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The Huygens SFP Volume Renderer

The SFP Renderer by SVI generates realistic 3D scenes, based on a 3D microscopy image, which is interpreted as a distribution of fluorescent material. The computational work is done by the Simulated Fluorescence Process (SFP) algorithm, simulating what happens when the material is excited and how the subsequently emitted light travels to the observer.

The SFP renderer
The SFP renderer


The properties of this algorithm allow rendering of the object at different depths, unveiling layers beneath the object's surface. The SFP algorithm does not require detection of surfaces, sharp gradients or any kind of segmentation, and is therefore very well suited for direct rendering of 3D microscopy data. An enormous speedup of the SFP Renderer is achieved through the use of GPUs, available as from Huygens version 19.04.

Principle

The SFP volume rendering algorithm inteprets the image intensity as a distribution of fluorescent dye. By modeling a physical light / matter interaction process the scene is rendered, showing the data as it would have appeared under the same conditions in reality.

The algorithm works as follows:
  • In the first stage the fluorescent distribution is illuminated (excited) by a light source located at infinity. Because the dye absorbs the excitation light, the areas facing the light source will be more excited. A table is placed below the object so shadows are visible.
  • In the second stage the light emitted by the object and the table propagates towards the viewer. The light which passes through the dye gets absorbed, so objects can be obscured from view by other objects.
Note that each channel of a multichannel image is interpreted as a dye with different properties (transparencies, color, brightness, etc.).

For details, see SFP algorithm


3D SFP render animation of a cell cluster (data recorded by Dr. Nicolas Fête, Bioimaging and Optics Platform, Swiss Federal Institute Of Technology).


Usage

The SFP renderer is highly customizable, giving the user the possibility to determine many parameters that play a role in the scene. The following options can be set:

  • Twist, tilt, zoom & pan: Adjust the viewing angle and camera position.
  • Time frame: Select the time frame for time series images.
  • Detector: Select the detector for multi-detector images.
  • Penetration depth: Determines the general "hardness" of the object. When light travels through the object, it is attenuated according to the properties and local density of the material. The length scale on which this attenuation takes place is called the penetration depth.
  • Channel parameters:
    • Excitation transparency: Determines the transparency of a certain channel for excitation light. When excitation light is absorbed by an object, it casts a shadow on itself and all the objects beneath it (relative to the lighting direction) for all channels.
    • Emission transparency: Determines the transparency of a certain channel for emission light. When emission light is absorbed by an object, it blocks the view of objects behind it (relative to the viewer) for all channels.
    • Shadow transparency: Determines the "hardness" of the shadow on the table. For a low transparency the shadow will be very dark and sharp, and for a high transparency it will be bright and smooth.
    • Object brightness: The brightness of the fluorescent material of the channel.
    • Soft threshold: By setting a threshold only voxels of sufficient intensity are taken into account.
    • Color mode: A color selection for the material represented by the channel.
  • Camera tracking: Let the excitation lighting direction follow the camera.
  • Light twist & tilt: Adjust the excitation lighting direction (azimuth and zenith).
  • Table: Choose whether or not the table underneath the object should be included in the scene.
  • Table distance: Adjust the distance between the object and the table.
  • Table reflection: Adjust the degree of reflection of the table.
  • Table size: Adjust the size of the table.
  • Table color & brightness: Adjust the color of the table through hue, saturation, and brightness.
  • Background color & brightness: Adjust the color of the background through hue, saturation, and brightness.
  • First scene: Set the render parameters of the first scene of the movie.
  • Last scene: Set the render parameters of 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 framerate (fps) of the movie.
  • Render size: Set the size (in pixels) of the SFP scene. If set to "Canvas", fills the window.

All scene settings, i.e. both the render options and all parameters, can be exported to a template file via File → Save scene template.... The template files have the extension .hgsv and can be applied to any image that is loaded in the SFP Renderer. Keep in mind that the sampling sizes of the data affect the transparency.

Rendering a movie

The Huygens Movie Maker allows you to create sophisticated animations using the Sfp Renderer and the other Huygens Visualization renderers.


Animated SFP 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 SFP 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 rame 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. Note that all the time frames of a Time Series images can be used for animations.

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

Further examples

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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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