Volume Viewer

Run the View > Image > ND View > Volume View command to display the current Z-stack as a 3D model using perspective projection.

Introduction

There are the following rendering engines available in the software. If possible, select the Optimal renderer which is described primarily in the following sections. Display the 3D Settings window to select the renderer.

Optimal

The default and recommended engine optimized for displaying large datasets.

Standard

A full-featured engine suitable for graphic cards supporting DirectX 10 or newer.

Compatibility

An engine with limited capabilities, but supported by most graphic cards.

Basic Operations

(requires: Optimal )

Rotation
  1. Click and drag directly in the volume image to freely rotate it.

  2. Select a specific rotation mode in the side toolbar (Side Toolbar ).

  3. Open the rotation panel found in the context menu of the Rotate around custom axis mode to rotate to basic planes or rotate using a precise orientation or rotation axis.

Shift

Use the secondary mouse button to move the volume image within the screen.

Zoom

Turn the mouse wheel to zoom the model in/out.

Crop

The basic workflow is this:

  1. Click the Bounding box button.

  2. Press the Ctrl key, place the cursor over one side of the 3D model (it gets red) and move the cutting plane. To drag two planes at once, move the corner ball.

Tip

Use the Ctrl + Shift + mouse button to move parallel cropping planes at the same time.

For more information about cropping and slicing please see: Crop & Slice.

Volume info

Displays information about the calibration and volume dimensions at the bottom of the image window. It also displays the Zoom info and the navigation cube (or axes) to help you determine the current orientation of the volume.

  • Open the context menu over the icon to switch between the navigation cube/axis and to turn on/off the additional information. Switching between the cube and the axis can also be done via the context menu revealed directly over the cube/axis.

  • Click on an axis, a cube wall, or a cube corner to rotate the object so that it faces you.

  • Double-click to the volume view to reset it to the default position.

Bounding box

Displays/hides a box around the 3D image.

Show Grid

Shows or hides the graticule. Define visible graticule planes in the Grid & Scale section of the Volume Options panel.

Show Scale

Displays/hides a scale around the bounding box. To adjust the scale parameters, reveal the context menu over this icon. Details can be found here Displaying a Grid.

3D measurement

Measures distances inside the volume image. The View > Analysis Controls > Annotations and Measurements panel will open with the Length 3D tool selected. When measuring centroids, the start/end of the measuring line automatically snaps to the center of the closest centroid.

Note

To measure distances more precisely, switch to Slices View (View > Image > ND View > Slices View ), make the measurement in the particular Z-plane, and switch back to Volume View.

Blending Mode

Different rendering techniques can be used to display the Z sequence as a volume. Some combinations of the following techniques are available depending on which renderer is selected.

Alpha

Uses the physical principles of light absorbing so that only the surface voxels are visible.

Alpha & Shade

Alpha blending in combination with the Shaded Volume (see below).

MaxIP

Maximum Intensity Projection. Only voxels with the highest intensity in the observation direction are displayed.

MinIP

Minimum Intensity Projection. Only voxels with the lowest intensity in the observation direction are displayed.

Depth Coding

Turns on/off the volume color gradient. Use the drop-down menu next to the icon to choose a gradient, Show depth code legend or Reverse gradient.

Show smooth volume

Click on this button to show the volume smoothed or raw (non-interpolated).

Edge Enhancement

Turns the edge enhancement function on/off. This function reduces the opacity of the haze around the objects so that they are more contrasting and sharper. Open the context menu over the icon and move the slider of the selected channel to the right to increase the enhancement power.

Full-res

Low resolution is recommended for basic volume previewing. When precise static details are to be visualized, switch to high resolution (uses up to half of the available RAM). The most noticeable changes between these two modes are observed in large images (beyond the graphic card capabilities).

If the image is fully loaded into the memory of the graphics card, High resolution is turned on, the viewer shows the maximum quality and the button is automatically disabled. If the memory capabilities are exceeded, two more modes appear - Highest Possible Resolution (optimized for the highest resolution without downsampling; can be slower) and Balanced Resolution vs Speed (resolution can be lower; speed performance should be sufficient).

Create Image Cache for Time Loop

Use this button if your image sequence contains the time dimension and you would like to observe it. The visualization will be pre-loaded to memory and therefore smooth and fast enough.

Full screen

This option switches the volume viewer to full screen mode. You can abort this mode by pressing Esc.

Tip

When using two monitors, the Volume Options panel can be controlled from one monitor and the 3D volume can be in full screen on the other monitor.

Snapshot

Opens the Snapshot window where you can select the resolution and click OK to create a snapshot of the current volume scene in that resolution.

Show Movie Maker

This button runs the Movie Maker application. It enables the user to create AVI movies of the 3D model.

See Creating a Movie from Volume View.

Anaglyph

This button turns on/off the anaglyph 3D view. Press the arrow next to the button to display the menu with possible color combinations (depending on the type of your anaglyph glasses).

Open 3D settings

Opens the 3D Settings window used for choosing a volume renderer and other 3D parameters. For details please see 3D Settings.

Open volume options

Opens/closes the Volume Options panel.

Show volume view help

Displays the help page.

Basic Operations (Standard renderer)

(requires: Standard)

Rotation
  1. Select a rotation mode, e.g. Free Rotation, in the toolbar.

  2. Drag the volume by the primary mouse button and rotate it.

Rotation to a specific position

(requires: Standard), (requires: Optimal )

  1. Display the Volume Options (Standard renderer) panel.

  2. Expand the View angle pull-down menu.

  3. Define the position manually or click one of the predefined views.

Shifts

Use the secondary mouse button to move the model within the screen.

Zoom

Use the mouse wheel to zoom the model.

Crop

The basic workflow is this:

  1. Click the Show bounding box button.

  2. Press the Ctrl key, place the cursor over one side of the 3D model (it gets red) and move the cutting plane.

Tip

Use the Ctrl + Shift + secondary mouse button to move parallel cropping planes at the same time.

Tip

(requires: Optimal )

Use the Ctrl key + secondary mouse button to move the whole cropping box freely.

Tip

(requires: Compatibility)

Or, you can enter the cropping mode by selecting the tool. In this mode, you don't need to hold Ctrl for cropping.

See Cropping Tools .

Crop a single channel

Select the channel you will crop in the Channels section of the Volume Options (Standard renderer) panel and proceed with the cropping. With the Compatibility renderer, the subvolume buttons are on the right tool bar.

Hold Ctrl to select multiple channels.

Show bounding box, Show box

Displays/hides a box bounding the 3D image.

Show Axis

(requires: Compatibility)

Displays the XYZ axis model orientation.

Show Grid

Shows or hides the graticule. Define visible graticule planes in the Grid & Scale section of the Volume Options panel.

Show Scale

(requires: Standard), (requires: Optimal )

Displays/hides a scale around the bounding box.

Show Z Scale

(requires: Compatibility)

This button displays/hides the Z scale in the image window. Press the arrow button to open a menu with additional options.

Show volume info

(requires: Standard), (requires: Optimal )

Displays information about the calibration and volume dimensions at the bottom of the image window. It also displays the the navigation axes (or cube) to help you determine the current orientation of the volume.

  • Select between the cube and the axes via a context menu.

  • Click on an axis, a cube wall, or a cube corner to rotate the object so that it faces you.

  • Double-click to the volume view to reset it to the default position.

Show volume dimensions

(requires: Compatibility)

This button displays information about the calibration and volume dimensions at the bottom of the image window.

Generate acceleration data file

(requires: Optimal )

Generates the volume acceleration h5 file used for fast reloading of oversized volume datasets. Once the file is generated, the icon changes to indicating that the file is recorded in the file manager (see below).

Manage acceleration files

(requires: Optimal )

Opens the Full-Res Acceleration Files dialog window managing all volume acceleration h5 files. Table with the files is sorted after clicking on the selected table header indicating the data order with a triangle icon. Use to delete the selected file or use Delete Selected or Delete All.

Show centroid instead of binary

(requires: Compatibility)

Displays/hides a centroid for each binary object in the 3D image. Adjust the Centroid size in the nearby pull-down menu.

Open Z-LUTs for Volume View

(requires: Optimal )

Opens the Z-LUTs for Volume View panel (see: View > Visualization Controls > Z-LUTs for Volume View ).

Calculate additional slices in Z axis for better quality (for highly undersampled datasets only)

(requires: Compatibility)

This button enhances the quality of under-sampled datasets by calculating additional slices in the Z-axis.

Create Image Cache for Time Loop

Use this button if your image sequence contains the time dimension and you would like to observe it. The visualization will be pre-loaded to memory and therefore smooth and fast enough.

Switch to full screen mode rendering

This option switches the volume viewer to fullscreen mode. You can abort this mode by pressing Esc.

Tip

(requires: Standard), (requires: Optimal )

When using two monitors, the Volume Options (Standard renderer) panel can be controlled from one monitor and the 3D Volume can be in full screen on the other monitor.

Show Movie Maker

This button runs the Movie Maker application. It enables the user to create AVI movies of the 3D model.

See Creating a Movie from Volume View.

Show Help

Displays the help page.

Opening large volume datasets

When an image with a large volume dataset is opened, it generates a volume acceleration h5 file, which is then employed to quickly reload the volume datasets. Two icons appear on the main toolbar:

Generate acceleration data file

(requires: Optimal )

Generates the volume acceleration h5 file used for fast reloading of oversized volume datasets. Once the file is generated, the icon changes to indicating that the file is recorded in the file manager (see below).

Manage acceleration files

(requires: Optimal )

Opens the Full-Res Acceleration Files dialog window managing all volume acceleration h5 files. Table with the files is sorted after clicking on the selected table header indicating the data order with a triangle icon. Use to delete the selected file or use Delete Selected or Delete All.

Time-to-Volume Projection

Timelapse images can be projected inside the volume viewer to illustrate time displacements. If more dimensions are available, select Time from the first drop-down menu in the Volume Options and choose a suitable blending mode. Click to set the first timelapse frame as the highest/lowest one in the sequence.

Note

For renderers other than Optimal, select the time dimension in the first combo box found in the top toolbar.

Side Toolbar

(requires: Optimal )

Center view around picked point

If you select this function or hold down Alt, clicking in the volume image automatically centers the view based on the clicked position.

Fix rotation center to data center

If turned on, the volume image is rotated from the center of the object. If turned off, the object rotates around the focal point based on the observer perspective.

Rotate around object axis X

Restricts rotation direction only to the X axis.

Rotate around object axis Y

Restricts rotation direction only to the Y axis.

Rotate around object axis Z

Restricts rotation direction only to the Z axis.

Rotate around custom axis

Restricts rotation based on the values set in the Rotation axis (X, Y, Z) fields. Use the secondary mouse-click over the icon to reveal the window with shortcuts to the basic planes, Orientation settings (Yaw, Pitch, Roll) and Rotation axis settings. To make the window visible at all times, activate the pin button.

Crop/slice

Turns the crop/slice mode on/off. Hold down Ctrl and move the desired plane with the left mouse button. The Crop/Slice panel, revealed by the secondary-mouse click over the icon, is closely described here: Crop & Slice.

Binary

Displays the binary layer of the 3D image. Use the key shortcut Ctrl + B.

Color

Displays the color layer of the 3D image. Use the key shortcut Ctrl + R.

Overlay

Displays the color layer and the binary layer of the 3D image at once. Use the key shortcut Ctrl + V.

Colorize by 3D Objects

This function is used to distinguish between binary objects by colorizing each 3D object with a different color. This function can be turned on/off in the context menu over the 3D image where it is also possible to change the color of each binary 3D object (Change Binary 3D Object Color).

Sync binaries with channels

If a single channel is selected for display, only binary layers attached to it are displayed and vice versa. More information about attaching binary layers to channels can be found here: Attaching Binary Layers to Channels.

Binary layers

Opens the View > Analysis Controls > Binary Layers panel.

3D binary objects

Opens the 3D Object Measurement tab displaying values of measured features for each 3D object in the image (see: Measure > 3D Object Measurement ).

Add binary

Opens one of the thresholding methods to create 3D binaries from the current volume image:

Volume Options

(requires: Optimal )

Volume Options

Click this button on the image toolbar to display the Volume Options panel which contains the following options:

Dimension

Z-stack/Time/Frame

Selects the dimension used for the volume viewing. If frame is selected, it can be chosen in the navigation bar below the image. Time projection is closely described here: Time-to-Volume Projection.

Z-zoom

Adjusts the Z-step height of the image Z sequence.

The first frame is highest, The first frame is lowest

Click the button to set the first frame as the highest/lowest one in the sequence.

Image

Opacity slider

Sets the opacity of the image. If a binary layer is present, it is left intact.

Reset

Resets the image opacity back to its default value.

Edge Enhancement

The switch turns the edge enhancement function on/off. This function reduces the opacity of the haze around the objects so that they are more contrasting and sharper. Move the slider of the selected channel to the right to increase the enhancement power. Hold down Shift to move all active sliders at once. This function can be used only with Alpha and Alpha & Shade blending.

Maximum Intensity Projection

Displays only voxels with the highest intensity in the observation direction on plane(s) selected using the first three buttons (XY, XZ, YZ). To display all planes at once click Show all. To hide all planes, click Hide all.

Crop & Slice

Off

Cropping and slicing is turned off when this tab is selected.

Crop

Crops the image using an orthogonal () or arbitrary () plane.

Box: Hold down Ctrl and move the mouse to select a plane. Then click and drag the plane while still holding Ctrl and release the mouse button to create the crop. To drag two planes at once, move the corner ball.

Plane: Hold down Ctrl and move the ball to set the center of the arbitrary crop. Then move the cone on the opposite end of the line to tilt the cropping plane. Release Ctrl to create the crop.

To reset any crop or cropping groups, click Reset. To create a new document from the current crop, click Extract.

Cropping Groups 
Both the channels (color squares) and the binary layers (color circles) can be cropped. Double-click on a channel (color square) or binary layer (color circle with the letter B) in this field or drag it into the area to create a new cropping group (a new row is created). Crop is then performed only on the selected cropping group.

Slice

Select one or more slicing planes ( XY, XZ, YZ), hold down Ctrl, click on the plane and move it to position the slice. When working with the Custom slice, hold down Ctrl and move the ball to set the center of the slicing plane. Then move the cone on the opposite end of the line to tilt the slicing plane. Release Ctrl to create the slice. To reset the slices back to default, click Reset.

Binary

Surface

Opacity slider 
Sets the opacity of the binary layer.

Hide front faces 
Hides the binary front faces so that the inside of the binary volume is more visible.

Mesh

Mesh line thickness slider 
Adjusts the thickness of the mesh line.

Density 
Sets the density of the triangular mesh.

Remeshing 
Remeshing adjusts the grid to the most regular equilateral triangles. Uniform remeshing makes all triangles the same size; it adaptively adjusts the size of the triangles and thus the density of the mesh according to the local complexity of the shape. Adaptive remeshing has a minimum triangle size the same as uniform, so it is allowed to reduce the grid density on large simple areas, but does not densify around details. This is because the mesh is mainly used to achieve binary transparency, so that a dense, opaque mesh does not form around fine details.

Centroid

Centroid radius slider 
Adjusts the size of the binary centroid(s).

Grid & Scale

Detailed description can be found here: Displaying a Grid.

Volume Options (Standard renderer)

(requires: Standard)

Note

If you use the Compatibility renderer, these tools are placed on the right image tool bar, otherwise in the Volume Options (Standard renderer) panel.

Volume Options

Click this button on the image toolbar to display the Volume Options (Standard renderer) panel which contains the following options:

Free rotation

Click and drag over the model for free rotation.

, Rotation around the selected axis

Restricts rotation direction only to the selected object axis.

User-defined rotation axis

Rotate the model around a user-defined axis. Click the arrow to display a context menu where you shall define coordinates of the second point of the axis. The first point is the origin of the 3D model.

View Plane, View

Display the pull-down menu in the top image tool bar and select which plane will be facing you from the six predefined views (side views and horizontal projections). The Default view is slightly rotated so that the structure of the sample can be overviewed.

View Angle

Defines the 3D image rotation using three values (Yaw, Pitch, Roll). Or you can select a predefined plane as in the View Plane menu.

Z-zoom

Adjusts the Z-step height of the image Z sequence.

The first frame is highest, The first frame is lowest

Use these two buttons to set the first frame as the highest/lowest one in the sequence.

Blending

Different rendering techniques can be used to display the Z sequence as a volume. Some combinations of the following techniques are available depending on which renderer is selected.

Alpha

Alpha Blending. Uses the physical principles of light absorbing so that only the surface voxels are visible.

Alpha & Shade

Alpha blending in combination with the Shaded Volume (see below).

MaxIP

Maximum Intensity Projection. Only voxels with the highest intensity in the observation direction are displayed.

MinIP

Minimum Intensity Projection. Only voxels with the lowest intensity in the observation direction are displayed.

Accumulated intensity projection

Accumulates voxel intensities in the observation direction. The result is often over-saturated, therefore you can adjust the display intensity in the 3D Settings window.

Z Depth Coding

A color gradient perpendicular to the Z-stack planes is applied to the volume. The lower part of the volume is colored with different colors than the top part based on the selected color gradient. It makes it easier to distinguish the object position within the whole Z sequence.

You can select a color gradient from the nearby pull-down menu.

Shaded Volume

(requires: Standard)

Uses the physical principles of light absorbing and reflectance. The object surface becomes more distinguishable.

Enable Depth Coding, Disable Depth Coding

Turns on/off the volume color gradient. Use the drop-down menu next to the icon to choose a gradient, Reverse gradient or Show depth code legend.

Full-res

Low resolution is recommended for basic volume previewing. When precise static details are to be visualized, switch to high resolution (uses up to half of the available RAM). The most noticeable changes between these two modes are observed in large images (beyond the graphic card capabilities).

If the image is fully loaded into the memory of the graphics card, High resolution is turned on, the viewer shows the maximum quality and the button is automatically disabled. If the memory capabilities are exceeded, two more modes appear - Highest Possible Resolution (optimized for the highest resolution without downsampling; can be slower) and Balanced Resolution vs Speed (resolution can be lower; speed performance should be sufficient).

Show smooth volume

Click on this button to smooth the 3D volume.

Show non-interpolated volume

Click on this button to display raw, non-interpolated 3D volume.

Anaglyph 3D stereo (left / right eye)

This button enables/disables the anaglyph 3D view. Press the arrow next to the button to display the menu with possible color combinations (depending on the type of your anaglyph glasses).

Toggle light visibility

(requires: Standard) (requires: Compatibility)

Press the button to switch the light on. Move the light freely around using the left mouse button. Double-click on the light to pin it to the scene (stays in its place, 3D volume moves) or to the volume (light moves together with the 3D volume). Change the light intensity with the mouse wheel when the cursor is over the light. Context menu over the light can be used to Reset Light Settings.

Enable Edge Enhancement

(requires: Standard) (requires: Optimal )

Turns the edge enhancement function on/off. This function reduces the opacity of the haze around the objects so that they are more contrasting and sharper. Move the slider of the selected channel to the right to increase the enhancement power.

Crop & Cut

(requires: Standard) (requires: Optimal )

See Cropping Tools .

Grid & Scale

(requires: Standard) (requires: Optimal )

See Displaying a Grid.

Displaying a Grid

Grid and Scale (Optimal renderer)

(requires: Optimal )

Grid

Grid is activated in the right toolbar. Parameters of the grid can be adjusted in the window revealed by a secondary-mouse click over the icon or in the Volume Options.

Grid can be set to Back, showing the grid on the bottom and far sides of the volume, or to User defined where the grid position is adjusted by holding Shift and clicking and moving the grid plane. User can set which grid planes are shown by clicking on the buttons (, , ). Grid density can be set automatically (Auto switch on) or specified manually in the edit box.

Colors of the bounding box, grid line and scale axes are set below after clicking on the squares. When you hover over a square, a tool tip shows which element the color will be assigned to. To reset the colors back to default, click .

Scale

Scale is activated in the right toolbar. Its parameters can be adjusted in the window revealed by a secondary-mouse click over the icon or in the Volume Options.

Outside adds a scale ruler to the outside of the bounding box. Center adds a scale ruler into the center of the bounding box. Focus locks the scale ruler in the center of the image window. Only the dimensions selected using the three axis buttons (X, Y, Z) are shown.

Grid and Scale (Standard renderer)

(requires: Standard)

Grid

If switched on, grids are shown in the volume view.

On back surface

Shows a grid on the bottom and distant sides of your current volume view.

Planes inside

Displays/hides the XY, YZ, and XZ planes (use the toggle switches). Each plane is carrying an automatic or manually defined grid. Hold down Shift to evoke a small cube. Drag the yellow ball of the cube to alter the zero grid position. Drag the arrow ends to move the grid just in the selected axis direction.

Scale

If switched on, a labeled scale is shown in the volume view.

Ruler

Shows a labeled ruler on the edge of the prism marking each grid line with its distance from 0.

Axis aligned Density, Screen aligned Density

Shows a labeled scale aligned with the volume view axis or with the screen.

XYZ, Z

Defines which axes are labeled when Ruler is selected.

Invert Z-Values

Changes the direction of the Z ruler.

Density

Adjusts the density of the grid or scale if Auto is switched to off.

Auto

Automatically calculates a suitable spacing of the grid and the scale.

Line, Line Color

Changes the color of the grid/plane line.

Font, Font Color

Changes the color of the grid/scale and its labels.

Grid (Compatibility renderer)

(requires: Compatibility)

The grid is called Graticules in the Compatibility renderer. Click the Show Grid button in the image tool bar to display it. Reveal the pull-down menu of the button to display the following options.

XY plane, YZ plane, XZ plane

Select which planes will contain the graticule.

Bounding Box

Displays the grid on all sides of the box displayed behind the volume. With the Always on Top option selected, it is the contrary.

Halved bounding box

Displays the grid on three sides of the box. With the Always on Top option selected, the opposite sides of the box are used.

Graticules Properties

Displays a window with graticule settings.

Type

Select which planes will be visible. You can combine them with other planes. Check the Bounding Box option to show the graticules on all sides of the box. The Halved bounding box displays graticules on three sides of the box.

Appearance

Adjust the graticule visibility. The graticule can be shown at the top or in the background.

Line colors

Select a color for each axis individually.

Density

Specify value and units of graticule density. Check the Automatically adjust density option to let the system set the graticule density automatically. The information about the current graticule size is displayed in the bottom right corner of the image window.

Moving the graticule 
(requires: Compatibility)

To move the graticule freely, hold down the Shift key, grab the graticule and drag it to a new position. If you need to adjust the graticule position only in some directions, hold down the Shift key. An axis system scheme appears. Point the mouse cursor on one of the axes or planes you want to fix. The selected plane (or axis) becomes highlighted. Now hold the primary mouse button and move the mouse cursor. The graticule will move accordingly in the selected plane or axis direction.

Binary and Measurement

(requires: Standard)

Define 3D Threshold

Opens the 3D threshold window used for segmentation of 3D objects.

Spot Detection 3D

Detects bright/dark circular objects within a 3D space. Please see: Spot Detection for more information.

Colorize Binary by 3D Objects

This function is used to distinguish between binary objects by colorizing each 3D object with a different color. This function can be turned on/off in the context menu over the 3D image where it is also possible to change the color of each binary 3D object (Change Binary 3D Object Color).

3D Object Measurement

Opens the 3D Object Measurement tab displaying values of measured features for each 3D object in the image (see: Measure > 3D Object Measurement ).

View Binary

Displays the binary layer of the 3D image. Use the key shortcut Ctrl + B.

View Color

Displays the color layer of the 3D image. Use the key shortcut Ctrl + R.

View Overlay

Displays the color layer and the binary layer of the 3D image at once. Use the key shortcut Ctrl + V.

Open Binary Toolbar

Opens the Binary Toolbar (View > Analysis Controls > Binary Toolbar ).

Show/hide centroids

Displays/hides a centroid for each binary object in the 3D image. Adjust the Centroid size in the combo box in the dialog window.

3D Manual Measurement

Measures distances inside the 3D image. The View > Analysis Controls > Annotations and Measurements panel will open with the Length 3D tool selected. When measuring centroids, the start/end of the measuring line automatically snaps to the center of the closest centroid.

Note

To measure distances more precisely, switch to Slices View (View > Image > ND View > Slices View ), make the measurement in the particular Z-plane, and switch back to Volume View.

Cropping Tools

(requires: Standard)

Display the Volume Options panel which contains the following tools:

Show/Hide

Displays or hides any cropping and cutting made on the 3D image.

Reset Crop

Removes any crop changes made on the image and returns the cut planes into their default position.

Extract

Extracts a new document from the current view limited by the crop/cut tools.

Ortho

This mode crops the 3D image perpendicularly. Hold down Ctrl and move the desired plane with the left mouse button.

Arbitrary

This mode crops the 3D image freely. Hold down Ctrl and move the yellow ball to position the center of the cropping plane and then move the yellow cone to tilt the plane which is illustrated by the white circular grid.

Both

Both orthogonal and arbitrary crops are enabled at the same time (see above).

Note

If you restrict the volume size using the cropping tools, you can shift the result inside the original volume in all three directions. Press Ctrl + Shift and then click and drag over a plane determining the shift direction. Color lines with crosses indicate the shift axis.

XY, XZ, YZ

A plane delimited by two axes can be used for cutting through the 3D image. Hold down Ctrl and drag the cutting plane in the direction of the remaining axis.

Any

Any plane can be used to cut through the 3D image. Hold down Ctrl and move the yellow ball to position the center of the cutting plane and then move the yellow cone to tilt the plane.

Channels

Select which channels will be cropped. This option is available only with Ortho cropping.

3D Settings

Click the 3D Settings button on the image toolbar to adjust the settings of the volume renderer.

3D Settings (Optimal Renderer)

Renderer

Switches between the engines.

See Introduction.

Behavior
Preload image data before playback

Data are preloaded automatically before each playback of a time dimension. If not selected, smoother playback of volume images containing the time dimension can be provided by clicking on the Create image cache for time loop button.

Save 'Volume Options' to the file

Saves individual settings of each image (view angle, crop, etc.) to the image file.

Enable autorotation

If checked, the manually spun volume will continue spinning.

Quality
Interactive mode frame rate

is used to adjust the optimal frame rate used when moving the 3D model.

Anti-aliasing

Anti-aliasing is used to smooth the edges of the lines to minimize the distortion artifacts when representing a high-resolution volume at a lower resolution.

Full-Res

Set conditions for activation of the Full-res button.

RAM usage limit

Sets how much of the RAM memory can the full-res mode use. For optimal running, it is best to keep as much of the document ready in RAM as possible, but please keep in mind that the system and other processes within NIS-Elements also need some memory to run.

Details

Sets the quality of displaying images. The level of detail in full-res varies according to the current view angle and especially the zoom factor. This factor determines how pixelated the data can be. In practice, this means that at a value of 1 the highest quality will be preferred. At a value of 5, you will need to zoom in for detail, but the smaller data volume will make the viewing much faster.

Full-res caching mode

Sets how to handle preloading of oversized datasets.

Always ask

The user is prompted every time there is a need to generate the acceleration file.

Lazy

Only portions of the dataset which are needed for the current view load automatically. It displays the image faster than the Preload option at first, but it subsequent manipulation is slower.

Preload

Always preloads the whole dataset. It takes some time when the image is opened, but all subsequent actions are fast.

Open large files directly in full-res mode

If volumetric data exceeds the available RAM, the Full-res button in the Volume Options panel will be enabled and pressed automatically.

Check available storage for full-res cache

Full-res (for oversized datasets) loads data in smaller blocks and uses cache (auxiliary *.h5 file) for faster reloading. If this check box is selected, the space available for this cache is verified when the document is opened.

Colors

By clicking on these color rectangles you can define the background color and color of the labels. A background gradient can be defined by selecting two different background colors. Click on the button to set all colors to their default values.

Text Options

These options influence the axes displayed around the bounding box and other texts displayed in the Volume Viewer (Zoom, Size, Calibration).

Font

Sets the text font type.

Size

Sets the size of the text.

Help

Opens this help page.

3D Settings (Standard Renderer)

Renderer

Switches between the engines. Options change based on the selected engine.

Quality
Still image resolution

This resolution is used for static viewing (which usually allows the highest quality).

Interactive mode resolution

This resolution is used when moving with the 3D model.

Shaded volume lighting

Choose one of the lighting modes.

Lighting of binary objects

Lighting presets are available in this combo box. Illumination is adapted according to the selected binary surface. Balanced mode automatically balances light irrespective of the surface type.

Accum. intensity projection

Modifies (multiplies by a coefficient) the pixel intensity sums created by the AccumulatedIP blending mode.

Colors

By clicking on these color rectangles you can define the background color, bounding box color, and color of the labels. Click to set all colors to their default values.

Text Options

These options influence the axes displayed around the bounding box and other texts displayed in the Volume Viewer (Zoom, Size, Calibration).

Font

Sets the text font type.

Size

Sets the size of the text.

Help

Opens this help page.

3D Settings (Compatibility Renderer)

Note

The 3D Settings button only if you have a high-performance graphic card with DirectX 9.0c support, Shader Model 3.0.

Show detailed tooltips on toolbar buttons

Check this item to display detailed tooltips.

Use advanced renderer

If an advanced graphic card is detected in your computer, this option becomes available. Choose it to make use of the extra capabilities of the card. The resulting image will be nicer and the performance faster.

Note

If this option is turned off, a stripe pattern may appear in the volume render.

Still image resolution

This resolution is used for static viewing (which usually allows the highest quality).

Interactive mode resolution

This resolution is used when moving with the 3D model.

Shaded volume lighting

Choose one of the lighting modes: Balanced, Matte, or Shiny.

Accum. intensity projection

Select the intensity of accumulating the pixel values: High, Medium, or Low.

Help

Opens this help page.