User Interface 3D View
The 3D workbench opens the 3D view, which can be combined with up to three orthogonal 2D views. The viewer is only available if you have loaded or acquired a z-stack.
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1 |
Toolbar |
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2 |
Image Views |
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3 |
View Options |
See also
3D Toolbar
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Parameter |
Description |
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Selects the number and layout of views. |
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Toggles the visibility of the bounding box, coordinate axis and scale bar around the volume in the view. With the arrow on the right, you can toggle the elements individually. |
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Bounding Box |
Activated: Displays the bounding box around the volume. |
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Coordinate Axis |
Activated: Displays the coordinate axis in the image view. |
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Coordinate Axis Scale |
Activated: Displays the scale bar for coordinate axis in the image view. |
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Automatically sets a zoom factor where the entire image is displayed to fill the view. |
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Displays the volume from the left. |
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Displays the image from the top. |
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Displays the image from the front. |
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Resets the view to the default. |
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Activates the interaction mode that enables you to move the slices with the mouse. |
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Activates the panning mode to fixate and move the volume in the view. |
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Activates the rotation mode to rotate the 3D image in any way within the image view. This is the default mode when you enter the 3D view. |
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Activated: Enables the spin mode which allows you to set the 3D volume in continuous motion. |
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Creates a 2D image of the current view and copies it to the clipboard. |
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3D Rendering Tab
On this tab you can specify which projection/rendering mode you want to use to display the 3D volume. There are 5 view modes available. Additionally, you have transparency settings for your displayed volume.
Rendering
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Parameter |
Description |
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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. |
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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. |
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Maximum |
Activates the Maximum intensity projection mode where only the pixels with the highest intensity are displayed along the observation axis. |
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Surface |
Activates the Surface mode where the program calculates solid surfaces ("isosurfaces") from the gray values, which emphasizes particularly flat structures (e.g. cell walls of plant cells). |
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Mixed |
Activates a mixed mode which is a combination of transparency rendering and surface reconstruction mode. This means that even highly complex spatial relationships can be displayed convincingly. |
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Precise/Fast |
Adjusts the level of detail of the 3D volume.
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Background Color |
Sets the background color for the 3D view by clicking on the color field and selecting the desired color. |
Transparency
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Parameter |
Description |
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Channels |
Selects the channel of a multichannel image for which you want to set the transparency. |
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Opacity Curve |
Changes the opacity of the volume by manipulating the opacity transfer function. Changing the lower point of the curve changes and updates the Threshold. Changing the upper point of the curve changes and updates the Maximum value. |
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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. |
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Maximum |
Sets the level of opacity (0-100 percent). |
Appearance Tab
Here you can define the appearance of the 3D volume. With the reset button 
on top of the sections of the tab, you can reset the parameters to their default values.
Light
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Parameter |
Description |
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Brightness |
Sets the brightness of the light source. |
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Enable Tone Mapping |
Activated: Enables tone mapping during the rendering of the image data. Tone mapping refers to the compression of the dynamic range of high contrast images (HDR). The contrast range is reduced in order to display digital HDR images on output devices with a more limited dynamic range. In most cases, tone mapping increases brightness and contrast of the rendering result and makes colors more vibrant. |
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Enable Directional Light |
Activated: Enables full lighting for volumetric rendering. A directional light illuminates all structures in a scene with parallel light rays from a specific direction, similar to sun light. The light disregards the distance between the light itself and the structures, so the light does not diminish with distance. |
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Azimuth |
Only visible if Enable Directional Light is activated. |
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Elongation |
Only visible if Enable Directional Light is activated. |
Projection
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Parameter |
Description |
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View Angle |
Adjusts the view angle of the projection. |
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Scale Z |
Adjusts the scaling in z, i.e. the height of the displayed z stack. |
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Reverse Z-Axis |
Activated: Reverses the z axis for displaying the image. |
Slices Tab
On this tab you can toggle the display of slices though the volume in the 3D view and define settings for the individual slices in the 3D and 2D views.
3D Options
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Parameter |
Description |
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Slice Table |
Displays the different slices through the volume. The settings on the rest of the tab are always applied to the currently selected slice. The eye symbol in front of the entry toggles the visibility of the slice in the 3D view. |
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Clip Front |
Clips the front of the volume. |
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Clip Back |
Clips the back of the volume. |
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Appearance |
Changes the appearance of the currently selected slice. You can change the color by clicking in the color field and have several display options available in the dropdown. |
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Colored |
The graphical representation of the slice is displayed in color. |
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Textured Opaque |
Black pixels do not let any light through, meaning that the render data behind them are not displayed. |
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Transparent |
The data that are touched by the clipping plane are displayed as they are in Transparency render mode, but in two dimensions. The ramp for the transparency is linear here. Black pixels are transparent. |
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Binary |
The data above the threshold value that are touched by the clipping plane are displayed as a white area. Black pixels are non-transparent. |
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Invisible |
Sets the plane invisible. |
2D Options
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Parameter |
Description |
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Thickness |
Defines the thickness for the slice currently selected in the table. |
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Projection Mode |
Selects the projection mode for the 2D views. The data display also depends on the defined thickness of the respective slice. |
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Maximum Intensity |
Uses maximum intensity projection, i.e. only the pixels with the highest intensity are displayed. |
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Minimum Intensity |
Uses minimum intensity projection, i.e. only the pixels with the lowest intensity are displayed. |
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Average Intensity |
Uses an average intensity projection where the average intensity is displayed for each pixel. |
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Interpolation |
Selects the interpolation method, i.e. how the values of individual pixels on the screen are calculated based on the pixels of the image. This is particularly relevant/visible if there are more screen pixels than image pixels and therefore several pixels on the screen are calculated from the “same” image pixel. The data display also depends on the defined thickness of the respective slice. |
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Linear |
Uses a linear interpolation for the value of each screen pixel between individual image pixels. The zoomed image is smoothed and is useful for images that have rather natural/smooth transitions and no hard boundaries, e.g. light microscopy images. |
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Nearest Neighbor |
Each screen pixel is assigned exactly the value of the image pixel that is closest to the screen pixel. Even when zoomed in, this type of display only shows exactly what is present in the source image. There is no smoothing and no suggestion of smooth transitions that are not present in the source material. This type of display is ideal if you expect hard boundaries and transitions, e.g. in materials, chips or other components. |
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Line Opacity |
Sets the opacity of the lines in the 2D views. |
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Transform
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Parameter |
Description |
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Position |
Changes the position of the currently selected slice. Each slice is moved in its respective dimension (e.g. the XY slice is moved in x direction) and the views are updated accordingly. If you change the position of the slice directly in one of the 2D views, the values are updated here accordingly. |
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Yaw |
Rotates the currently selected slice around the vertical axis. The 2D view affected by the respective transformation updates accordingly. |
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Pitch |
Rotates the currently selected slice around the lateral axis. The 2D view affected by the respective transformation updates accordingly. |
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Roll |
Rotates the image around the longitudinal axis of the currently selected slice. The 2D view affected by the respective transformation updates accordingly. |