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 in collaboration with the
Zuse Institute Berlin (ZIB), and commercially distributed by
Thermo Fisher Scientific.
Overview
Amira is an extendable software system for
scientific visualization,
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, enc ...
, 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.
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 mic ...
in
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 ...
and
materials science,
molecular biology,
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, q ...
,
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 he ...
,
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 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 dete ...
s, or
rapid prototyping or
3D printing
3D printing or additive manufacturing is the construction of a three-dimensional object from a CAD model or a digital 3D model. It can be done in a variety of processes in which material is deposited, joined or solidified under computer ...
, to name a few.
Other key Amira features are
multi-planar and
volume 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 illusion of depth in an image by means of stereopsis for binocular vision. The word ''stereoscopy'' derives . Any stereoscopic image is ...
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 and
informatics. The Scientific Visualization department’s mission is to help solve computationally and scientifically challenging tasks in
medicine,
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 ...
,
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
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 mo ...
, 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
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 re ...
),
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 Inve ...
(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
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 wi ...
.
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, developme ...
,
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 ...
,
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 interdiscipli ...
.
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
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 c ...
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
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 prefecture ...
, 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
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. Arter ...
, 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 it ...
*
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 a ...
*
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 the ...
*
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 tra ...
*
Diffusion MRI/
Tractography
*
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 an ...
*
Endocrinology
*
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 mic ...
in life and materials sciences
*
Molecular biology
*
Neuroscience
*
Orthopedics
*
Otolaryngology
*
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
References
External links
Official WebsiteUse Case Gallery
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