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The Simulated Fluorescence Process (SFP) is a computing algorithm used for scientific visualization of 3D data from, for example, fluorescence microscopes. By modeling a physical light/matter interaction process, an image can be computed which shows the data as it would have appeared in reality when viewed under these conditions.
The algorithm considers a virtual light source producing excitation light that illuminates the object. This casts shadows either on parts of the object itself or on other objects below it. The interaction between the excitation light and the object provokes the emission light, which also interacts with the object before it finally reaches the eye of the viewer. [1] [2]
Rendering or image synthesis is the process of generating a photorealistic or non-photorealistic image from a 2D or 3D model by means of a computer program. The resulting image is referred to as a rendering. Multiple models can be defined in a scene file containing objects in a strictly defined language or data structure. The scene file contains geometry, viewpoint, textures, lighting, and shading information describing the virtual scene. The data contained in the scene file is then passed to a rendering program to be processed and output to a digital image or raster graphics image file. The term "rendering" is analogous to the concept of an artist's impression of a scene. The term "rendering" is also used to describe the process of calculating effects in a video editing program to produce the final video output.
Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye. There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy, along with the emerging field of X-ray microscopy.
In 3D computer graphics, ray tracing is a technique for modeling light transport for use in a wide variety of rendering algorithms for generating digital images.
Tomography is imaging by sections or sectioning that uses any kind of penetrating wave. The method is used in radiology, archaeology, biology, atmospheric science, geophysics, oceanography, plasma physics, materials science, cosmochemistry, astrophysics, quantum information, and other areas of science. The word tomography is derived from Ancient Greek τόμος tomos, "slice, section" and γράφω graphō, "to write" or, in this context as well, "to describe." A device used in tomography is called a tomograph, while the image produced is a tomogram.
Scientific visualization is an interdisciplinary branch of science concerned with the visualization of scientific phenomena. It is also considered a subset of computer graphics, a branch of computer science. The purpose of scientific visualization is to graphically illustrate scientific data to enable scientists to understand, illustrate, and glean insight from their data. Research into how people read and misread various types of visualizations is helping to determine what types and features of visualizations are most understandable and effective in conveying information.
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set, typically a 3D scalar field.
Parallel rendering is the application of parallel programming to the computational domain of computer graphics. Rendering graphics can require massive computational resources for complex scenes that arise in scientific visualization, medical visualization, CAD applications, and virtual reality. Recent research has also suggested that parallel rendering can be applied to mobile gaming to decrease power consumption and increase graphical fidelity. Rendering is an embarrassingly parallel workload in multiple domains and thus has been the subject of much research.
A total internal reflection fluorescence microscope (TIRFM) is a type of microscope with which a thin region of a specimen, usually less than 200 nanometers can be observed.
A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection, and attenuation or absorption, to study the properties of organic or inorganic substances. "Fluorescence microscope" refers to any microscope that uses fluorescence to generate an image, whether it is a simple set up like an epifluorescence microscope or a more complicated design such as a confocal microscope, which uses optical sectioning to get better resolution of the fluorescence image.
Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser scanning confocal microscopy (LSCM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation. Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures within an object. This technique is used extensively in the scientific and industrial communities and typical applications are in life sciences, semiconductor inspection and materials science.
Huygens software refers to different multiplatform microscope image processing packages from Scientific Volume Imaging, made for restoring 2D and 3D microscopy images or time series and analyzing and visualizing them.
Two-photon excitation microscopy is a fluorescence imaging technique that is particularly well-suited to image scattering living tissue of up to about one millimeter in thickness. Unlike traditional fluorescence microscopy, where the excitation wavelength is shorter than the emission wavelength, two-photon excitation requires simultaneous excitation by two photons with longer wavelength than the emitted light. The laser is focused onto a specific location in the tissue and scanned across the sample to sequentially produce the image. Due to the non-linearity of two-photon excitation, mainly fluorophores in the micrometer-sized focus of the laser beam are excited, which results in the spatial resolution of the image. This contrasts with confocal microscopy, where the spatial resolution is produced by the interaction of excitation focus and the confined detection with a pinhole.
Patrick M. Hanrahan is an American computer graphics researcher, the Canon USA Professor of Computer Science and Electrical Engineering in the Computer Graphics Laboratory at Stanford University. His research focuses on rendering algorithms, graphics processing units, as well as scientific illustration and visualization. He has received numerous awards, including the 2019 Turing Award.
Chemical imaging is the analytical capability to create a visual image of components distribution from simultaneous measurement of spectra and spatial, time information. Hyperspectral imaging measures contiguous spectral bands, as opposed to multispectral imaging which measures spaced spectral bands.
Voreen is an open-source volume visualization library and development platform. Through the use of GPU-based volume rendering techniques it allows high frame rates on standard graphics hardware to support interactive volume exploration.
Super-resolution microscopy is a series of techniques in optical microscopy that allow such images to have resolutions higher than those imposed by the diffraction limit, which is due to the diffraction of light. Super-resolution imaging techniques rely on the near-field or on the far-field. Among techniques that rely on the latter are those that improve the resolution only modestly beyond the diffraction-limit, such as confocal microscopy with closed pinhole or aided by computational methods such as deconvolution or detector-based pixel reassignment, the 4Pi microscope, and structured-illumination microscopy technologies such as SIM and SMI.
Computer-generated imagery (CGI) is a specific-technology or application of computer graphics for creating or improving images in art, printed media, simulators, videos and video games. These images are either static or dynamic. CGI both refers to 2D computer graphics and 3D computer graphics with the purpose of designing characters, virtual worlds, or scenes and special effects. The application of CGI for creating/improving animations is called computer animation, or CGI animation.
Amira is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo.
Visual computing is a generic term for all computer science disciplines dealing with the 3D modeling of graphical requirements, for which extenuates to all disciplines of the Computational Sciences. While this is directly relevance to the software visualistics of Microservices, Visual Computing also includes the specializations of the subfields that are called Computer Graphics, Image Processing, Visualization, Computer Vision, Computational Imaging, Augmented Reality, and Video Processing, upon which extenuates into Design Computation. Visual computing also includes aspects of Pattern Recognition, Human-Computer Interaction, Machine Learning, Robotics, Computer Simulation, Steganography, Security Visualization, Spatial Analysis, Computational Visualistics, and Computational Creativity. The core challenges are the acquisition, processing, analysis and rendering of visual information. Application areas include industrial quality control, medical image processing and visualization, surveying, multimedia systems, virtual heritage, special effects in movies and television, and ultimately computer games, which is central towards the visual models of User Experience Design. Conclusively, this includes the extenuations of large language models (LLM) that are in Generative Artificial Intelligence for developing research around the simulations of scientific instruments in the Computational Sciences. This is especially the case with the research simulations that are between Embodied Agents and Generative Artificial Intelligence that is designed for Visual Computation. Therefore, this field also extenuates into the diversity of scientific requirements that are addressed through the visualized technologies of interconnected research in the Computational Sciences.
Fluorescence imaging is a type of non-invasive imaging technique that can help visualize biological processes taking place in a living organism. Images can be produced from a variety of methods including: microscopy, imaging probes, and spectroscopy.
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