2D-5D visualization and analysis software

Amira for Life & Biomedical Sciences

Thermo Scientific Amira Software is a powerful, multifaceted 2D-5D platform for visualizing, manipulating, and understanding life science research data from many image modalities, including CT, MRI, 3D Microscopy, and other techniques.

With incredible speed and flexibility, Amira Software enables advanced 2D-5D bioimaging workflows in research areas ranging from structural and cellular biology, to tissue imaging, neuroscience, preclinical imaging, and bioengineering.

Understanding living cells and their processes requires analysis of data from various imaging systems and modalities that all use different file formats. Each experimental setup can represent a unique challenge to process the data. Multi-scale dynamic processes require tracking of various sized objects, from diffraction-limited particles to entire cells. There can be a few dozen to tens of thousands objects in each data set. In addition, intracellular processes are supported by sub-cellular structures that also need to be identified and quantified.
Amira Software provides a comprehensive array of tools for the flexible and accurate analysis of time series data of cellular processes. It enables researchers to perform dedicated segmentation workflows on their intra- and intercellular images and apply powerful automated object tracking solution.

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C Elegans cell and its nuclei

C Elegans cell and its nuclei. Images collected with TLS-SPIM, Liang Gao lab, Stony Brook University.

Studying the brain and neuro-functions requires the knowledge of a vast selection of experimental methods, from cell preparation to image acquisition and analysis.
Amira Software aims at supporting researchers in the most frequently used image analysis techniques, such as filament tracing and editing, DTI analysis, brain perfusion analysis, and object tracking. Combining Amira Software's versatility, with state-of-the-art 3D visualization and image processing, enables researchers to create custom workflows that extract exactly the desired type of information from an image.

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Alzheimer's molecule

Preclinical image analysis relies on augmenting structural information from micro-CT or MRI systems with functional data from PET, SPECT or optical imaging instrumentation. Analysis of novel drug candidates requires pinpointing the location of dynamic processes acquired with functional modalities in images of the animal’s anatomy from structural modalities over time.
Amira Software enables the fusion of any type of preclinical image data. Co-registered images can be segmented and analyzed using Amira Software’s vast library of image analysis filters and algorithms. Image segmentation and quantification workflows can be applied to entire time series of image data of dynamic processes. With Amira Software’s professional-grade visualization tools, structural information from CT and MRI can be augmented and rendered jointly with segmentation results and functional images to create visualization of physiological processes that reveal the underlying mechanisms in an intuitive animation.

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Mouse bones segmentation
Courtesy of National Laboratory Animal Center - National Applied Research Laboratories, Taiwan.

The Xtra Library provides a collection of add-ons (recipes, scripts, demos) dedicated to specific use cases and workflows, that will help you improve your daily use of Amira Software and dramatically increase your efficiency.

Go to the Xtra Library


Key features

  • Handle any modality, at any scale, of any size:

- Bio-Formats
- Bitmap formats
- Microscopy: electron and optical
- Medical and neuroimage formats
- Molecular formats
- Other acquisition devices (MRI, radiography, etc.)

  • Finite element modeling, geometric modeling, CAD
  • Support for multi-data/multi-view, multi-channel, time series, very large data
  • Scaling, calibration, conversion, re-sampling
  • Image enhancement, comprehensive filtering and convolution, Fourier frequency transforms
  • Artifact reduction algorithms
  • Advanced multi-mode 2D/3D automatic registration
  • Image stack alignment, arithmetic, correlation, fusion
  • Interactive high-quality volume and multichannel visualization
  • Orthogonal, oblique, cylindrical and curved slicing
  • Contouring and iso-surface extraction
  • Maximum Intensity or other types of projections
  • Vector and tensor visualization
  • Objects and tracks
  • Molecular visualization
  • Thresholding and auto-segmentation, object separation, automatic labeling
  • Region growing, snakes, interpolation, wrapping, smoothing
  • Morphological processing, including watershed and basins
  • Machine Learning-based segmentation
  • Automatic tracing of individual fibers and filaments
  • Skeletonization and filament network extraction
  • Interactive tools for generation or editing of segmentation and spatial graphs
  • 3D surface reconstruction
  • Grid generation for FEA/CFD
  • Intuitive recipe creation, customization, automated replay
  • Built-in measurements, including counts, volumes, areas, perimeters, aspect ratios and orientations
  • User-defined measures
  • Results viewer with spreadsheet tool and charting
  • Automatic individual feature measurements, 3D localization and spreadsheet selection
  • Automated statistics, distribution graphs
  • Feature filtering using any measurement criterion
  • Data registration, deformation, comparison and measurements
  • Animation and video generation
  • Advanced key frame and object animation
  • Mix images, geometric models, measurements and simulations
  • Annotations, measures legends, histograms and curve plots
  • Export spreadsheets, 3D models, high-quality images
  • Active and passive 3D stereo vision
  • Single and tiled screen display
  • Immersive environment
  • Custom C++ modules development
  • MATLAB™ bridge
  • Python scripting API

Amira Software is for Research Use Only. Not for use in diagnostic procedures.