Volume Viewer

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

Basic Operations

(requires: mod.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

  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.

Bounding box

Displays/hides a box around the 3D image.

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.

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.

Show volume view help

Displays the help page.

Basic Operations (Standard renderer)

(requires: mod.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.

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

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

Crop a single channel

Select one of the subvolume buttons on the right tool bar and proceed with the cropping.

Hold Ctrl to select multiple channels.

Show bounding box, Show box

Displays/hides a box bounding the 3D image.

Show Axis

Displays the XYZ axis model orientation.

Show Z Scale

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

Show volume dimensions

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

Show centroid instead of binary

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

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:

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 (Standard renderer) 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.

Volume Options (Standard renderer)

(requires: mod.standard)

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.

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.

Z-zoom

Adjusts the Z-step height of the image Z 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

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

Lighting appearance can be changed via the 3D Settings button.

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.

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

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.

3D Settings

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

3D Settings (Standard 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.