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The SFP Renderer

Chromosomes in a grain pollen nucleus as visualized with the SFP algorithm. Image courtesy: Dr. O. A. Mayboroda.

This volume renderer avaliable in the Huygens Software is based on taking the 3D microscopy image as a distribution of fluorescent material, simulating what happens if the material is excited and how the subsequently emitted light travels to the observer. The computational work is done by the Simulated Fluorescence Process (SFP) algorithm. The unique properties of this algorithm enable it to create depth cue rich images from unprocessed data. Because it does not rely on boundaries or sharp gradients, it is eminently suited to render 3D microscopic data sets.
Since the SFP algorithm is bases on ray-tracing it does not require a special graphical board as the polygon based techniques do.



(Image: 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)

Principle

In the Simulated Fluorescence Process (SFP) volume rendering algorithm the data is taken as a distribution of fluorescent dye. By modeling a physical light/matter interaction process an image is computed showing the data as it would have appeared in reality when viewed under these conditions.

The algorithm works like follows: In the first stage the fluorescent distribution is illuminated (excited) by a light source at infinity. Because the dye absorbs the excitation light areas towards the light source will be stronger excited than other areas. Underneath the distribution a flat slab of dye, usually referred to as 'table', is added to visualize cast shadows.
In the second stage the light emitted by the distribution and the table propagates towards the viewer. Light which passes through dye gets absorbed, so areas towards the viewer contribute most to the image.
The transparency factors in the excitation and emission phases can be controlled independently.

In case there are more than one channel present, each channel is taken as a dye with different properties (transparencies, color, brightness).

Read more on Simulated Fluorescence Process .

Tutorial

Free SFPTutorial : illustrated tutorial for Free Sfp , the freeware version of the SFP renderer, that covers the main rendering parameters of the SFP renderer explained here.

Use

By default the first channel (ch-0) is the red object, the second channel is (ch-1) is the green object and the third (ch-2) is the blue object.

The properties of the interaction between object and light (transparency), both for excitation and emission, as well as the viewpoint, can be adapted interactively by the user to produce different sceneries. Since the volume rendering process is rather computationally intensive, a preview image is displayed. Apart from the viewpoint settings and the optional zooming, the following sliders affect the image:

• Transparencies:
  • Excitation: The transparency of the object for the excitation light. The less transparency the more shadow is casted on the subsequent voxels and on the table.
  • Emission: The transparency of the object for the emission light. The lower the transparency for the emission light the more difficult it is to peer inside or trough the object.
• The Characteristic object size affects both the excitation and the emission transparency. While traveling through the object, the light intensity is attenuated to some degree. This enables us to define some definition for penetration depth at which the light intensity is decreased to some extent, say 10% of its initial value. This penetration depth should be in line with the object size. A transparent object is small with respect to the penetration depth. Thus for the same physical properties of the light one object can be transparent while the other is oblique due to its size. To find a reasonable range in transparencies the object size may be altered. At start-up the object size is computed from the microscopic sampling sizes and number of pixels the image is composed off. If your image has not the correct parameters (for example a tiff series) the object size is set according to the default parameters as set by the Huygens Essential software and may not be related to the actual object size.
• Material efficiency: The efficiency of the individual channels (here represented as materials) to interact with the incident light beam.

Use the Run button to start the actual rendering. The result can be saved as a tiff-image ( File > Save ).

Perspective/Parallel views

In the perspective view, objects which are far away are smaller than those nearby. Since we use perspective views in real life perspective viewpoints give more information about depth and are easier to interpret.

In the parallel view, sometimes also referred to as `Orthographic camera view', all objects appear at the same scale. The rendering process is simpler and therefore the SFP scene will be updated more quickly.

Rendering a movie

The Huygens Movie Maker allows you to easily create sophisticated animations of your multi-channel 3D images using the Sfp Renderer and the other powerful 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.

Without the Movie Maker the SFP Renderer has the option to make simple animations of your image, changing the view point in different frames. Select the viewpoint coordinates for the first frame, then click Set > Home. Select now the viewpoint coordinates for the last frame, and click Set > End. (You can now go to the last or the first frame by clicking Go > End or Go> Home). Select all the rendering parameters, including the total number of rendered frames for the movie (Options > Animation frame count). Finally, click Animate, and select a directory to save the tiff frames to. You can later load and edit these tiff images with your favourite animation tool. For instance, you can use the 'convert' tool from ImageMagick (http://www.imagemagick.org) to make a GIF animation, using

convert -delay 20 animatedSfp*.tiff animatedSfp.gif

You can now place this single file GIF animation directly on your web page, as most of the internet browsers currently avaliable can handle this kind of movie files:



See another small video sample: SfpRend200.gif (851 kB 2008-09-15 14:53)

See Make Animation for more details.

If your image is a Time Series , you can also make an animation along time coordinates.

Free volume renderer

Free Sfp , the FreeWare version of this component, uses the parallel view. The perspective view is avaliable in Huygens Essential , Huygens Professional and Huygens Scripting .

Further examples

See:

• Image Restoration
• http://www.pfid.org/html/gal/chromo.shtml?en

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