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Tomo3D View

The Tomo3D view combines a 3D viewer with up to three orthogonal 2D views. The Tomo3D is only available if you have loaded or acquired a z-stack.

1

Left Toolbar
Toolbar to manipulate the image display. For more information, see Left Toolbar (Tomo3D).

2

Image View
Area where you interact with the image views and set the cut lines with the mouse. You can display up to four different views, including a 3D and different 2D views. The number of image views can be set in the Ortho Display tab, the type can be set by the dropdown in the top left corner of each view. The individual views can be synchronized with the Synchronize View Area of 2D Panes checkbox in the Dimensions tab.

3

Snap button
Creates a 2D image of the currently displayed image views. All annotations are burned in automatically.

4

Bottom Toolbar
Toolbar to manipulate the image display, see Bottom Toolbar (Tomo3D).

5

View Options
Area for general and specific view options.

Left Toolbar (Tomo3D)

Parameter

Description

Top thumb wheel vertical control with stacked horizontal bars and small magnifier icon
Top thumb wheel

Zooms in or out of the image.

Dark blue square icon with white crosshair and four small filled circles at the crosshair ends
Rotate

Enables you to rotate the 3D image in any way you wish within the space.

Rotate icon: diagonal pointer cursor on dark square background
Zoom

Enables you to increase or reduce the zoom factor of the image area.

Move icon: white hand cursor on dark square background
Panning

Enables you to pan the 3D image.

Vertical gradient bar with horizontal segments and a small circular crosshair icon near the top
Bottom thumb wheel

Rotates the 3D image around the horizontal (X) axis.

Bottom Toolbar (Tomo3D)

Control element

Description

Segmented light gray horizontal control bar on dark blue background with small circular rotation icon at right
Left thumb wheel

Rotates the 3D volume around the vertical (Y) axis.

White house icon centered in a dark rounded square button
Home view

Switches back to the start view from any view.

A top view of the 3D volume is displayed. Lateral movements and the zoom factor are adjusted so that the 3D volume can be seen at the center of the image area.

White overlapping stacked-rectangles icon in a dark rounded square button
Show bounding box

Shows or hides a bounding box around the 3D volume.

Blue square with white plus sign and a small white vertical rectangle to its right
Draw cutlines

Activated: Displays the cutlines in the 3D viewer.
Deactivated: The cutlines are not displayed in the 3D viewer.

Horizontal rounded gray bar with vertical gradient stripes on dark background and a small white line icon at top-left
Right thumb wheel

Rotates the 3D volume around the (Z) axis perpendicular to the screen plane.

Ortho Display Tab (Tomo3D)

Parameter

Description

Cut Lines

Sets the positions (pixel values) for the section lines using the X/Y/Z sliders or input fields.
Alternatively you can also adjust the positions directly in the image area. To adjust the positions, move the mouse over a section line in the image. Hold down the left mouse button and move the mouse.

-

Mid

Positions the relevant slider at the center of the view.

Line Width

Only visible if the Show All mode is activated.
Enter the thickness of the section lines in pixels using the sliders or input fields. This results in a maximum intensity projection being displayed over the selected pixel width.
You can also adjust the width directly in the image area. To adjust the width, move the mouse over a section line in the image until a small arrow is displayed. Hold down the left mouse button and move the mouse.

Cut Line Opacity

Only visible if the Show All mode is activated.
Here you can enter the degree of opacity of the section lines from 0% (invisible) to 100% (completely opaque).

Views

Only visible if the Show All mode is activated.
Sets the number and allocation of views in the Image View.

-

Six blue view-layout icons: 4 views; 1 view; 2 vertical; 2 horizontal; 3 vertical; 3 horizontal

Displays four views.

-

Displays four views icon

Displays one view.

-

Displays one view icon

Displays two vertically separated views.

-

Displays two vertically separated views icon

Displays two horizontally separated views.

-

Displays two horizontally separated views icon

Displays three vertically separated views.

-

blue rounded square with three white horizontal bars and three small white squares

Displays three horizontally separated views.

3D Tab (Tomo3D)

Here you can specify which projection/rendering mode you want to use to display the 3D volume. There are three view modes available. To activate the desired view mode, click on the corresponding button.

Parameter

Description

Transparency

Activates the Transparency rendering mode where the structures in the image are rendered in a similar fashion as in the Volume mode. This render mode is particularly suitable for dense image data. The key difference is an applied edge enhancement filter to allow more focus on relevant structures within the data while simultaneously fading out homogenous and less important areas.

Volume

Activates the Volume mode where the structures in the image are rendered as three-dimensional objects and illuminated by means of a virtual light source. This allows a realistic and, in contrast to the maximum projection mode, a quantitative display of the volume.

Maximum

Activates the Maximum intensity projection mode where only the pixels with the highest intensity are displayed along the observation axis.

Create Image Tab (Tomo3D)

This tab enables you to create an image of the current view(s).

Parameter

Description

Resolution

Selects the resolution for the image. You have the following options:

  • Current Resolution
  • 720 x 576 (SD)
    (SD = Standard Definition)
  • 1024 x 768
  • 1920 x 1080 (HD)
    (HD = High Definition)
  • 4096 x 3072 (4K)

Create

Creates an image of the current view and opens it in ZEN.

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