Wherever 3-dimensional data sets need to be processed, for example in medicine, biology, and engineering, amira offers fascinating new opportunities. State-of-the-art visualization techniques allow you to gain detailed insight into your data. Graphics hardware is efficiently utilized to display large data sets at interactive speed.
Powerful automatic and interactive segmentation tools support processing of 3D image data. Innovative, fast, and robust reconstruction algorithms make it easy to create polygonal models from segmented objects.
In addition, true volumetric tetrahedral meshes can be generated, suitable for advanced finite element simulations. Simulation results as well as other data defined on a variety of different grids can be investigated using a large set of powerful visualization methods.
Who uses amira?
- R&D groups working with 3D image data, e.g. in biology, medicine, material science, quality control, physics or geophysics.
- R&D groups performing numerical simulations like finite element analysis, computational fluid dynamics, or physics simulations.
- R&D groups working in chemistry and biochemistry.
AmiraDev
The amira Developer Edition, amiraDev™, allows clients to extend the functionality of amira Standard Edition to meet custom requirements. Specific graphic representation, new readers or writers, or new computational algorithms can be added. Such custom extensions can be used with the amira Standard Edition. amiraDev allows scientists and researchers to customize the visualization to meet needs of specific projects. Building on amiraDev saves time in the completion of visualization tasks.
From now, people working in medical imaging, biology, confocal microscopy, 3D geometry reconstruction, engineering, CFD, FEM, geosciences, and so on... can develop custom extensions for the amira visualization system. amiraDev allows the user to add new components such as file read and write routines, modules for visualizing data, and modules for processing data. New modules and new data classes can be defined as subclasses of existing ones.
amiraDev is a superset of the amira Standard Edition. It additionally provides all the C++ header files needed to compile custom extensions. For developing custom extensions, amiraDev users need a C++ development environment, such as Microsoft© Visual Studio on Windows, or a C++ compiler on UNIX.
AmiraMol
amiraMol™ adds advanced tools for the visualization of Molecules. amiraMol combines amira's strong capabilities for 3D data visualization like hardware-accelerated volume rendering with specific tools for molecular visualization and data analysis. Molecular surfaces, sequence alignment or configuration density computation are only a few examples. Due to amira's innovative user interface using the features of amiraMol is easy. amiraMol comes with self-running demos and step-by-step tutorials for the most common molecular visualization tasks.
Features of amiraMol Beta version:
- Visualization of static molecules as well as time dependent data (trajectories).
- Computation and visualization of configuration densities from trajectories
- The following file formats are supported for molecular data input:
- PDB
- MDL
- Tripos
- UniChem
- PSF/DCD (CHARMM, trajectories)
- amira's native file format ZibMolFile (trajectories)
- Flexible and fast ball and stick visualization, flexible color schemes
- "BondAngle-style" visualization
- Flexible and convenient tools to select and display parts of a molecule
- Extraction and visualization of molecular surfaces (van der Waals surfaces and solvent accessible surfaces)
- Visualization of back bone and secondary structures
- Visualization of additional quantities like scalar or vector fields with color coding
- Simultaneous display of multiple molecules
- Measuring of lengths and angles in molecules
- Sequence and structural alignment of molecules
- All molecular visualization tools can be arbitrarily combined with the standard Amira modules like volume rendering, slicing, or iso-surfaces.
AmiraVR
amiraVR™ is a specialized and extended version of the amira® visualization system which is dedicated for use in immersive installations like large-screen stereoscopic projections, CAVE® or Holobench® systems. amiraVR offers these features:
- Support for single and multiple screen display systems.
- Support for single or multi-pipe rendering on all platforms.
- Easy and flexible customization for specific display system geometry.
- Support of active and passive stereoscopic displays.
- Head-tracking for correct perspective viewing
- Support for tracked hand-held input-devices like the 6-DOF Wand TM
- Control of Amira functionality via 3D user interface components.
- Control of 2D user interfaces with 3D devices (Virtual Mouse).
- Scriptable using TCL.
- Programmers API (amiraDEV).
- Full binary compatibility with AmiraDev custom modules.
With its unique set of features amiraVR represents both a VR (Virtual Reality) ready application for scientific and medical visualization in immersive environments, and a development platform which allows to build VR applications as easy as never before.
AmiraDeconv
amiraDECONV™ is an extension product for the amira visualization system. It adds tools for the deconvolution of 3D microscopic images. Deconvolution is the process of increasing image quality and resolution by computationally compensating artefacts of the recording process. While so-called blind deconvolution uses an individual measured point spread function, non-blind algorithms work on the basis of only a few recording parameters (like numerical aperture or zoom factor). amira DECONV offers these features:
- Fast non-blind deconvolution of microscopic images.
- Tools for extraction and averaging point spread functions from bead measurements.
- Automatic generation of point spread functions.
- Fast blind deconvolution of microscopic images.
- Support for confocal and widefield data.
- Documentation on optimising recording parameters and using the deconvolution.
- Support for non-power-of two dimensions as well as large data sets.
