The Huygens SFP Renderer
Generate realistic 3D scenes of fluorescent material
Huygens SFP Renderer 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.
Rendering of the object isperformed at different depths, unveiling layers beneath the object's surface. The 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. Since Huygens 19.04 (released in Spring 2019), the SFP Renderer has gained a significant speed improvement using GPU acceleration.
Huygens SFP renderer window showing a mouse blastocysts acquired with a Leica Digital Light Sheet microscope, and deconvolved with Huygens using an appropriate Light Sheet PSF and the CMLE algorithm. Courtesy of Dr. Marc Duque Ramirez and Dr. Ritsuya Niwayama (Hiiragi group) and Dr. Stefan Terjung (ALMF) from the EMBL Heidelberg, Germany.
SFP and surface rendering
New in Huygens version 19.10 is the ability to add an isosurface to the SFP Renderer scene. (Structure on the right with an additional isosurface has been placed in the SFP scene for comparison).
Perhaps the most important parameter in the SFP renderer is the penetration depth. This parameter sets the absorption and emission transparencies for all channels at the same time.
A new feature in Huygens 19.10 is the ability to add cutting planes in the SFP renderer. These will virtually cut away parts of your image, allowing you to look inside.
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Simulated Fluorescence Process Principle
The SFP volume rendering algorithm interprets 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. In the first stage of the algorithm 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 multi-channel image is interpreted as a dye with different properties (transparencies, color, brightness, etc.). For details, see SFP algorithm.
In the SFP Renderer excitation of and subsequent emission of light by fluorescent materials is simulated. Each subsequent voxel in the light beam is affected by shadowing from its predecessors. The transparency of the object for the emission light controls to what extent the viewer can peer inside the object.
Perhaps the most important parameter in the SFP renderer is the penetration depth. This parameter sets the absorption and emission transparencies for all channels at the same time. In the example on the left, you can see a rendering of two mouse blastocysts with a low penetration depth. The excitation light is absorbed by the object almost immediately, and the objects appear very solid. The objects also cast a hard shadow. When we increase the penetration depth, we get the image on the right. The light now has a chance to penetrate deeper into the object, revealing internal structures and giving the image and overall softer and more transparent look. The shadow is now also softer and reflects the internal structure of the objects.
SFP renderings of mouse blastocysts showing the effect of the penetration depth parameter. The scene on the left has a low penetration depth, while the scene on the right has a high penetration depth.
Adding an isosurface
A new feature in Huygens 19.10 is the ability to add an isosurface to the SFP scene. This surface is similar to the surfaces found in the SFP Renderer. However, in the SFP scene, the surface has more advanced interactions with the excitation and emission light, creating a much greater sense of space and depth. The surface is effectively interpreted as a completely impenetrable barrier for both excitation and emission light, and thus casts hard shadows on the SFP material beneath it and on the table. It is also partially obscured by SFP material which might be in front of it. Finally, the surface can also cast shadows on itself, so interesting renderings and animations can be made even without any fluorescent material.
An added isosurface layer over the right object. Courtesy of Dr. Marc Duque Ramirez and Dr. Ritsuya Niwayama (Hiiragi group) and Dr. Stefan Terjung (ALMF) from the EMBL Heidelberg, Germany.
Using cutting planes
Another new feature in Huygens 19.10 is the ability to add cutting planes in the SFP renderer. These will virtually cut away parts of your image, allowing you to look inside. Up to 6 cutting planes can be added at the same time, and each cutting plane can be placed in an arbitrary position and orientation. In the image in the top right you can see the interface with which you can select and alter cutting planes. In the images below you can see the effects of adding one and then two cutting planes to an SFP scene. By combining cutting planes, you can cut wedges, cubes, and slices. By animating these you can make very information rich animations as well.
SFP rendering of a mouse blastocyst. In the image on the left, no cutting planes are used. In the middle image a single cutting plane is used with a plane normal roughly pointing towards the camera. In the right-hand image an additional cutting plane is used, with a plane normal pointing roughly upward. Image courtesy of Dr. Marc Duque Ramirez, Dr. Ritsuya Niwayama (Hiiragi group), and Dr. Stefan Terjung (ALMF) from the EMBL in Heidelberg, Germany.
Rendering a movie
The Huygens Movie Maker allows you to create sophisticated animations using the MIP, SFP and Surface renderers. However, the SFP Renderer can also create simple animations on its own by transitioning between two custom keyframes.
Stitched and Fused light sheet image of a chicken embryo, rendered in the Huygens SFP renderer with an isosurface and moving cutting planes. Courtesy of Prof. Christophe Marcelle, Mrs. Marie Julie Dejardin (INMG) & Dr. Denis Ressnikoff (CIQLE), Université Lyon 1, France.