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TomoPy
TomoPy is an open-sourced Python toolbox to perform tomographic data processing and image reconstruction. Overview Tomographic reconstruction creates three-dimensional views of an object by combining two-dimensional images taken from multiple directions, for example in how a computer-aided tomography scanner allows 3D views of the heart or brain. Data collection can be rapid, but the required computations are massive. Further, many common experimental perturbations can degrade the quality of tomographs, unless corrections are applied. Unless automated tools make these corrections, beamline In accelerator physics, a beamline refers to the trajectory of the beam of particles, including the overall construction of the path segment (guide tubes, diagnostic devices) along a specific path of an accelerator facility. This part is eithe ... staff can be overwhelmed by data that can be collected far faster than corrections and reconstruction can be performed. To address the needs fo ...
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Tomographic Reconstruction
Tomographic reconstruction is a type of multidimensional inverse problem where the challenge is to yield an estimate of a specific system from a finite number of projection (linear algebra), projections. The mathematical basis for tomographic imaging was laid down by Johann Radon. A notable example of applications is the operation of computed tomography#Tomographic reconstruction, reconstruction of CT scan, computed tomography (CT) where cross-sectional images of patients are obtained in non-invasive manner. Recent developments have seen the Radon transform and its inverse used for tasks related to realistic object insertion required for testing and evaluating computed tomography use in airport security. This article applies in general to reconstruction methods for all kinds of tomography, but some of the terms and physical descriptions refer directly to the reconstruction of X-ray computed tomography. Introducing formula The projection of an object, resulting from the tomograph ...
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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 ...
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C (programming Language)
C (''pronounced like the letter c'') is a General-purpose language, general-purpose computer programming language. It was created in the 1970s by Dennis Ritchie, and remains very widely used and influential. By design, C's features cleanly reflect the capabilities of the targeted CPUs. It has found lasting use in operating systems, device drivers, protocol stacks, though decreasingly for application software. C is commonly used on computer architectures that range from the largest supercomputers to the smallest microcontrollers and embedded systems. A successor to the programming language B (programming language), B, C was originally developed at Bell Labs by Ritchie between 1972 and 1973 to construct utilities running on Unix. It was applied to re-implementing the kernel of the Unix operating system. During the 1980s, C gradually gained popularity. It has become one of the measuring programming language popularity, most widely used programming languages, with C compilers avail ...
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Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ...
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OS X
macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and laptop computers it is the second most widely used desktop OS, after Microsoft Windows and ahead of ChromeOS. macOS succeeded the classic Mac OS, a Mac operating system with nine releases from 1984 to 1999. During this time, Apple cofounder Steve Jobs had left Apple and started another company, NeXT, developing the NeXTSTEP platform that would later be acquired by Apple to form the basis of macOS. The first desktop version, Mac OS X 10.0, was released in March 2001, with its first update, 10.1, arriving later that year. All releases from Mac OS X 10.5 Leopard and after are UNIX 03 certified, with an exception for OS X 10.7 Lion. Apple's other operating systems ( iOS, iPadOS, watchOS, tvOS, audioOS) are derivatives of macOS. A p ...
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Image Processing
An image is a visual representation of something. It can be two-dimensional, three-dimensional, or somehow otherwise feed into the visual system to convey information. An image can be an artifact, such as a photograph or other two-dimensional picture, that resembles a subject. In the context of signal processing, an image is a distributed amplitude of color(s). In optics, the term “image” may refer specifically to a 2D image. An image does not have to use the entire visual system to be a visual representation. A popular example of this is of a greyscale image, which uses the visual system's sensitivity to brightness across all wavelengths, without taking into account different colors. A black and white visual representation of something is still an image, even though it does not make full use of the visual system's capabilities. Images are typically still, but in some cases can be moving or animated. Characteristics Images may be two or three- dimensional, such as a ...
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BSD-new
BSD licenses are a family of permissive free software licenses, imposing minimal restrictions on the use and distribution of covered software. This is in contrast to copyleft licenses, which have share-alike requirements. The original BSD license was used for its namesake, the Berkeley Software Distribution (BSD), a Unix-like operating system. The original version has since been revised, and its descendants are referred to as modified BSD licenses. BSD is both a license and a class of license (generally referred to as BSD-like). The modified BSD license (in wide use today) is very similar to the license originally used for the BSD version of Unix. The BSD license is a simple license that merely requires that all code retain the BSD license notice if redistributed in source code format, or reproduce the notice if redistributed in binary format. The BSD license (unlike some other licenses e.g. GPL) does not require that source code be distributed at all. Terms In addition to ...
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Tomography
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. In many cases, the production of these images is based on the mathematical procedure tomographic reconstruction, such as X-ray computed tomography technically being produced from multiple projectional radiographs. Many different reconstruction algorithms exist. Most algorithms fall into one of two categories: filtered back projection (FBP) and iterative reconstruction (IR). These procedures give inexact results: ...
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X-ray Computed Tomography
X-rays (or rarely, ''X-radiation'') are a form of high-energy electromagnetic radiation. In many languages, it is referred to as Röntgen radiation, after the German scientist Wilhelm Conrad Röntgen, who discovered it in 1895 and named it ''X-radiation'' to signify an unknown type of radiation.Novelline, Robert (1997). ''Squire's Fundamentals of Radiology''. Harvard University Press. 5th edition. . X-ray wavelengths are shorter than those of ultraviolet rays and longer than those of gamma rays. There is no universally accepted, strict definition of the bounds of the X-ray band. Roughly, X-rays have a wavelength ranging from 10  nanometers to 10  picometers, corresponding to frequencies in the range of 30  petahertz to 30  exahertz ( to ) and photon energies in the range of 100  eV to 100  keV, respectively. X-rays can penetrate many solid substances such as construction materials and living tissue, so X-ray radiography is widely used in medica ...
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Beamline
In accelerator physics, a beamline refers to the trajectory of the beam of particles, including the overall construction of the path segment (guide tubes, diagnostic devices) along a specific path of an accelerator facility. This part is either * the line in a linear accelerator along which a beam of particles travels, or * the path leading from particle generator (e.g. a cyclic accelerator, synchrotron light sources, cyclotrons, or spallation sources) to the experimental end-station. Beamlines usually end in experimental stations that utilize particle beams or synchrotron light obtained from a synchrotron, or neutrons from a spallation source or research reactor. Beamlines are used in experiments in particle physics, materials science, life science, chemistry, and molecular biology, but can also be used for irradiation tests or to produce isotopes. Beamline in a particle accelerator In particle accelerators the beamline is usually housed in a tunnel and/or unde ...
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Data Processing
Data processing is the collection and manipulation of digital data to produce meaningful information. Data processing is a form of '' information processing'', which is the modification (processing) of information in any manner detectable by an observer.Data processing is distinct from ''word processing'', which is manipulation of text specifically rather than data generally. The term "Data Processing", or "DP" has also been used to refer to a department within an organization responsible for the operation of data processing programs. Data processing functions Data processing may involve various processes, including: * Validation – Ensuring that supplied data is correct and relevant. * Sorting – "arranging items in some sequence and/or in different sets." * Summarization(statistical) or (automatic) – reducing detailed data to its main points. * Aggregation – combining multiple pieces of data. * Analysis – the "collection, organization, ...
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