Amira 3D Software Extensions

Go further in visualizing and understanding your life sciences data

Amira is a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding data from computed tomography, microscopy, MRI, and many other imaging modalities.

Amira offers optional specialized extensions, which respectively address different specific applications, ranging from advanced neuroscience studies, to immersive virtual reality

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Amira Neuro

Diffusion Tensor Imaging

This extension offers specialized modules to analyze images obtained from CT or MR imaging. Diffusion weighted MR imaging (DWI) is used to image the rate of water diffusion in tissues like brain or muscle. This extension allows the user to compute the apparent diffusion coefficient (ADC), fractional anisotropy (FA), and directionally encoded color (DEC) maps. Diffusion tensor imaging (DTI) aims at localizing and visualizing fiber tracts in the human or primate brain and is supported by several modules. Brain perfusion analysis is supported based on tracking a contrast bolus in a time series of MR or CT images.

Amira Molecular

Molecular visualization and analysis

This extension combines Amira's strong capabilities for 3D data visualization, such as hardware-accelerated volume rendering, with specific tools for molecular visualization and analysis, such as molecular surfaces, sequence alignment, configuration density computation and molecule trajectory animation. Due to Amira's innovative user interface, using the features of the Molecular Extension is easy. The Amira Molecular Extension comes with self-running demos and step-by-step tutorials for the most common molecular visualization tasks.

Amira Quantification+

Advanced quantitative information

The Quantification+ Extension delivers high-level tools for obtaining and visualizing advanced quantitative information on 3D images. This extension offers the whole range of software tools needed to perform automated segmentation, convolution, object separation, and to extract statistical and geometrical information.

Amira Skeletonization

Reconstruction and analysis of networks

This free-of-charge extension supports reconstruction and analysis of vascular, dendritic, and fracture networks. It combines specific micro-detailed image mosaic management with advanced automatic and semi-automatic tools for reconstruction of a 3D vessel network from, for example, confocal microscopy or electron microscopy image acquisition. The Skeletonization Extension delivers a unique set of features for the researcher who studies and analyzes neurons or micro-vascular networks.

Amira Mesh

3D geometry generation

The Mesh Extension offers advanced features for scientists working with complex surface analysis, volume reconstruction using tetrahedral grids, vector field visualization, and complex tensor computation. This package is designed especially for Finite Element Modeling (FEM), for computational analysis of 3D regular fields, brain science, and 3D fluid dynamics simulations.

Amira Very Large Data

Out-of-core data management

The Very Large Data Extension allows Amira to deal with large data sets that exceed the available main memory, e.g., on computers with only a small amount of RAM or when using a 32-bit operating system. Using volumes of interest and multi-resolution technology, the Very Large Data Extension overcomes these limitations and allows interactive visualization and processing of large data volumes. Depending on the available resources, this extension allows exploration of image volumes greater than 8 GB, and has been successfully tested with data sets larger than 300 GB.

Multi-Component Analysis

Whenever there is the need to analyze image stacks with numerous similar components this extension provides you with the necessary tools. The modules of this extension enable a complete workflow, from generating the binary image by using local thresholds, separating clustered items, up to the extraction of shape parameters from them. The extension comes with a comprehensive tutorial explaining all required and extensional steps in the workflow.

Amira Developer

Develop advanced custom modules for Amira

The Developer Extension allows you to extend Amira by developing custom data types, visualization or processing modules, and input/output routines through a well-documented C++ API. The object-oriented language together with the open design makes this extension the ideal answer to specific technical requirements.

Amira VR

For Collaborative and Immersive Virtual Reality

The Amira VR Extension enables advanced data visualization and analysis with large tiled displays as well as immersive VR configurations like CAVEs. The VR Extension supports efficient multi-threaded rendering on multi-pipe systems and distributed rendering on cluster systems at optimal performance with minimal bandwidth requirements. It also supports active or passive stereo, edge blending, head tracking, 3D interaction for using Amira capabilities with a true immersive experience.

Amira for life sciences application brochure

Read how Amira software allows to get more detailed insight in life sciences data sets.

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Check out the detailed specifications of Amira for FEI Systems, the dedicated Amira edition tailored for FEI Instruments.

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