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ClearVolume
ClearVolume is an open source real-time live 3D visualization library designed for high-end volumetric light sheet microscopes. ClearVolume enables the live visualization of microscope data - allowing the biologists to immediately decide whether a sample is worth imaging. ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the FiJi/ ImageJ2/KNIME ecosystem. See also * FiJi * KNIME * Light sheet fluorescence microscopy * Volume rendering 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. A typ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Volume Rendering
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. A typical 3D data set is a group of 2D slice images acquired by a CT, MRI, or MicroCT scanner. Usually these are acquired in a regular pattern (e.g., one slice for each millimeter of depth) and usually have a regular number of image pixels in a regular pattern. This is an example of a regular volumetric grid, with each volume element, or voxel represented by a single value that is obtained by sampling the immediate area surrounding the voxel. To render a 2D projection of the 3D data set, one first needs to define a camera in space relative to the volume. Also, one needs to define the opacity and color of every voxel. This is usually defined using an RGBA (for red, green, blue, alpha) transfer function that defines the RGBA value for every possible voxel value. For example, a volu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Light Sheet Fluorescence Microscopy
Light or visible light is electromagnetic radiation that can be perceived by the human eye. Visible light is usually defined as having wavelengths in the range of 400–700 nanometres (nm), corresponding to frequencies of 750–420 terahertz, between the infrared (with longer wavelengths) and the ultraviolet (with shorter wavelengths). In physics, the term "light" may refer more broadly to electromagnetic radiation of any wavelength, whether visible or not. In this sense, gamma rays, X-rays, microwaves and radio waves are also light. The primary properties of light are intensity, propagation direction, frequency or wavelength spectrum and polarization. Its speed in a vacuum, 299 792 458 metres a second (m/s), is one of the fundamental constants of nature. Like all types of electromagnetic radiation, visible light propagates by massless elementary particles called photons that represents the quanta of electromagnetic field, and can be analyzed as both waves and particles ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java (programming Language)
Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C/C++
The C and C++ programming languages are closely related but have many significant differences. C++ began as a fork of an early, pre- standardized C, and was designed to be mostly source-and-link compatible with C compilers of the time. Due to this, development tools for the two languages (such as IDEs and compilers) are often integrated into a single product, with the programmer able to specify C or C++ as their source language. However, C is ''not'' a subset of C++, and nontrivial C programs will not compile as C++ code without modification. Likewise, C++ introduces many features that are not available in C and in practice almost all code written in C++ is not conforming C code. This article, however, focuses on differences that cause conforming C code to be ill-formed C++ code, or to be conforming/well-formed in both languages but to behave differently in C and C++. Bjarne Stroustrup, the creator of C++, has suggested that the incompatibilities between C and C++ should be r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LabVIEW
Laboratory Virtual Instrument Engineering Workbench (LabVIEW) is a system-design platform and development environment for a visual programming language from National Instruments. The graphical language is named "G"; not to be confused with G-code. The G dataflow language was originally developed by LabVIEW. LabVIEW is commonly used for data acquisition, instrument control, and industrial automation on a variety of operating systems (OSs), including Microsoft Windows as well as various versions of Unix, Linux, and macOS. The latest versions of LabVIEW are LabVIEW 2022 Q3 (released in July 2022) and LabVIEW NXG 5.1 (released in January 2021). NI released the free for non-commercial use LabVIEW and LabVIEW NXG Community editions on April 28th, 2020. Dataflow programming The programming paradigm used in LabVIEW, sometimes called G, is based on data availability. If there is enough data available to a subVI or function, that subVI or function will execute. Execution flow is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fiji (software)
Fiji (''Fiji Is Just ImageJ'') is an open source image processing package based on ImageJ2. Fiji's main purpose is to provide a distribution of ImageJ2 with many bundled plugins. Fiji features an integrated updating system and aims to provide users with a coherent menu structure, extensive documentation in the form of detailed algorithm descriptions and tutorials, and the ability to avoid the need to install multiple components from different sources. Fiji is also targeted at developers, through the use of a version control system, an issue tracker, dedicated development channels, and a rapid-prototyping infrastructure in the form of a script editor which supports BeanShell, Jython, JRuby, Clojure, Groovy, JavaScript, and other scripting languages, as well as just-in-time Java development. Plugins Many plugins exist for ImageJ, that have a wide range of applications, but also a wide range of quality. Further, some plugins require specific versions of ImageJ, specific version ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ImageJ
ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation (LOCI, University of Wisconsin). Its first version, ImageJ 1.x, is developed in the public domain, while ImageJ2 and the related projects SciJava, ImgLib2, and SCIFIO are licensed with a permissive BSD-2 license. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging to radiological image processing, multiple imaging system data comparisons to automated hematology systems. ImageJ's plugin architecture and built-in development environment has made it a popular platform for teaching image processing. ImageJ can be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
KNIME
KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept. A graphical user interface and use of JDBC allows assembly of nodes blending different data sources, including preprocessing ( ETL: Extraction, Transformation, Loading), for modeling, data analysis and visualization without, or with only minimal, programming. Since 2006, KNIME has been used in pharmaceutical research, it also used in other areas such as CRM customer data analysis, business intelligence, text mining and financial data analysis. Recently attempts were made to use KNIME as robotic process automation (RPA) tool. KNIME's headquarters are based in Zurich, with additional offices in Konstanz, Berlin, and Austin (USA). History The Development of KNIME was started January 2004 by a team of software engine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Science
Computational science, also known as scientific computing or scientific computation (SC), is a field in mathematics that uses advanced computing capabilities to understand and solve complex problems. It is an area of science that spans many disciplines, but at its core, it involves the development of models and simulations to understand natural systems. * Algorithms ( numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve science (e.g., biological, physical, and social), engineering, and humanities problems * Computer hardware that develops and optimizes the advanced system hardware, firmware, networking, and data management components needed to solve computationally demanding problems * The computing infrastructure that supports both the science and engineering problem solving and the developmental computer and information science In practical use, it is typically the application of computer simulation and other f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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