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Surface Renderer

The Huygens Surface Renderer is a powerful 3D visualization tool that enables the visualization of iso-surfaces of volumes.

The Surface renderer showing an isolated Rat Hepatocyte couplet (recorded by Dr. Permsin Marbet at the Department of Anatomy, University of Basel, Switzerland, in the lab of Prof. Lukas Landmann)
The Surface renderer showing an isolated Rat Hepatocyte couplet (recorded by Dr. Permsin Marbet at the Department of Anatomy, University of Basel, Switzerland, in the lab of Prof. Lukas Landmann)


An iso-surface is a 3D surface representation of points with equal intensities in a 3D stack; it is the 3D equivalent of a contour line (see figure below). The iso-surface envelops voxels with intensities above a certain threshold. If those voxels are distributed in groups that are not spatially connected, they will be considered and labeled as independent objects.

A contour line for an interpolated value of 5. Because 5 is much closer to 6 than to 12, the distance of the contour to the voxel with value 12 is larger than the distance to the bottom-right voxel with value 6.
A contour line for an interpolated value of 5. Because 5 is much closer to 6 than to 12, the distance of the contour to the voxel with value 12 is larger than the distance to the bottom-right voxel with value 6.


Shading enhances the perception of 3D shapes and texture. Alongside the iso-surfaces, the Surface Renderer can also render a MIP projection and cross-sectional slices.

A schematic overview of surface rendering. The orientation of the surface determines the shading.
A schematic overview of surface rendering. The orientation of the surface determines the shading.


Starting from version 19.04, the Surface Renderer} supports GPU acceleration. This greatly reduces render times. Note that GPU-based surface renders can differ from CPU-based surface renders. The most important difference is that GPU renders use a perspective projection (diverging rays, objects farther away are smaller), whereas CPU renders use an orthogonal projection (parallel rays, objects farther away stay the same size).

To start the Surface Renderer, right-click on a thumbnail and select 3D Visualization → Surface renderer from the pop-up menu. Alternatively, choose the corresponding icon from the taskbar or select the Visualization → Surface renderer from the main menu.

Usage

The Surface renderer is highly customizable, giving the user the ability to set many parameters that play a role in the scene. The following parameters can be set:
  • Twist, tilt, zoom & pan: Adjust the viewing angle and camera position.
  • Time frame: Select the time frame in a time series image.
  • Detector: Select the detector in a multi-detector image.
  • Channel parameters:
    • Soft threshold: Only voxels above a certain intensity are taken into account during rendering.
    • Color mode: A color selection for the material represented by each channel.
    • Use watershed (surface): Toggles watershed segmentation.
    • Sigma (surface): Sets the watershed sigma (see Watershed segmentation).
    • Threshold (surface): Adjust the threshold level for the channel surface, i.e. the threshold for the iso-surface.
    • Seed (surface): Only objects with an intensity higher than the seed level remain, while the rest are discarded.
    • Garbage volume (surface): Objects that contain fewer voxels than defined by the garbage volume parameter will not be rendered. This is useful for filtering out tiny objects in noisy images.
    • Transparency (surface): Adjust the transparency of the channel surface.
    • Brightness (surface): Adjust the brightness of the channel surface.
    • Channel (surface): Set the channel for this surface. Up to three channels can be rendered using the different surface pipes, or the same channel surface can be rendered with different thresholds.
    • Hue (surface): Using the hue range slider the range of hues used for the surface for the selected surface can be set.
    • Threshold (MIP): Set the soft threshold level of the MIP.
    • Transparency (MIP): Adjust the transparency of the MIP.
    • Brightness (MIP): Adjust the brightness of the MIP.
    • Channel (MIP): Set the MIP channel. Only a single channel MIP can be added.
    • Hue & saturation (MIP): Using the hue & saturation sliders the color of the MIP can be set.
    • Transparency (Slicer): Adjust the transparency of the slice.
    • Brightness (Slicer): Adjust the brightness of the slice.
    • Orientation (Slicer): Set the orientation of the slice. For now only orthogonal orientations are allowed.
    • Position (Slicer): Set the position of the slicer perpendicular to the slicing surface.
    • Show (Slicer): Toggle the slicer. For now only the first channel can be sliced.
  • First scene: Set the render parameters for the first scene of the movie.
  • Last scene: Set the render parameters for the last scene of the movie.
  • Set number of movie frames: Set the number of frames that will be included in the movie.
  • Set movie frame rate: Set the number of frames per second of the movie.

Rendering a movie

The Huygens Movie Maker allows you to create sophisticated animations using the MIP, SFP and Surface renderers. Note that all the time frames of Time Series images can be selected for animations.


Animated surface rendering of an isolated Rat Hepatocyte couplet recorded by Dr. Permsin Marbet at the Department of Anatomy, University of Basel, Switzerland, in the lab of Prof. Lukas Landmann.



However, the Surface renderer can also create simple animations on its own by transitioning between two custom keyframes. Set the render parameters for the first frame and click the Movie tab, Set view → First scene. Now adjust the parameters for the final frame, and click SET view → Last scene. The frame count and frame rate can also be set in the Movie tab. Finally press the animate button to render the movie as an AVI or as a series of Tiff files.

The exported AVI files use the MJPEG codec and can be played by most video players.

See Make Animations for more details.

For further information, see Surface Renderer Tutorial.

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Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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