Amira (software)

Amira (ah-MEER-ah) 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. == Overview == Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. It is used by researchers and engineers in academia and industry. It is a tool for processing, analysis and visualization of data from various modalities; e.g. micro-CT, PET, Ultrasound. It is used in many fields, such as microscopy in biology and materials science, molecular biology, quantum physics, astrophysics, computational fluid dynamics (CFD), finite element modeling (FEM), non-destructive testing (NDT), and many more. One of the key features, besides data visualization, is Amira's set of tools for image segmentation and geometry reconstruction. This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis, density analysis, shape analysis, or the generation of 3D computer models for visualization, numerical simulations, or rapid prototyping or 3D printing. Other key Amira features are multi-planar and volume visualization, image registration, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data, skeletonization, spatial graph analysis, and stereoscopic rendering of 3D data over multiple displays and immersive virtual reality environments, including CAVEs. As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge. == History == === 1993–1998: Research software === Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department's mission is to help solve computationally and scientifically challenging tasks in medicine, biology, engineering and materials science. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products' interactivity, flexibility, and ease-of-use for non-computer scientists. Therefore, the development of a new software system was started in a research project within a medically oriented, multi-disciplinary collaborative research center. Based on experiences that Tobias Höllerer had gained in late 1993 with the new graphics library IRIS Inventor, it was decided to utilize that library. The development of the medical planning system was performed by Detlev Stalling, who later became the chief software architect of Amira. The new software was called "HyperPlan", highlighting its initial target application – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. The software was based on libraries such as OpenGL (originally IRIS GL), Open Inventor (originally IRIS Inventor), and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit. The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in medical image computing, medical visualization, neurobiology, confocal microscopy, flow visualization, molecular analytics and computational astrophysics. === 1998–today: Commercially supported product === The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB's primary mission was algorithmic research. Therefore, the spin-off company Indeed – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff. In Feb 1998 the HyperPlan software was given the new, application-neutral name "Amira". This name is not an acronym, but was chosen for being pronounceable in different languages and providing a suitable connotation, namely "to look at" or "to wonder at", from the Latin verb "admirare" (to admire), which reflects a basic situation in data visualization. A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths. Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years. In 2003 both Indeed – Visual Concepts GmbH, as well as TGS, Inc. were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury's newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences. In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. This brought the two software sisters Amira and Avizo back into one hand. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. In 2016 FEI has been bought by Thermo Fisher Scientific and became part of its Materials & Structural Analysis division in early 2017. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. In the meantime, the number of scientific articles using the Amira / Avizo software, is in the order of 10 thousands. == Amira options == === Microscopy option === Specific readers for microscopy data Image deconvolution Exploration of 3D imagery obtained from virtually any microscope Extraction and editing of filament networks from microscopy images === DICOM reader === Import of clinical and preclinical data in DICOM format === Mesh option === Generation of 3D finite element (FE) meshes from segmented image data Support for many state-of-the-art FE solver formats High-quality visualization of simulation mesh-based results, using scalar, vector, and tensor field display modules === Skeletonization option === Reconstruction and analysis of neural and vascular networks Visualization of skeletonized networks Length and diameter quantification of network segments Ordering of segments in a tree graph Skeletonization of very large image stacks === Molecular option === Advanced tools for the visualization of molecule models Hardware-accelerated volume rendering Powerful molecule editor Specific tools for complex molecular visualization === Developer option === Creation of new custom components for visualizing or data processing Implementation of new file readers or writers C++ programming language Development wizard for getting started quickly === Neuro option === Medical image analysis for DTI and brain perfusion Fiber tracking supporting several stream-line based algorithms Fiber separation into fiber bundles based on user defined source and destination regions Computation of tensor fields, diffusion weighted maps Eigenvalue decomposition of tensor fields Computation of mean transit time, cerebral blood flow, and cerebral blood volume === VR option === Visualization of data on large tiled displays

Sample (graphics)

In computer graphics, a sample is an intersection of a channel and a pixel. The diagram below depicts a 24-bit pixel, consisting of 3 samples for Red, Green, and Blue. In this particular diagram, the Red sample occupies 9 bits, the Green sample occupies 7 bits and the Blue sample occupies 8 bits, totaling 24 bits per pixel. Note that the samples do not have to be equal size and not all samples are mandatory in a pixel. Also, a pixel can consist of more than 3 samples (e.g. 4 samples of the RGBA color space). A sample is related to a subpixel on a physical display.

International Medical Education Directory

The International Medical Education Directory (IMED) was a public database of worldwide medical schools. The IMED was published as a joint collaboration of the Educational Commission for Foreign Medical Graduates (ECFMG) and the Foundation for Advancement of International Medical Education and Research (FAIMER). The information available in IMED was derived from data collected by the Educational Commission for Foreign Medical Graduates (ECFMG) throughout its history of evaluating the medical education credentials of international medical graduates. Using these data as a starting point, Foundation for Advancement of International Medical Education and Research (FAIMER) began developing IMED in 2001 and made it publicly available in April 2002. In April 2014, IMED was merged with the Avicenna Directory to create the World Directory of Medical Schools. The World Directory is now the definitive list of medical schools in the world, as IMED and Avicenna were discontinued in 2015.

Data commingling

Data commingling, in computer science, occurs when different items or kinds of data are stored in such a way that they become commonly accessible when they are supposed to remain separated. In cloud computing, this can occur where different customer data sits on the same server. Data that is commingled can present a security vulnerability. Data commingling can also occur due to high speed data transmission mixing. In this situation, data of one security level can inadvertently or purposely be mixed with data of a lower or higher security level on the same transmission portal. Portal vehicles can be wire, fiber optics, microwave or various radio frequency transmission portals. This commingling can cause breaches of security and become a source of legal issues to any entity, corporation or individual. Data commingling can also occur when personal computers and personal software programs are used for business, security, government, etc. uses. In the early formulation stages of entities, non-profit or profit corporations, LLC's, LLP's, etc., the creation and use of stand-alone computers and stand-alone networks, "absolutely unconnected" to involved individuals, is the easiest, and safest way to prevent Data Commingling.

Lost Art-Database

The Lost Art-Datenbank is an online database published by the German Lost Art Foundation (Deutsches Zentrum Kulturgutverluste. It contains information on cultural objects looted from Jewish collectors or transferred due to Nazi persecution during the Nazi era. Until 2015, it was managed by the Koordinierungsstelle für Kulturgutverluste (Magdeburg Coordination Office). == Creation == Following the Washington Conference of 1998, and the commitments to provide more transparency regarding looted art, Germany launched the Lost Art Database in 2000 order to help Holocaust victims and their families track down artworks that had been looted from them or lost due to Nazi persecution. == Functionality == The Lost Art Database lists art and books and other cultural objects that were lost, seized, stolen or forceably sold during the Nazi era. The database is divided into search requests from victims' families, heirs or institutions and "found" reports from cultural institutions on items with unresolved provenance gaps from the Nazi periods. The section on reports of finds lists objects that are known to have been unlawfully seized or relocated as a result of the war. In addition, reports are published here on cultural objects for which an uncertain or incomplete provenance may indicate a possible unlawful seizure or war-related relocation. The publication of reports in the Lost Art Internet Database is carried out on behalf of and with the consent of the reporting persons and institutions. The responsibility for the content of the reports lies with these legal or natural persons. There have been controversies over which items should be included in the database. Lost Art is based on the Washington Principles adopted in 1998, which Germany has committed itself to implementing (Joint Declaration, 1999). The Lost Art Database is considered a key resource in the search for looted art and the victims of persecution. Every item in the Lost Art Database has an identifier, known as a Lost Art ID. Proveana is the linked research database. == Other lost art databases == Other countries have launched databases to help identify Nazi looted art. Each database has its own area of focus. The German Lost Art Database allows families or heirs to submit information. Other countries have databases that focus on looted artworks that have not been found or artworks that were repatriated to the national authorities after the defeat of the Nazis but were never returned to their original owners. Other databases have been created for stolen antiquities, looted art from colonial era, art stolen from Syria, Iraq, Ukraine, or from museums or collectors.

Confidential computing

Confidential computing is a security and privacy-enhancing computational technique focused on protecting data in use. Confidential computing can be used in conjunction with storage and network encryption, which protect data at rest and data in transit respectively. It is designed to address software, protocol, cryptographic, and basic physical and supply-chain attacks, although some critics have demonstrated architectural and side-channel attacks effective against the technology. The technology protects data in use by performing computations in a hardware-based trusted execution environment (TEE). Confidential data is released to the TEE only once it is assessed to be trustworthy. Different types of confidential computing define the level of data isolation used, whether virtual machine, application, or function, and the technology can be deployed in on-premise data centers, edge locations, or the public cloud. It is often compared with other privacy-enhancing computational techniques such as fully homomorphic encryption, secure multi-party computation, and Trusted Computing. Confidential computing is promoted by the Confidential Computing Consortium (CCC) industry group, whose membership includes major providers of the technology. == Properties == Trusted execution environments (TEEs) "prevent unauthorized access or modification of applications and data while they are in use, thereby increasing the security level of organizations that manage sensitive and regulated data". Trusted execution environments can be instantiated on a computer's processing components such as a central processing unit (CPU) or a graphics processing unit (GPU). In their various implementations, TEEs can provide different levels of isolation including virtual machine, individual application, or compute functions. Typically, data in use in a computer's compute components and memory exists in a decrypted state and can be vulnerable to examination or tampering by unauthorized software or administrators. According to the CCC, confidential computing protects data in use through a minimum of three properties: Data confidentiality: "Unauthorized entities cannot view data while it is in use within the TEE". Data integrity: "Unauthorized entities cannot add, remove, or alter data while it is in use within the TEE". Code integrity: "Unauthorized entities cannot add, remove, or alter code executing in the TEE". In addition to trusted execution environments, remote cryptographic attestation is an essential part of confidential computing. The attestation process assesses the trustworthiness of a system and helps ensure that confidential data is released to a TEE only after it presents verifiable evidence that it is genuine and operating with an acceptable security posture. It allows the verifying party to assess the trustworthiness of a confidential computing environment through an "authentic, accurate, and timely report about the software and data state" of that environment. "Hardware-based attestation schemes rely on a trusted hardware component and associated firmware to execute attestation routines in a secure environment". Without attestation, a compromised system could deceive others into trusting it, claim it is running certain software in a TEE, and potentially compromise the confidentiality or integrity of the data being processed or the integrity of the trusted code. == Technical approaches == Technical approaches to confidential computing may vary in which software, infrastructure and administrator elements are allowed to access confidential data. The "trust boundary," which circumscribes a trusted computing base (TCB), defines which elements have the potential to access confidential data, whether they are acting benignly or maliciously. Confidential computing implementations enforce the defined trust boundary at a specific level of data isolation. The three main types of confidential computing are: Virtual machine isolation Application isolation, also known as process isolation Function isolation, also known as library isolation Virtual machine isolation removes the elements controlled by the computer infrastructure or cloud provider, but allows potential data access by elements inside a virtual machine running on the infrastructure. Application or process isolation permits data access only by authorized software applications or processes. Function or library isolation is designed to permit data access only by authorized subroutines or modules within a larger application, blocking access by any other system element, including unauthorized code in the larger application. == Threat model == As confidential computing is concerned with the protection of data in use, only certain threat models can be addressed by this technique. Other types of attacks are better addressed by other privacy-enhancing technologies. === In scope === The following threat vectors are generally considered in scope for confidential computing: Software attacks: including attacks on the host’s software and firmware. This may include the operating system, hypervisor, BIOS, other software and workloads. Protocol attacks: including "attacks on protocols associated with attestation as well as workload and data transport". This includes vulnerabilities in the "provisioning or placement of the workload" or data that could cause a compromise. Cryptographic attacks: including "vulnerabilities found in ciphers and algorithms due to a number of factors, including mathematical breakthroughs, availability of computing power and new computing approaches such as quantum computing". The CCC notes several caveats in this threat vector, including relative difficulty of upgrading cryptographic algorithms in hardware and recommendations that software and firmware be kept up-to-date. A multi-faceted, defense-in-depth strategy is recommended as a best practice. Basic physical attacks: including cold boot attacks, bus and cache snooping and plugging attack devices into an existing port, such as a PCI Express slot or USB port. Basic upstream supply-chain attacks: including attacks that would compromise TEEs through changes such as added debugging ports. The degree and mechanism of protection against these threats varies with specific confidential computing implementations. === Out of scope === Threats generally defined as out of scope for confidential computing include: Sophisticated physical attacks: including physical attacks that "require long-term and/or invasive access to hardware" such as chip scraping techniques and electron microscope probes. Upstream hardware supply-chain attacks: including attacks on the CPU manufacturing process, CPU supply chain in key injection/generation during manufacture. Attacks on components of a host system that are not directly providing the capabilities of the trusted execution environment are also generally out-of-scope. Availability attacks: confidential computing is designed to protect the confidentiality and integrity of protected data and code. It does not address availability attacks such as Denial of Service or Distributed Denial of Service attacks. == Use cases == Confidential computing can be deployed in the public cloud, on-premise data centers, or distributed "edge" locations, including network nodes, branch offices, industrial systems and others. === Data privacy and security === Confidential computing protects the confidentiality and integrity of data and code from the infrastructure provider, unauthorized or malicious software and system administrators, and other cloud tenants, which may be a concern for organizations seeking control over sensitive or regulated data. The additional security capabilities offered by confidential computing can help accelerate the transition of more sensitive workloads to the cloud or edge locations. === Multi-party analytics === Confidential computing can enable multiple parties to engage in joint analysis using confidential or regulated data inside a TEE while preserving privacy and regulatory compliance. In this case, all parties benefit from the shared analysis, but no party's sensitive data or confidential code is exposed to the other parties or system host. Examples include multiple healthcare organizations contributing data to medical research, or multiple banks collaborating to identify financial fraud or money laundering. Oxford University researchers proposed the alternative paradigm called "Confidential Remote Computing" (CRC), which supports confidential operations in Trusted Execution Environments across endpoint computers considering multiple stakeholders as mutually distrustful data, algorithm and hardware providers. === Confidential generative AI === Confidential computing technologies can be applied to various stages of a generative AI deployments to help increase data or model privacy, security, and regulatory compliance. TEEs and remote attestation can protect the integrity of data during AI model training, keep

Mixed raster content

Mixed raster content (MRC) is a method for compressing images that contain both binary-compressible text and continuous-tone components, using image segmentation methods to improve the level of compression and the quality of the rendered image. By separating the image into components with different compressibility characteristics, the most efficient and accurate compression algorithm for each component can be applied. MRC-compressed images are typically packaged into a hybrid file format such as DjVu and sometimes PDF. This allows for multiple images, and the instructions to properly render and reassemble them, to be stored within a single file. Some image scanners optionally support MRC when scanning to PDF. A typical manual states that without MRC, the image is generated in a single process, with text and graphics not distinguished. With MRC, separate processes are used for text, graphics, and other elements, producing clearer graphics and sharper text, at the price of slightly slower processing. MRC is recommended to optimise the scanning of documents with harder-to-read text or lower-quality graphics. MRC can also reduce the size of the scanned file, though higher compression using JBIG2 can sometimes lead to character substitution errors in scanned documents. == File format == A form of MRC is defined by international standard bodies as ISO/IEC 16485, or ITU recommendation T.44 (accessible free of charge). It defines a file format with bilevel masks and two data layers in each "stripe" of the image. The mask can be encoded in ITU T.4, JBIG1, or JBIG2, while the images can be JPEG, JBIG1, or run-length encoded color. The format is loosely based on JPEG, with a APP13 segment registered for this purpose. It is not known whether this file format is actually used, as formats like DjVu and PDF have their own ways of defining layers and masks.