Amira (pronounce: Ah-meer-ah) is a software platform for 3D and 4D data visualization, processing, and analysis. It is being actively developed by

Thermo Fisher Scientific Thermo Fisher Scientific Inc. is an American supplier of scientific instrumentation, reagents and consumables, and software services. Based in Waltham, Massachusetts, Thermo Fisher was formed through the merger of Thermo Electron and Fisher S ...

in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by

Overview

Amira is an extendable software system for

scientific visualization Scientific visualization ( also spelled scientific visualisation) is an interdisciplinary branch of science concerned with the visualization of scientific phenomena.Michael Friendly (2008)"Milestones in the history of thematic cartography, stat ...

data analysis Data analysis is a process of inspecting, cleansing, transforming, and modeling data with the goal of discovering useful information, informing conclusions, and supporting decision-making. Data analysis has multiple facets and approaches, enco ...

, and presentation of 3D and 4D data. It is used by thousands of researchers and engineers in academia and industry around the world. Its flexible user interface and modular architecture make it a universal tool for processing and analysis of data from various modalities; e.g.

micro-CT X-ray microtomography, like tomography and X-ray computed tomography, uses X-rays to create cross-sections of a physical object that can be used to recreate a virtual model (3D model) without destroying the original object. The prefix ''micro-'' ...

PET A pet, or companion animal, is an animal kept primarily for a person's company or entertainment rather than as a working animal, livestock, or a laboratory animal. Popular pets are often considered to have attractive appearances, intelligence, ...

Ultrasound Ultrasound is sound waves with frequency, frequencies higher than the upper audible limit of human hearing range, hearing. Ultrasound is not different from "normal" (audible) sound in its physical properties, except that humans cannot hea ...

. Its ever-expanding functionality has made it a versatile data analysis and visualization solution, applicable to and being used in many fields, such as

microscopy Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of micr ...

biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary i ...

and materials science,

molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...

quantum physics Quantum mechanics is a fundamental theory in physics that provides a description of the physical properties of nature at the scale of atoms and subatomic particles. It is the foundation of all quantum physics including quantum chemistry, qua ...

astrophysics Astrophysics is a science that employs the methods and principles of physics and chemistry in the study of astronomical objects and phenomena. As one of the founders of the discipline said, Astrophysics "seeks to ascertain the nature of the h ...

, 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 In digital image processing and computer vision, image segmentation is the process of partitioning a digital image into multiple image segments, also known as image regions or image objects ( sets of pixels). The goal of segmentation is to simpl ...

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 Visualization or visualisation may refer to: *Visualization (graphics), the physical or imagining creation of images, diagrams, or animations to communicate a message * Data visualization, the graphic representation of data * Information visualiz ...

numerical simulation Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be deter ...

s, or

rapid prototyping Rapid prototyping is a group of techniques used to quickly fabricate a scale model of a physical part or assembly using three-dimensional computer aided design (CAD) data. Construction of the part or assembly is usually done using 3D printin ...

3D printing 3D printing or additive manufacturing is the Manufacturing, construction of a three-dimensional object from a computer-aided design, CAD model or a digital 3D modeling, 3D model. It can be done in a variety of processes in which material is ...

, to name a few. Other key Amira features are multi-planar and

volume Volume is a measure of occupied three-dimensional space. It is often quantified numerically using SI derived units (such as the cubic metre and litre) or by various imperial or US customary units (such as the gallon, quart, cubic inch). The de ...

visualization,

image registration Image registration is the process of transforming different sets of data into one coordinate system. Data may be multiple photographs, data from different sensors, times, depths, or viewpoints. It is used in computer vision, medical imaging, milit ...

, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data,

skeletonization Skeletonization is the state of a dead organism after undergoing decomposition.The Australian Museum. (2018). Decomposition-Body Changes. Retrieved from: https://australianmuseum.net.au/about/history/exhibitions/death-the-last-taboo/decomposit ...

, spatial graph analysis, and

stereoscopic Stereoscopy (also called stereoscopics, or stereo imaging) is a technique for creating or enhancing the depth perception, illusion of depth in an image by means of stereopsis for binocular vision. The word ''stereoscopy'' derives . Any stere ...

rendering of 3D data over multiple displays and immersive virtual reality environments, including

CAVEs A cave or cavern is a natural void in the ground, specifically a space large enough for a human to enter. Caves often form by the weathering of rock and often extend deep underground. The word ''cave'' can refer to smaller openings such as sea ...

. 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 Mathematics is an area of knowledge that includes the topics of numbers, formulas and related structures, shapes and the spaces in which they are contained, and quantities and their changes. These topics are represented in modern mathematics ...

and

informatics Informatics is the study of computational systems, especially those for data storage and retrieval. According to ACM ''Europe and'' ''Informatics Europe'', informatics is synonymous with computer science and computing as a profession, in which ...

. The Scientific Visualization department’s mission is to help solve computationally and scientifically challenging tasks in

medicine Medicine is the science and practice of caring for a patient, managing the diagnosis, prognosis, prevention, treatment, palliation of their injury or disease, and promoting their health. Medicine encompasses a variety of health care pract ...

engineering Engineering is the use of scientific method, scientific principles to design and build machines, structures, and other items, including bridges, tunnels, roads, vehicles, and buildings. The discipline of engineering encompasses a broad rang ...

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

environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products’

interactivity Across the many fields concerned with interactivity, including information science, computer science, human-computer interaction, communication, and industrial design, there is little agreement over the meaning of the term "interactivity", but m ...

, 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 Open Inventor, originally IRIS Inventor, is a C++ object-oriented retained mode 3D graphics toolkit designed by SGI to provide a higher layer of programming for OpenGL. Its main goals are better programmer convenience and efficiency. Open Inven ...

, 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 OpenGL (Open Graphics Library) is a cross-language, cross-platform application programming interface (API) for rendering 2D and 3D vector graphics. The API is typically used to interact with a graphics processing unit (GPU), to achieve hardwa ...

(originally

IRIS GL IRIS GL (Integrated Raster Imaging System Graphics Library) is a proprietary graphics API created by Silicon Graphics (SGI) in the early 1980s for producing 2D and 3D computer graphics on their IRIX-based IRIS graphical workstations. Later SGI rem ...

Open Inventor Open Inventor, originally IRIS Inventor, is a C++ object-oriented retained mode 3D graphics toolkit designed by SGI to provide a higher layer of programming for OpenGL. Its main goals are better programmer convenience and efficiency. Open Invent ...

(originally

), and the

graphical user interface The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicator such as primary notation, inste ...

libraries

X11 The X Window System (X11, or simply X) is a windowing system for bitmap displays, common on Unix-like operating systems. X provides the basic framework for a GUI environment: drawing and moving windows on the display device and interacting wi ...

Motif (software) In computing, Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and Unix-like operating systems. The Motif look a ...

, and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the

Qt toolkit Qt (pronounced "cute") is cross-platform software for creating graphical user interfaces as well as cross-platform applications that run on various software and hardware platforms such as Linux, Windows, macOS, Android or embedded systems wit ...

. 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 Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions and disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular biology, development ...

confocal microscopy Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser confocal scanning microscopy (LCSM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a sp ...

flow visualization Flow visualization or flow visualisation in fluid dynamics is used to make the flow patterns visible, in order to get qualitative or quantitative information on them. Overview Flow visualization is the art of making flow patterns visible. ...

, molecular analytics and

computational astrophysics Computational astrophysics refers to the methods and computing tools developed and used in astrophysics research. Like computational chemistry or computational physics, it is both a specific branch of theoretical astrophysics and an interdiscip ...

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 Latin (, or , ) is a classical language belonging to the Italic branch of the Indo-European languages. Latin was originally a dialect spoken in the lower Tiber area (then known as Latium) around present-day Rome, but through the power of the ...

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 CeBIT was the largest and most internationally representative computer expo. The trade fair was held each year on the Hanover fairground, the world's largest fairground, in Hanover, Germany. In its day, it was considered a barometer of cur ...

tradeshow in

Hannover Hanover (; german: Hannover ; nds, Hannober) is the capital and largest city of the German States of Germany, state of Lower Saxony. Its 535,932 (2021) inhabitants make it the List of cities in Germany by population, 13th-largest city in Germa ...

, Germany on SGI

IRIX IRIX ( ) is a discontinued operating system developed by Silicon Graphics (SGI) to run on the company's proprietary MIPS workstations and servers. It is based on UNIX System V with BSD extensions. In IRIX, SGI originated the XFS file system and ...

and Hewlett-Packard UniX (HP-UX) booths. Versions for

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 ...

and

Microsoft Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the

Bordeaux Bordeaux ( , ; Gascon oc, Bordèu ; eu, Bordele; it, Bordò; es, Burdeos) is a port city on the river Garonne in the Gironde department, Southwestern France. It is the capital of the Nouvelle-Aquitaine region, as well as the prefectur ...

, France and

San Diego San Diego ( , ; ) is a city on the Pacific Ocean coast of Southern California located immediately adjacent to the Mexico–United States border. With a 2020 population of 1,386,932, it is the List of United States cities by population, eigh ...

, 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 This list of life sciences comprises the branches of science that involve the scientific study of life – such as microorganisms, plants, and animals including human beings. This science is one of the two major branches of natural science, the ...

business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to

Melbourne Melbourne ( ; Boonwurrung/Woiwurrung: ''Narrm'' or ''Naarm'') is the capital and most populous city of the Australian state of Victoria, and the second-most populous city in both Australia and Oceania. Its name generally refers to a met ...

, 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 Berlin ( , ) is the capital and largest city of Germany by both area and population. Its 3.7 million inhabitants make it the European Union's most populous city, according to population within city limits. One of Germany's sixteen constitue ...

, 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

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 Cerebral circulation is the movement of blood through a network of cerebral arteries and veins supplying the brain. The rate of cerebral blood flow in an adult human is typically 750 milliliters per minute, or about 15% of cardiac output. Arterie ...

, and cerebral blood volume

VR option

*Visualization of data on large tiled displays or in immersive Virtual Reality (VR) environments *Support of 3D navigation devices *Fast multi-threaded and distributed rendering

Very large data option

*Support for visualization of image data exceeding the available main memory, using efficient out-of-core data management *Extensions of many standard modules, such as orthogonal and oblique slicing, volume rendering, and isosurface rendering, to work on out-of-core data

Application areas

Anatomy Anatomy () is the branch of biology concerned with the study of the structure of organisms and their parts. Anatomy is a branch of natural science that deals with the structural organization of living things. It is an old science, having its ...

Biochemistry Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology and ...

Biophysics Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. ...

Cellular microbiology Cellular microbiology is a discipline that bridges microbiology and cell biology. The term "cellular microbiology" was coined by the authors of the book of the same title published in 1996. Cooperation and mutual dependency between microbiology ...

Computational fluid dynamics Computational fluid dynamics (CFD) is a branch of fluid mechanics that uses numerical analysis and data structures to analyze and solve problems that involve fluid flows. Computers are used to perform the calculations required to simulate th ...

Cryo-electron tomography Electron cryotomography (CryoET) is an imaging technique used to produce high-resolution (~1–4 nm) three-dimensional views of samples, often (but not limited to) biological macromolecules and cells. CryoET is a specialized application of t ...

Diffusion MRI Diffusion-weighted magnetic resonance imaging (DWI or DW-MRI) is the use of specific MRI sequences as well as software that generates images from the resulting data that uses the diffusion of water molecules to generate contrast in MR images. It ...

Tractography In neuroscience Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions and disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular b ...

Embryology Embryology (from Greek ἔμβρυον, ''embryon'', "the unborn, embryo"; and -λογία, '' -logia'') is the branch of animal biology that studies the prenatal development of gametes (sex cells), fertilization, and development of embryos and ...

Endocrinology Endocrinology (from '' endocrine'' + '' -ology'') is a branch of biology and medicine dealing with the endocrine system, its diseases, and its specific secretions known as hormones. It is also concerned with the integration of developmental event ...

* Finite Element Modelling *

Histology Histology, also known as microscopic anatomy or microanatomy, is the branch of biology which studies the microscopic anatomy of biological tissues. Histology is the microscopic counterpart to gross anatomy, which looks at larger structures vis ...

* Materials science *

Medical imaging Medical imaging is the technique and process of imaging the interior of a body for clinical analysis and medical intervention, as well as visual representation of the function of some organs or tissues (physiology). Medical imaging seeks to rev ...

Microscopy Microscopy is the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of micr ...

in life and materials sciences *

Molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...

Neuroscience Neuroscience is the scientific study of the nervous system (the brain, spinal cord, and peripheral nervous system), its functions and disorders. It is a multidisciplinary science that combines physiology, anatomy, molecular biology, development ...

Orthopedics Orthopedic surgery or orthopedics ( alternatively spelt orthopaedics), is the branch of surgery concerned with conditions involving the musculoskeletal system. Orthopedic surgeons use both surgical and nonsurgical means to treat musculoskeletal ...

Otolaryngology Otorhinolaryngology ( , abbreviated ORL and also known as otolaryngology, otolaryngology–head and neck surgery (ORL–H&N or OHNS), or ear, nose, and throat (ENT)) is a surgical subspeciality within medicine that deals with the surgical a ...

Preclinical imaging Preclinical imaging is the visualization of living animals for research purposes, such as drug development. Imaging modalities have long been crucial to the researcher in observing changes, either at the organ, tissue, cell, or molecular level, i ...

Urology Urology (from Greek οὖρον ''ouron'' "urine" and '' -logia'' "study of"), also known as genitourinary surgery, is the branch of medicine that focuses on surgical and medical diseases of the urinary-tract system and the reproductive org ...

References

External links

Official Website

Use Case Gallery

{{Image Processing Software 3D graphics software 3D imaging Computer vision software Data visualization software Graphics software Image processing software Image segmentation Medical software Mesh generators Science software Software that uses Qt Virtual reality