Understanding cell structure and mechanisms

Understanding cell structure and mechanisms 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.

Thermo Scientific Amira Software provides a comprehensive array of tools for the flexible and accurate analysis of time series data of cellular mechanisms. It enables researchers to perform dedicated segmentation workflows on their intra- and intercellular images and apply powerful automated object tracking solution.

Imaging data

Workflow using Avizo Software

Processing

Workflow using Avizo Software

Visualization

Workflow using Avizo Software

Analysis

Workflow using Avizo Software

Customization

Confidence

Thanks to powerful segmentation and image processing capabilities and workflows, and after 20+ years of collaboration with the scientific community and thousands of researchers, it has been now proven that our digital imaging-based workflows provide reliable answers to biomedical and life science research.

Customization

Customization

Because your needs are unique and keep evolving, our software solutions are fully flexible and open to customization. Thanks to our scripting interface (Python, TCL), bridge with MATLAB, and our programming API, you can expand our software solution and integrate your own IP (Intellectual Property). And, if needed, our professional service team can help you design unique solutions tailored to your needs.

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Support

Thanks to our dedicated professional support team, you get access to our top experts to ensure that no question is left unanswered. And with our training, consulting options, and ever-expanding collection of tutorials and how-to’s, you can reduce your learning curve and focus on getting the answers you are pursuing.

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Automation

Thanks to our automation capabilities, and with the addition of our always expanding online repository of add-ons (Xtra Gallery), you can encapsulate repeatable workflows into easy-to-reproduce recipes. With the addition of artificial intelligence, analysis can be performed by non-image processing experts, allowing them to save time on complex analysis while ensuring results consistency.


Use cases

 

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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 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 Software’s 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.

 

Multi-channel and time-series visualization

With our new Xplore5D extension for Amira Software, life scientists can easily visualize, correlate, and process large multichannel and time series data in one platform, without worrying about image size or memory limits. With its smart file format, Xplore5D allows you to compress all imaging data without losing precious information collected during acquisition.

Learn more

 

High-content screening

Amira Software enables multi-channel quantitative 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, you are able to use a template-matching algorithm to automatically detect and trace these fine filaments in noisy cryo-EM or DualBeam instrument data. In addition, Amira Software enables you 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 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 Software’s 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.

 

Multi-channel and time-series visualization

With our new Xplore5D extension for Amira Software, life scientists can easily visualize, correlate, and process large multichannel and time series data in one platform, without worrying about image size or memory limits. With its smart file format, Xplore5D allows you to compress all imaging data without losing precious information collected during acquisition.

Learn more

 

High-content screening

Amira Software enables multi-channel quantitative 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, you are able to use a template-matching algorithm to automatically detect and trace these fine filaments in noisy cryo-EM or DualBeam instrument data. In addition, Amira Software enables you 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.

 

Services

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Introductory training

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

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

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Advanced training

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

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

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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 can customize and expand our software solutions at various levels.


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Testimonials

Matthia A. Karreman at EMBL and DKFZ, Heidelberg, Germany, uses Amira Software

This testimonial highlights the way Amira Software supported Matthia A. Karreman, MSc, PhD at EMBL and DKFZ, Heidelberg, Germany, in her project on multimodal correlative microscopy to efficiently target single tumor cells in vivo.

Matthia A. Karreman, MSc, PhD
EMBL and DKFZ, Heidelberg, Germany


Heidelberg University uses Amira Software

 

"Amira Software helps to set up complex data processing workflows. The first aim was to enhance the contrast of viral and cellular membranes. We applied a combination of 3D non-local means filter and the Membrane Enhancement Filter implemented in Amira Software. An initial automated segmentation was achieved using the Top-hat segmentation tool. This initial segmentation was further manually refined utilizing a Wacom graphics tablet. Based on the refined membrane segmentation, a 3D surface was calculated using unconstrained smoothing, and the surface was visualized as 3D model."

By Steffen Klein (Chlanda lab, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany)

 

Read more


Resources

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.

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

Golgi apparatus of green alga Chlamydomonas reihardtii, flas-frozen without any artificial staining or fixatives, and thinned by cryo-FIB milling.

SARS-CoV-2 virion budding and assembly at the ERGIC membrane. A 3D volume rendering is shown for each area with cellular and viral membranes in green and magenta respectively, viral spike proteins in yellow, and viral ribonucleoproteins in cyan.

Amira Software provides a comprehensive toolset for the flexible and accurate analysis of time series data of cellular processes.

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.

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

Golgi apparatus of green alga Chlamydomonas reihardtii, flas-frozen without any artificial staining or fixatives, and thinned by cryo-FIB milling.

SARS-CoV-2 virion budding and assembly at the ERGIC membrane. A 3D volume rendering is shown for each area with cellular and viral membranes in green and magenta respectively, viral spike proteins in yellow, and viral ribonucleoproteins in cyan.

Amira Software provides a comprehensive toolset for the flexible and accurate analysis of time series data of cellular processes.

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

    Contact us

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

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