Iterative reconstruction

Iterative reconstruction

Iterative reconstruction refers to iterative algorithms used to reconstruct 2D and 3D images in certain imaging techniques. For example, in computed tomography an image must be reconstructed from projections of an object. Here, iterative reconstruction techniques are usually a better, but computationally more expensive alternative to the common filtered back projection (FBP) method, which directly calculates the image in a single reconstruction step. In recent research works, scientists have shown that extremely fast computations and massive parallelism is possible for iterative reconstruction, which makes iterative reconstruction practical for commercialization. == Basic concepts == The reconstruction of an image from the acquired data is an inverse problem. Often, it is not possible to exactly solve the inverse problem directly. In this case, a direct algorithm has to approximate the solution, which might cause visible reconstruction artifacts in the image. Iterative algorithms approach the correct solution using multiple iteration steps, which allows to obtain a better reconstruction at the cost of a higher computation time. There are a large variety of algorithms, but each starts with an assumed image, computes projections from the image, compares the original projection data and updates the image based upon the difference between the calculated and the actual projections. === Algebraic reconstruction === The Algebraic Reconstruction Technique (ART) was the first iterative reconstruction technique used for computed tomography by Hounsfield. === Iterative Sparse Asymptotic Minimum Variance === The iterative sparse asymptotic minimum variance algorithm is an iterative, parameter-free superresolution tomographic reconstruction method inspired by compressed sensing, with applications in synthetic-aperture radar, computed tomography scan, and magnetic resonance imaging (MRI). === Statistical reconstruction === There are typically five components to statistical iterative image reconstruction algorithms, e.g. An object model that expresses the unknown continuous-space function f ( r ) {\displaystyle f(r)} that is to be reconstructed in terms of a finite series with unknown coefficients that must be estimated from the data. A system model that relates the unknown object to the "ideal" measurements that would be recorded in the absence of measurement noise. Often this is a linear model of the form A x + ϵ {\displaystyle \mathbf {A} x+\epsilon } , where ϵ {\displaystyle \epsilon } represents the noise. A statistical model that describes how the noisy measurements vary around their ideal values. Often Gaussian noise or Poisson statistics are assumed. Because Poisson statistics are closer to reality, it is more widely used. A cost function that is to be minimized to estimate the image coefficient vector. Often this cost function includes some form of regularization. Sometimes the regularization is based on Markov random fields. An algorithm, usually iterative, for minimizing the cost function, including some initial estimate of the image and some stopping criterion for terminating the iterations. === Learned Iterative Reconstruction === In learned iterative reconstruction, the updating algorithm is learned from training data using techniques from machine learning such as convolutional neural networks, while still incorporating the image formation model. This typically gives faster and higher quality reconstructions and has been applied to CT and MRI reconstruction. == Advantages == The advantages of the iterative approach include improved insensitivity to noise and capability of reconstructing an optimal image in the case of incomplete data. The method has been applied in emission tomography modalities like SPECT and PET, where there is significant attenuation along ray paths and noise statistics are relatively poor. Statistical, likelihood-based approaches: Statistical, likelihood-based iterative expectation-maximization algorithms are now the preferred method of reconstruction. Such algorithms compute estimates of the likely distribution of annihilation events that led to the measured data, based on statistical principle, often providing better noise profiles and resistance to the streak artifacts common with FBP. Since the density of radioactive tracer is a function in a function space, therefore of extremely high-dimensions, methods which regularize the maximum-likelihood solution turning it towards penalized or maximum a-posteriori methods can have significant advantages for low counts. Examples such as Ulf Grenander's Sieve estimator or Bayes penalty methods, or via I.J. Good's roughness method may yield superior performance to expectation-maximization-based methods which involve a Poisson likelihood function only. As another example, it is considered superior when one does not have a large set of projections available, when the projections are not distributed uniformly in angle, or when the projections are sparse or missing at certain orientations. These scenarios may occur in intraoperative CT, in cardiac CT, or when metal artifacts require the exclusion of some portions of the projection data. In Magnetic Resonance Imaging it can be used to reconstruct images from data acquired with multiple receive coils and with sampling patterns different from the conventional Cartesian grid and allows the use of improved regularization techniques (e.g. total variation) or an extended modeling of physical processes to improve the reconstruction. For example, with iterative algorithms it is possible to reconstruct images from data acquired in a very short time as required for real-time MRI (rt-MRI). In Cryo Electron Tomography, where the limited number of projections are acquired due to the hardware limitations and to avoid the biological specimen damage, it can be used along with compressive sensing techniques or regularization functions (e.g. Huber function) to improve the reconstruction for better interpretation. Here is an example that illustrates the benefits of iterative image reconstruction for cardiac MRI.

InstallCore

InstallCore (stylized as installCore) was an installation and content distribution platform created by ironSource, considered potentially unwanted programs (PUP) by a number of anti-malware vendors. It included a software development kit (SDK) for Windows and Mac OS X. The program allowed those using it for distribution to include monetization by advertisements or charging for installation, and made its installations invisible to the user and its anti-virus software. The platform and its programs have been rated potentially unwanted programs (PUP) or potentially unwanted applications (PUA) by anti-malware product vendors since 2014, and by Windows Defender Antivirus since 2015. The platform was primarily designed for efficient web-based deployment of various types of application software. As of August 2012, InstallCore was managing 100 million installations every month, offering services for paid, unpaid, and free software by using the SDK version. == History == The InstallCore team introduced the first version of the SDK at the beginning of 2011. The SDK was a fork of the FoxTab installer and had only basic Installation features. InstallCore was discontinued as part of a company flotation in late 2020. == Criticism and malware classification == InstallCore and its software packages have been classified as potentially unwanted programs (PUP) or potentially unwanted applications (PUA), by anti-malware product vendors and Windows Defender Antivirus from 2014–2015 onwards, with many stating that it installs adware and other additional PUPs. Malwarebytes identified the program as "a family of bundlers that installs more than one application on the user's computer". It has been described as "crossing the line into full-blown malware" and a "nasty Trojan".

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Markov chain geostatistics

Markov chain geostatistics uses Markov chain spatial models, simulation algorithms and associated spatial correlation measures (e.g., transiogram) based on the Markov chain random field theory, which extends a single Markov chain into a multi-dimensional random field for geostatistical modeling. A Markov chain random field is still a single spatial Markov chain. The spatial Markov chain moves or jumps in a space and decides its state at any unobserved location through interactions with its nearest known neighbors in different directions. The data interaction process can be well explained as a local sequential Bayesian updating process within a neighborhood. Because single-step transition probability matrices are difficult to estimate from sparse sample data and are impractical in representing the complex spatial heterogeneity of states, the transiogram, which is defined as a transition probability function over the distance lag, is proposed as the accompanying spatial measure of Markov chain random fields.

Corinna Cortes

Corinna Cortes (born 31 March 1961) is a Danish computer scientist known for her contributions to machine learning. She is a Vice President at Google Research in New York City. Cortes is an ACM Fellow and a recipient of the Paris Kanellakis Award for her work on theoretical foundations of support vector machines. == Early life and education == Corinna Cortes was born in 1961 in Denmark. Cortes received her Master of Science degree in physics from University of Copenhagen in 1989. She received her PhD in computer science from the University of Rochester in 1993 for research supervised by Randal C. Nelson. == Career and research == Cortes joined AT&T Bell Labs as a researcher in 1993. Since 2003, she has served as Vice President of Google Research, New York City, and since 2011, as adjunct professor at the UCPH Department of Computer Science. She is serves as an editorial board member of the journal Machine Learning. Cortes' research covers a wide range of topics in machine learning, including support vector machines (SVM) and data mining. SVM is one of the most frequently used algorithms in machine learning, which is used in many practical applications, including medical diagnosis and weather forecasting. At AT&T, Cortes was a contributor to the design of Hancock programming language. === Awards and honours === In 2008, she jointly with Vladimir Vapnik received the Paris Kanellakis Award for the development of a highly effective algorithm for supervised learning known as support vector machines (SVM). She was named an ACM Fellow in 2023 for theoretical and practical contributions to machine learning, industrial leadership and service to the field. == Personal life == Corinna has two children and is also a competitive runner.

Qlone

Qlone is a 3D scanning app based on photogrammetry for creation of 3D models on mobile devices. The resultant 3D models can be exported for external use. Qlone was featured at the Apple Worldwide Developers Conference in 2021. It was also featured on BBC Click. == Qlone features == === 3D scanning === 3D scanning with Qlone requires the use of an included mat design. The user prints the mat onto a sheet of paper, then places the object to be scanned in the centre of the mat. An augmented reality dome within the Qlone app guides the user through the subsequent scanning process. The iOS version of Qlone allows scanning without the mat. === 3D editing === Qlone's editing features allow users to adjust 3D scanned models using texture mapping, polygon mesh size simplification, digital sculpting, cleaning and smoothing, and artistic effects. === File export === Qlone exports directly to multiple 3D platforms including SketchFab, i.materialise, Lens Studio for Snapchat, Shapeways and CGTrader. Models can also be exported in different 3D formats for use in other 3D tools – OBJ, STL, FBX, USDZ, GLB (Binary gLTF), PLY, and X3D. == Use in Science, Education and Academia == Due to its inexpensive, simple and accessible nature for creating 3D models, Qlone was used in many academically educational and scientific research projects. The European Space Agency used Qlone to scan rocks in a Tele-Robotic rock collection experiment. Neurosurgeons from the University of Southern California and surgeons from Tulane University School of Medicine used Qlone to create 3D models of cadaveric specimens and anatomical models with the aim of increasing access to such components for enhancing anatomy training and allowing realistic surgical simulations for neurosurgeons and practitioners worldwide. Archaeologists from Texas A&M University used Qlone to create 3D replicas of artifacts and models and students from Vancouver iTech Preparatory Middle School used Qlone to create 3D scans of more than 100 artifacts from Fort Vancouver National Historic Site.

Apache cTAKES

Apache cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source Natural Language Processing (NLP) system that extracts clinical information from electronic health record unstructured text. It processes clinical notes, identifying types of clinical named entities — drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity has attributes for the text span, the ontology mapping code, context (family history of, current, unrelated to patient), and negated/not negated. cTAKES was built using the UIMA Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. == Components == Components of cTAKES are specifically trained for the clinical domain, and create rich linguistic and semantic annotations that can be utilized by clinical decision support systems and clinical research. These components include: Named Section identifier Sentence boundary detector Rule-based tokenizer Formatted list identifier Normalizer Context dependent tokenizer Part-of-speech tagger Phrasal chunker Dictionary lookup annotator Context annotator Negation detector Uncertainty detector Subject detector Dependency parser patient smoking status identifier Drug mention annotator == History == Development of cTAKES began at the Mayo Clinic in 2006. The development team, led by Dr. Guergana Savova and Dr. Christopher Chute, included physicians, computer scientists and software engineers. After its deployment, cTAKES became an integral part of Mayo's clinical data management infrastructure, processing more than 80 million clinical notes. When Dr. Savova's moved to Boston Children's Hospital in early 2010, the core development team grew to include members there. Further external collaborations include: University of Colorado Brandeis University University of Pittsburgh University of California at San Diego Such collaborations have extended cTAKES' capabilities into other areas such as Temporal Reasoning, Clinical Question Answering, and coreference resolution for the clinical domain. In 2010, cTAKES was adopted by the i2b2 program and is a central component of the SHARP Area 4. In 2013, cTAKES released their first release as an Apache Software Foundation incubator project: cTAKES 3.0. In March 2013, cTAKES became an Apache Software Foundation Top Level Project (TLP).