Biological image analysis for powerful data visualization and insights

Thermo Scientific Amira Software provides a comprehensive toolbox for advanced 2D-5D biological characterization. It enhances time efficiency, reliability, and reproducibility with automated tools for image data analysis in life science research.


Seamless import of imaging data

Stack of slides imported into Amira Software.
  • Seamless automatic import of images from multiple imaging modalities, optical and electron microscopy, CT, MRI, and others, including metadata.
  • Handling of multi-data/multi-view, multi-channel, time series, and very large datasets.
  • Full support of almost all established file types (BioFormats compatibility).

Filtering and pre-processing

  • AI-based and conventional image quality enhancement, including: 
    • Image enhancement, filtering, and convolution (Fourier frequency transforms)
    • Noise and artifact reduction Background correction
    • Image stack alignment, arithmetic operations, correlation, and fusion
  • Advanced 2D/3D multi-modal image registration
  • Finite element and geometric modeling, along with CAD integration
Noise reduction in Amira Software.

Visualize and explore imaging data

  • Interactive high-quality and high-precision visualization 
  • Embedding of quantitative information into visualization
  • Simultaneous multi-window visualization for better understanding of the data
  • Vector and tensor visualization 
  • Molecular visualization

AI-enabled segmentation tools

Amira Software features advanced AI-driven segmentation tools that ensure exceptional accuracy and efficiency in data analysis. Amira Software's specialized segmentation workroom combines innovative artificial intelligence with user-friendly annotation tools, streamlining the creation of ground truth data.

 

Amira Software provides flexible AI segmentation models, offering shallow models for rapid processing of simpler tasks and deep models for high-precision analysis of complex images. Training can be conducted in either 2D or 3D, tailored to your data needs. With its intuitive interface, superior accuracy, and efficient performance, Amira Software is an ideal solution for professionals in both research and industry.

AI-assisted segmentation in Amira Software of a Chlamydomonas sample dataset.

200+ built-in measurements

Cowpox virus-infected cells with particle density colormap created in Amira Software. Sample courtesy of Robert Koch Institute, Berlin, Germany

Analyze your imaging data and obtain quantitative information:

  • Intuitive recipe creation, customization, automated replay
  • More than 200 built-in measurements, including counts, volumes, areas, perimeters, aspect ratios, and orientations
  • User-defined measurements
  • Results viewer with spreadsheet tool and charting
  • Automatic individual feature measurements, 3D localization, and spreadsheet selection
  • Automated statistics and distribution graphs
  • Feature filtering using any measurement criterion
  • Data registration, deformation, comparison, and measurements

Presentation and animation

Export your analysis and visualization work to seamlessly publish and present it:

  • 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

 


Scripting and customization

Scripting and customization in Amira Software.

Easily and quickly adapt Amira Software to your specific needs:

  • Custom C++ modules development
  • MATLAB bridge
  • Python scripting API

Automated workflows

Automated image processing workflows are essential for efficient and reproducible scientific research and industrial applications.

 

Amira Software provides the capability to create image processing and analysis recipes in an intuitive way, allowing you to create, customize, and automate workflows, including AI-based, without any programming skills.

 

Save and reuse recipes for consistency and handle large datasets efficiently. You can even merge existing recipes with new recipes to increase productivity and simplify image analysis.

 

Amira Software's Image Recipe Designer enhances accuracy, reliability, and productivity to support your research.

Amira Software image recipe designer workroom. Data courtesy of Srigokul Upadhyayula, Howard Hughes Medical Institute (HHMI) and Harvard Medical School.

Digital volume correlation

Amira Software supports digital volume correlation (DVC), enabling researchers to measure non-contact, 3D volumetric displacement and strain data within biological tissues and implants under various conditions. This capability is crucial for studying the mechanical properties of bones and other structures, allowing for better understanding of strain transfer and failure mechanisms.


AI powered data analysis

Amira Software features advanced AI-driven segmentation tools for precise and efficient data analysis. Its segmentation workroom incorporates innovative AI, simplifying ground truth data creation with intuitive annotation tools.

 

Amira Software offers versatile AI models: shallow models for speed in simple tasks and deep models for high precision in complex image analysis. Training can be done in 2D or 3D based on your data needs.

 

With a user-friendly interface, high accuracy, and efficient processing, Amira Software is an ideal choice for research and industry professionals, transforming images into quantifiable insights.

AI-powered Amira Software.

Simulation and modeling

Brain surface editing with Amira Software.

Amira Software provides a robust meshing engine to create simulation inputs from 3D labeled images. It generates high-quality meshes with smoothed interfaces from large multi-material segmented images, preserving thin structures and topology. You have fine control over element size distribution. Meshes can be exported to major solver formats with boundary conditions, and Amira Software supports importing solver outputs for advanced post-processing and visualization.


Try Amira Software

For Research Use Only. Not for use in diagnostic procedures.