User:Cwietholt/Amira (Software) Draft

Amira (pronounce: Ah-meer-ah) is a software platform for 3D and 4D data visualization, processing, and analysis. It is being actively developed by Visage Imaging GmbH, Berlin and the Zuse-Institute, Berlin (ZIB).

Overview
Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. Amira is being developed and commercially distributed by Visage Imaging GmbH, Berlin in cooperation with the Zuse-Institute, Berlin (ZIB). It is used by several thousand researchers and engineers in academia and industry around the world. Amira’s flexible user interface and its modular architecture make it a universal tool for processing and analysis of data from various modalities and in various fields of application. 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 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, to name a few. 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 including CAVEs (Cave automatic virtual environments). 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
A Short History of the Visualization System Amira

1994-1998 Research Software
Amira’s roots go back to 1994 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, and engineering. 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, within a large multi-disciplinary research project the development of a new software system was started in early 1994, led by chief software architect Detlev Stalling. Initially the system 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. Software development was based on libraries such as OpenGL, SGI Open Inventor, and the graphical user interface libraries X11, Motif (widget toolkit), and ViewKit. Later, 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 neurobiology, confocal microscopy, flow visualization, molecule visualization and analysis 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 with the vision of making the extensive capabilities of the software available to researchers in industry and academia worldwide and to provide the product support and robustness needed in today’s fast-paced and competitive world.

The software was given the new, less application-specific name Amira. Amira is not an acronym but was chosen for being pronounceable in different languages, starting with an ‘A’, and having a positive connotation; Amira has a similarity with the Latin verb “admirare” (to admire), meaning “to look at and to wonder at”, which describes a typical situation in data visualization. In Arabic the word “Amira” means “princess”.

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 shown at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX). Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts selected the Bordeaux, France and San Diego, USA 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 as well as TGS 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. Amira continues to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. As in the beginning, the Amira roadmap continues to be driven by the interesting and challenging scientific questions that Amira users around the world are trying to answer, often at the leading edge in their fields.

Sometimes Amira is confused with a product named Avizo. Avizo is distributed by the Bordeaux based company VSG, another spin-off from Mercury Computer Systems, Inc. Avizo is based on a 2009 snapshot of the Amira source code that VSG licensed from Mercury Computer Systems and distributes for certain markets.

The latest version, Amira 5.4.2, was released in March 2012, with the next release planned for the middle of 2012.

Microscopy Option

 * Specific readers for microscopy data
 * Deconvolution
 * Exploration of 3D imagery obtained from virtually any microscope.
 * Edit and extract filament networks from your 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 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

VR Option

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

Very Large Data Option

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

Editors

 * CameraPath Editor: create a camera path using key-frames for animations and movies
 * Color Dialog: graphical interface for defining a color value
 * 2 Colormap Editors: modify the RGBA values of a discrete colormap
 * Curve Editor: creates and edits curves
 * Demo Manager: graphical interface to manage and control demos
 * Digital Image Filters: apply standard image processing filters
 * Filament Editor: skeletonize image data and modify spatial graphs
 * Grid Editor: edit and simplify tetrahedral grids
 * Image Crop Editor: crop 3D images, change bounding box, and voxel size
 * Landmark Editor: add, move, or delete markers in a landmark set
 * LineSet Editor: select, create, modify, and delete polylines
 * Multi-planar Viewer: view up to two data sets simultaneously in a 3+1 MPR viewer
 * Parameter Editor: add, change, or delete attributes of a data object
 * Plot Tool: graphical interface for displaying 2D plots
 * Segmentation Editor: interactive and semi-automatic tools for 3D image segmentation
 * Surface Simplification Editor: reduce the number of triangles of a surface
 * Surface Editor: modify triangles, remove intersections, assign boundary ids
 * Transform Editor: translate, rotate, or scale any 3D data object

Application Areas

 * Anatomy
 * Biochemistry
 * Biophysics
 * Cellular microbiology
 * Computational fluid dynamics
 * Cryo-electron tomography
 * Diffusion MRI/Fiber Tracking
 * Embryology
 * Endocrinology
 * Finite Element Modelling
 * Histology
 * Medical imaging research
 * Microscopy in life and material sciences
 * Molecular biology
 * Neuroscience


 * Nondestructive testing
 * Orthopedics
 * Otolaryngology
 * Preclinical imaging
 * Urology

Processing and Data Analysis

 * Surface and grid generation
 * 3D image segmentation
 * Image registration and slice alignment
 * Skeletonization and deconvolution
 * Multitude of quantification tools
 * Arithmetic operations
 * MATLAB integration
 * 2D and 3D image filtering
 * Surface generation
 * Finite element model (FEM) grid generation
 * Interactive and automatic segmentation
 * Interactive and automatic slice alignment
 * Image registration and morphing
 * Tensor computation
 * Skeletonization and tracing of neural and vascular networks
 * Deconvolution and z-drop correction
 * Powerful scripting interface
 * Dedicated editors for segmentation, tracing, and fusion

Visualization

 * Orthogonal and oblique slicing
 * Volume rendering
 * Surface rendering
 * Isolines and isosurfaces
 * Multi-channel imaging and fusion
 * Vector and tensor visualization
 * Support of structured / unstructured grids
 * Molecular simulation and visualization
 * Structured workflow visualization
 * Active and passive stereo support
 * Tiled screen support
 * Virtual reality navigation and tools

Presentation

 * Easy-to-use interactive 3D navigation
 * Tools for designing animated demos
 * Automation of complex animations and demonstrations
 * Embedded tools for movie generation
 * Active and passive 3D stereo vision
 * 2D and 3D annotation
 * Support for stereoscopic and auto-stereoscopic displays
 * Virtual reality navigation tools
 * Single and tiled screen display
 * Single or multi-pipe rendering
 * Support for “trackd” input devices
 * Geometry data
 * Scalar fields and all types of multidimensional images
 * Vector and flow data
 * Tensor fields
 * Molecular models
 * Simulation data on finite element models