ZEISS Knowledge Base

This module offers functionality to combine 3D and 2D visualization in one screen, enabling the user to render up to three 2D and one 3D view panes together in one new viewer (Tomo3D view). The 3D view features ray-casting-based volume rendering with transparency, volume and maximum intensity modes, flexible channel-wise adjustment of 3D view, background color and lighting. The position of the three orthogonal 2D view panes are synchronized with the 3D view, can be interactively positioned and are indicated by colored cut lines.

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.

Parameter	Description
Top thumb wheel	Zooms in or out of the image.
Rotate	Enables you to rotate the 3D image in any way you wish within the space.
Zoom	Enables you to increase or reduce the zoom factor of the image area.
Panning	Enables you to pan the 3D image.
Bottom thumb wheel	Rotates the 3D image around the horizontal (X) axis.

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.
-		Displays four views.
-		Displays one view.
-		Displays two vertically separated views.
-		Displays two horizontally separated views.
-		Displays three vertically separated views.
-		Displays three horizontally separated views.

Appearance Tab (Tomo3D)

Here you can define the appearance of the 3D volume. On the tabs available on this tab, select the setting that you want to change (e.g. Transparency).

Transparency Tab (Tomo3D)

Parameter	Description
Channel selection	Here you can select the channel of a multichannel image for which you want to set the transparency.
Threshold	Sets the lower threshold value in percent of the gray levels displayed. With this setting you specify the gray value range for the relevant channel that you want to be included in the rendered image.
Ramp	Sets the extent of the transition from completely transparent to completely opaque (0-100 percent).
Maximum	Sets the level of opacity (0-100 percent).
Histogram	Displays the settings that you enter using the sliders schematically. The x axis represents the gray level values and the y axis the opacity. You can also change the position of the curve using the mouse.
Reset	Resets all parameters to the original values.
Opacity 2D	Sets the opacity of the selected volume in the 2D views.

Background Tab

Parameter	Description
Background Color	Sets the background color for the 3D view. To do this, click on the color field and select the desired color.
Reset	Resets the background color.

Light Tab (Tomo3D)

Parameter	Description
Brightness	Sets the brightness of the light source.
Reset	Resets the brightness.

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.

Carl-Zeiss-Strasse 22

73447 Oberkochen

Germany

3Dxl Plus

Tomo3D View

Ortho Display Tab (Tomo3D)

Appearance Tab (Tomo3D)

Transparency Tab (Tomo3D)

Background Tab

Light Tab (Tomo3D)

3D Tab (Tomo3D)

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3Dxl Plus

Tomo3D View

Left Toolbar (Tomo3D)

Ortho Display Tab (Tomo3D)

Appearance Tab (Tomo3D)

Transparency Tab (Tomo3D)

Background Tab

Light Tab (Tomo3D)

3D Tab (Tomo3D)

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