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Thanks to accelerated innovations in microscopy, life scientists now have access to a growing suite of imaging tools and techniques. However, the trade-off in some cases is that imaging data size and volume may be significantly higher, especially with high-resolution or light sheet fluorescence microscopy.

The Xplore5D extension for Thermo Scientific Amira Software allows you to easily visualize, correlate, and process large multi-channel and time series data in one environment.

Amira Software is a powerful tool for visualizing, manipulating, and understanding life science research data from many image modalities, including light sheet fluorescence microscopy, electron microscopy, CT, MRI, and other techniques. With the inclusion of Xplore5D, Amira Software now addresses the growing challenges of handling large imaging data. Xplore5D offers you easy data conversion and compression with immediate visual feedback, allowing you to quickly interact with and communicate on large 3–4D+ data. Xplore5D enables you to build meaningful answers to complex research questions across structural and cellular biology, tissue imaging, neuroscience, preclinical imaging, and bioengineering.

Amira Software with Xplore5D will help you increase productivity and turn research and discovery into action.

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Techniques

Cell detection

Cellular spheroids are 3D cell cultures that represent in vivo tissue better than traditional cellular monolayers, improving the ability of researchers to study cancer, diabetes mellitus, or stem cells among many applications. However, cell analysis in such 3D multicellular objects is not accurately possible, especially without destroying the object of study. Amira Software can automatically separate the cells and perform volumetric, morphometric, and intensity measurements on individual cells and their nuclei in 3D image data of these spheroids. Amira Software also helps researchers with the analysis of conventional 2D cellular monolayers.

Correlative imaging

With its long-standing applications in multi-modality imaging techniques, Amira Software is the tool of choice for many researchers working with data from different imaging modalities. Amira architecture supports multi-volume data processing and visualization from the ground up. The automatic registration tools integrated into the standard edition of Amira Software with the Multi-Planar Workroom offer the flexibility of the most commonly used automated registration metrics and optimizers that allow for the adjustment of the registration parameters to meet the needs of your data.

Membrane detection

Amira Software accelerates segmentation by employing automated detection of cellular features, such as filaments and membranes. By performing advanced image analysis and statistics on the cryo-tomograms, Amira Software combines data from these individual structures, averaging out noise and increasing contrast to create a composite model with higher resolution.

High-content screening

Amira Software enables multi-channel quantitivative capabilities to investigate the most demanding scientific and experimental models used in HCS, including immuno-oncology, neuroscience, and organoid health. Thanks to its incredible speed and flexibility, Amira Software helps enable advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology, to neuronal and spheroid morphology in 3D models. To facilitate these advanced analyses, Amira Software features deep learning for improved training and prediction, including "intelligent denoising functionality".  

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Filament tracing

With Amira Software, researchers are able to use a template-matching algorithm to automatically detect and trace fine filaments. In addition, Amira Software enables scientists to reconstruct filamentous networks and edit the resulting graphs to remove image features erroneously identified as filaments or to add missing parts of a network. Graphs of filaments can then be quantified by measuring parameters such as amount, length, thickness, orientation, ranks, etc. Compelling 3D renderings can be created from the reconstructed model and the computed parameters.

Cell detection

Cellular spheroids are 3D cell cultures that represent in vivo tissue better than traditional cellular monolayers, improving the ability of researchers to study cancer, diabetes mellitus, or stem cells among many applications. However, cell analysis in such 3D multicellular objects is not accurately possible, especially without destroying the object of study. Amira Software can automatically separate the cells and perform volumetric, morphometric, and intensity measurements on individual cells and their nuclei in 3D image data of these spheroids. Amira Software also helps researchers with the analysis of conventional 2D cellular monolayers.

Correlative imaging

With its long-standing applications in multi-modality imaging techniques, Amira Software is the tool of choice for many researchers working with data from different imaging modalities. Amira architecture supports multi-volume data processing and visualization from the ground up. The automatic registration tools integrated into the standard edition of Amira Software with the Multi-Planar Workroom offer the flexibility of the most commonly used automated registration metrics and optimizers that allow for the adjustment of the registration parameters to meet the needs of your data.

Membrane detection

Amira Software accelerates segmentation by employing automated detection of cellular features, such as filaments and membranes. By performing advanced image analysis and statistics on the cryo-tomograms, Amira Software combines data from these individual structures, averaging out noise and increasing contrast to create a composite model with higher resolution.

High-content screening

Amira Software enables multi-channel quantitivative capabilities to investigate the most demanding scientific and experimental models used in HCS, including immuno-oncology, neuroscience, and organoid health. Thanks to its incredible speed and flexibility, Amira Software helps enable advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology, to neuronal and spheroid morphology in 3D models. To facilitate these advanced analyses, Amira Software features deep learning for improved training and prediction, including "intelligent denoising functionality".  

Learn more

Filament tracing

With Amira Software, researchers are able to use a template-matching algorithm to automatically detect and trace fine filaments. In addition, Amira Software enables scientists to reconstruct filamentous networks and edit the resulting graphs to remove image features erroneously identified as filaments or to add missing parts of a network. Graphs of filaments can then be quantified by measuring parameters such as amount, length, thickness, orientation, ranks, etc. Compelling 3D renderings can be created from the reconstructed model and the computed parameters.

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Products

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Amira Software
Life Sciences

  • Explore 2D-5D bioimaging data
  • Identify and understand structures
  • Obtain statistical information
  • Share reports and stunning animations

Krios Rx Cryo-TEM

  • Industry leading productivity and ease of use
  • Fixed 300 kV voltage for SPA only
  • Pharma-dedicated service package for guaranteed reliability

Aquilos 2 Cryo-FIB

  • Automation enables production of multiple lamellas
  • Target and extract your structure of interest with lift-out nano-manipulator
  • 3D visualization for high-resolution tomography

Apreo 2 SEM

  • High-performance SEM for all-round nanometer or sub-nanometer resolution
  • In-column T1 backscatter detector for sensitive, TV-rate materials contrast
  • Excellent performance at long working distance (10 mm)

Services

Amira-Avizo-Introductory-training_1160x600

Introductory training

Shorten your learning curve and maximize your investment with this introductory training specifically designed for new users of Amira Software.

The course consists of a lecture with hands-on sessions. The training material highlights the basic features and functionalities of Amira Software.

Learn more

Amira-Avizo-Custom-Dev_1160x600

Custom development

With over 25 years of experience in 3D and image processing and hundreds of custom projects delivered to organizations small and large, Thermo Fisher Scientific can provide you with a solution tailored to fit your specific needs.

We have the ability to customize and expand our software solutions at various levels

Learn more

Amira-Avizo-advanced-training_1160x600

Advanced training

Maximize your investment and reduce your time-to-results with this advanced training specifically designed for existing users of Amira Software.

The course consists of a lecture with hands-on sessions. The training material highlights advanced features and functionalities of Amira Software.

Learn more

Features

Import and process your imaging data

    • 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

    Easily segment your imaging data

    • 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

     

    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

    Visualize and explore your imaging data

    • 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

    Analyze your imaging data and obtain quantitative information

    • 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

     

    Easily and quickly adapt Amira Software to your specific needs

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

    Resources

    Amira Software can automatically count the cell nuclei which correspond to the cell count of the 3D spheroid cell cultures.
    Golgi apparatus of green alga Chlamydomonas reihardtii, flas-frozen without any artificial staining or fixatives, and thinned by cryo-FIB milling.
    Amira software solution for the analysis of time series data of cellular processes.
    Amira Software can automatically count the cell nuclei which correspond to the cell count of the 3D spheroid cell cultures.
    Golgi apparatus of green alga Chlamydomonas reihardtii, flas-frozen without any artificial staining or fixatives, and thinned by cryo-FIB milling.
    Amira software solution for the analysis of time series data of cellular processes.

    Contact us

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

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