Reveal the underlying physiological mechanisms

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.


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

Co-registration

One of the main reasons researchers are using preclinical imaging is in vivo distribution studies aimed at localizing therapeutic agents in drug or gene therapy. These agents are often tagged or made susceptible for tagging with radioactive nuclei for detection with PET or SPECT imaging instruments.

With its extensive, performance-optimized registration tools and its multi-volume architecture, Amira Software allows preclinical researchers to automatically co-register image data from any type of preclinical imaging instrumentation. Amira Software’s extensive toolbox of segmentation and quantification tools then allows for segmentation of the anatomical images and quantifying radiotracer uptake in the co-registered functional images.

 

Bone separation

Micro-CT image acquisition is one of the most popular imaging techniques for any type of bone research. One of the first steps for any bone analysis is bone segmentation and separation into individual bones.

Amira Software offers the tools to perform bone segmentation from the surrounding tissue. The segmented bones can then be separated with Amira Software’s advanced algorithms. The individual bones can then be measured using a customizable list of the many measurements that Amira Software provides, such as size, shape and orientation.

 

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 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. These 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.

 

Co-registration

One of the main reasons researchers are using preclinical imaging is in vivo distribution studies aimed at localizing therapeutic agents in drug or gene therapy. These agents are often tagged or made susceptible for tagging with radioactive nuclei for detection with PET or SPECT imaging instruments.

With its extensive, performance-optimized registration tools and its multi-volume architecture, Amira Software allows preclinical researchers to automatically co-register image data from any type of preclinical imaging instrumentation. Amira Software’s extensive toolbox of segmentation and quantification tools then allows for segmentation of the anatomical images and quantifying radiotracer uptake in the co-registered functional images.

 

Bone separation

Micro-CT image acquisition is one of the most popular imaging techniques for any type of bone research. One of the first steps for any bone analysis is bone segmentation and separation into individual bones.

Amira Software offers the tools to perform bone segmentation from the surrounding tissue. The segmented bones can then be separated with Amira Software’s advanced algorithms. The individual bones can then be measured using a customizable list of the many measurements that Amira Software provides, such as size, shape and orientation.

 

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 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. These 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.

 

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, 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.


Testimonials

VetCore, University of Veterinary Medicine uses Amira Software

"Research at Vetmeduni Vienna is quite diverse, covering both clinical and preclinical research areas. We are currently four people working in the imaging facility, providing equipment and supports for researchers in both image acquisition (widefield microscopy, CLSM, spinning disk confocal microscopy, soon also STORM super-resolution microscopy, microscopic X-ray computed tomography) and in data visualization and analysis. Amira Software allows you to build networks, enabling complex interactions between data objects. Biology is also complex, and biological interactions are complex networks. Complex questions require complex tools to address them. In this respect, analysis networks such as used in Amira Software outperform most other software approaches when it comes to complex data analysis. Furthermore, I like that Amira Software is quite open concerning integration of deep learning networks and scripting (Tcl, Matlab, Python,...)."

Stephan Handschuch, PhD
VetCore, University of Veterinary Medicine, Vienna



Resources

Understanding the passage of air through the upper airways is crucial for planning corrective rhinosurgery when undisturbed airflow is inhibited by persistent obstructions or deformities.

Micro-CT image acquisition is one of the most popular imaging techniques for any type of bone research. One of the first steps for any bone analysis is bone segmentation and separation into individual bones.

Discover how Amira-Avizo Software enables the whole 3D printing workflow, from 2D image stack import, to 3D reconstruction and 3D meshing, right through to 3D printer compatible formats export. Data courtesy of National University of Singapore.

Amira Software can automatically count the cell nuclei which correspond to the cell count of the 3D spheroid cell cultures.

Amira-Software-Preclinical_1160x600_image-card
Maximum intensity projection and surface reconstruction of a mouse thorax. Acquisition device: VAMP TomoScope® 30s+, Amira Software - Courtesy of Dr. Elizatea Stepina and Dr. Peter Hauff, Bayer Healthcare.
Amira-Software-coregistration_1160x600_image-card


Co-registration for distribution studies. CT/SPECT data courtesy of Dr. Nabil Boutagy of the Yale Translation Research Imaging Center.

Amira-Software-bone-separation_1160x600_image-card
Courtesy of National Laboratory Animal Center - National Applied Research Laboratories, Taiwan.

Understanding the passage of air through the upper airways is crucial for planning corrective rhinosurgery when undisturbed airflow is inhibited by persistent obstructions or deformities.

Micro-CT image acquisition is one of the most popular imaging techniques for any type of bone research. One of the first steps for any bone analysis is bone segmentation and separation into individual bones.

Discover how Amira-Avizo Software enables the whole 3D printing workflow, from 2D image stack import, to 3D reconstruction and 3D meshing, right through to 3D printer compatible formats export. Data courtesy of National University of Singapore.

Amira Software can automatically count the cell nuclei which correspond to the cell count of the 3D spheroid cell cultures.

Amira-Software-Preclinical_1160x600_image-card
Maximum intensity projection and surface reconstruction of a mouse thorax. Acquisition device: VAMP TomoScope® 30s+, Amira Software - Courtesy of Dr. Elizatea Stepina and Dr. Peter Hauff, Bayer Healthcare.
Amira-Software-coregistration_1160x600_image-card


Co-registration for distribution studies. CT/SPECT data courtesy of Dr. Nabil Boutagy of the Yale Translation Research Imaging Center.

Amira-Software-bone-separation_1160x600_image-card
Courtesy of National Laboratory Animal Center - National Applied Research Laboratories, Taiwan.

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

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