Animate (button bar) 47 Definition 27
Button bar 46 Set 35, 37
Calibration 48 Output tab 12, 46
Create 46
Definition 2
Image Plane 2, 9 P
Reslice (SliceViewer) 14
Size 47 Parallel Perspective (VoxelViewer) 25
Installation Perspective (VoxelViewer) 25
Add-In 3 Plane (SliceViewer)
Intensity (VoxelViewer) Select/move 7
Projections 21, 22 Zoom 8
Isosurface (VoxelViewer) Polygon length (VoxelViewer)
Isosurface Projection 22 Measure 26
Positions (VoxelViewer)
Measure 26
L Projection (VoxelViewer) 21

Light
Switch on 10, 24 R
Link
Measurement sheet (VoxelViewer) 27 Raycasting (VoxelViewer) 28
Representation
3D representation 10
M Slice (SliceViewer) 9
Voxel (VoxelViewer) 18, 28
Maximum intensity projection (VoxelViewer) 21 Reslice
Mean Intensity, Projection (VoxelViewer) 22 Image Stack (SliceViewer) 14
Measure (VoxelViewer) 26 Rotate 7, 11, 25
Measurement sheet (VoxelViewer) 27 Rotation 7, 11, 25
Minimal intensity projection (VoxelViewer) 21 Rotation tab (VoxelViewer) 44
MIP, mIP (VoxelViewer) 21
Model
54

3D image (VoxelViewer) 18 S
Fence view object (SliceViewer) 6
Mouse Select
Animate 15, 42 Plane (SliceViewer) 7
Rotate With Mouse 7, 11, 25 Projection (VoxelViewer) 21
Zoom With Mouse 8, 11, 25 View (SliceViewer) 9
Move Set
Model 7, 25 Home position 16, 42
Plane (SliceViewer) 7 Settings
Move to VoxelViewer 27
Home position 11, 26 Size
Multiple TIFF-File 45 Adjust 47
Group Size, Animation (VoxelViewer) 46
Maximum size, option (VoxelViewer) 29
Slice (SliceViewer) 9
Definition 9
 Index

Select/move 7
Smooth 50
Stack
Reslice (SliceViewer) 14
Start
Add-In 5, 18
Switch
Viewing mode (SliceViewer) 9
Switch on
Central Perspective (VoxelViewer) 25
Light 10, 24

T
Three-dimensional representation
SliceViewer 10
VoxelViewer 18
TIFF 45
Tile View (SliceViewer) 9
Tilt 7, 11, 25

V
View
3D-View in RGB 12, 46
Convert view as an image (SliceViewer)
Copy (SliceViewer) 16
Copy 12, 41
Group View (VoxelViewer) 46
Image From View 12, 16, 41
Viewing mode (SliceViewer) 9
Voxel
Binning 29
Definition 18

55
X
X-Slice (SliceViewer) 9

Y
Y-Slice (SliceViewer) 9

Z
Zoom 8, 11, 25
Z-Slice (SliceViewer) 9