The Huygens SFP Volume RendererThe Huygens SFP renderer by SVI evaluates the intensities of the 3D microscopy image as a distribution of fluorescent material. This renderer simulates how the object's excited matter emits light forming a scene.
The SFP renderer relies on the Simulated Fluorescence Process (SFP) algorithm to render the scene. The properties of this algorithm allow to render the object at different depths, unveiling layers under the object's surface. The SFP algorithm is not limited by boundaries or sharp gradients and is exclusively suited to render 3D microscopic data sets. Since the SFP algorithm is based on ray-tracing techniques it does not require a special graphic card.
PrincipleThe SFP volume rendering algorithm takes 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. Underneath the object, a flat slab of dye, usually referred to as 'table', is placed to cast shadows.
- 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 those areas facing the viewer contribute most to the image.
3D SFP render animation of a cell cluster (data recorded by Dr. Nicolas Fête, Bioimaging and Optics Platform, Swiss Federal Institute Of Technology).
UsageThe SFP renderer is highly customizable, giving the user the possibility to determine many parameters that play a role in the scene.
Apart from the viewpoint settings (tilt, twist, and zoom) the following options can be edited by the user:
- Time frame: a selection of the time frame (for time series).
- Object size: a definition of the penetration depth at which the light intensity is decreased to some extent. This penetration depth is related to the object size. A transparent object is small with respect to the penetration depth. At start-up the object size is computed from the microscopic sampling sizes and the image dimensions. If these parameters are missing in the image (for example in a tiff series) the object size is set to the Huygens default which may not be related to the actual object size.
- Channel parameters:
- Excitation transparency: the transparency of the object for the excitation light. The less transparency the more shadow is cast on the subsequent voxels and on the table.
- Emission transparency: the transparency of the object for the emission light. The lower the transparency the more difficult it is to peer inside or through the object.
- Object brightness: the brightness of the fluorescent material of the channel.
- Soft threshold: a limit of the fluorescent material that is visible.
- Color mode: a color selection for the material represented by the channel.
- Background color: a color selection for the background.
- Compute shadow: whether or not the object's shadow should be included in the scene.
- Table: whether or not the table underneath the object should be included in the scene.
- Table distance: distance between the object and the underlying table.
- Table reflection: reflection degree of the table. The more table reflection the more the table acts as a mirror.
- Table size: the size of the underlying table.
- Table color: a color selection for the table.
- First movie scene: the viewpoint of the first scene from which to make a movie.
- Last movie scene: the viewpoint of the last scene from which to make a movie. The movie will be automatically recorded interpolating positions between the 'First scene' and the 'Last scene'.
- Movie frames: the number of frames that will be included in the movie.
- Movie frame rate: the number of frames per second of the movie. Along with the 'Movie frames' it will determine the movie length.
- Light direction: the position of the light source.
- Light intensity: the intensity of the light source.
- Render size: the size (in pixels) of the SFP scene.
- Render mode: whether the scene will be rendered in fast mode, high quality mode, or not rendered. It also includes the animation button to render a movie.
Notice that the SFP renderer is equipped with a template reader and writer. This allows to save to a file the parameters of a scene and to read from a file the parameters of a scene.
Rendering a movieThe Huygens Movie Maker allows to easily create sophisticated animations of multi-channel 3D images 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.
Without the Movie Maker the SFP Renderer has the option to make simple animations, changing the SFP view point of the movie frames. In the SFP renderer, set viewpoint coordinates for the first frame, then switch to the Movie tab and click on the set 'First scene' button. Set now viewpoint coordinates for the last frame, and click on the set 'Last scene' button. To review the selected scenes click on the show 'First scene', 'Last scene' buttons. Select all the movie parameters, including the total number of rendered frames for the movie (Movie tab > Set number of movie frames). Finally, click on the Animate button, and select a destination directory for the movie.
Notice that all the time frames of Time Series images can be selected for animations.