Understanding brain and neuro-functions

Studying the brain and neuro-functions requires the knowledge of a vast selection of experimental methods, from cell preparation to image acquisition and analysis. Thermo Scientific Amira Software supports you 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 you to create custom workflows that extract exactly the desired type of information from an image.

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

Understanding the interconnectivity of the brain is essential for functional brain research. This allows researchers to better understand how different parts of the brain jointly orchestrate higher cognitive functions and motor skills.

With Amira Software, you are able to perform the entire DTI analysis workflow by first converting images into Talairach coordinates. You are then able to map multiple brain images onto a reference brain. Once the brain images are aligned, gradient images can be converted into a tensor field, and nerve fiber bundles can be tracked and visualized with our state-of-the-art visualization tools.

 

With Amira Software, you are able to trace, analyze, and quantify 3D images of filamentous structures such as neurons and blood vessels. Filamentous networks can be reconstructed, and measures such as length, thickness, orientation, ranks, etc., can be computed and visualized in compelling 3D renderings. Tracing can be performed automatically or interactively, depending on the application and needs.

Our template-matching algorithm allows automatic detection and tracing of fine filaments in noisy cryo-EM data. Amira Software also enables you to edit the resulting graphs to remove image features erroneously identified as a filament or to add missing parts of a network.

 

Brain perfusion studies help researchers and scientist to understand the impact of strokes or other brain tissue diseases such as Alzheimer and dementia. The exact location and duration of a stroke can determine functional impact of the event.

With Amira Software, you are able to analyze brain perfusion in perfusion-weighted MRI and CT images. This analysis includes computation of mean transit time (MTT), cerebral blood flow (CBF), and cerebral blood volume (CBV).

 

In vitro neuroscience research has grown considerably in neurodegenerative, neurogenesis, and neurotoxicology applications. Neurite outgrowth and synaptogenesis are the gold standards for evaluating health and functionality of neurons. However, even in vitro, identification of neuronal outgrowth morphology is difficult.

Researchers manually tracing neurites and synaptogenic spots face variability and non-scalability. Amira Software’s three-dimensional neuroscience abilities can accurately and efficiently quantify neuronal morphology in 3D models to facilitate the high-throughput demands of this research.

Learn more

Understanding the interconnectivity of the brain is essential for functional brain research. This allows researchers to better understand how different parts of the brain jointly orchestrate higher cognitive functions and motor skills.

With Amira Software, you are able to perform the entire DTI analysis workflow by first converting images into Talairach coordinates. You are then able to map multiple brain images onto a reference brain. Once the brain images are aligned, gradient images can be converted into a tensor field, and nerve fiber bundles can be tracked and visualized with our state-of-the-art visualization tools.

 

With Amira Software, you are able to trace, analyze, and quantify 3D images of filamentous structures such as neurons and blood vessels. Filamentous networks can be reconstructed, and measures such as length, thickness, orientation, ranks, etc., can be computed and visualized in compelling 3D renderings. Tracing can be performed automatically or interactively, depending on the application and needs.

Our template-matching algorithm allows automatic detection and tracing of fine filaments in noisy cryo-EM data. Amira Software also enables you to edit the resulting graphs to remove image features erroneously identified as a filament or to add missing parts of a network.

 

Brain perfusion studies help researchers and scientist to understand the impact of strokes or other brain tissue diseases such as Alzheimer and dementia. The exact location and duration of a stroke can determine functional impact of the event.

With Amira Software, you are able to analyze brain perfusion in perfusion-weighted MRI and CT images. This analysis includes computation of mean transit time (MTT), cerebral blood flow (CBF), and cerebral blood volume (CBV).

 

In vitro neuroscience research has grown considerably in neurodegenerative, neurogenesis, and neurotoxicology applications. Neurite outgrowth and synaptogenesis are the gold standards for evaluating health and functionality of neurons. However, even in vitro, identification of neuronal outgrowth morphology is difficult.

Researchers manually tracing neurites and synaptogenic spots face variability and non-scalability. Amira Software’s three-dimensional neuroscience abilities can accurately and efficiently quantify neuronal morphology in 3D models to facilitate the high-throughput demands of this research.

Learn more

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.


Resources

Visualization of the results of a Diffusion Tensor Imaging study of the human head Courtesy of Prof. Dr. Alexander Brawanski, University Hospital of Regensburg1001.

Visualization of a brain of Mus musculus.

Fertilizers effects on neuronal outgrowth and synapse expression by IUF – Leibniz Research Institute for Environmental Medicine.

Analysis of the neurites of a neurospheroid
Analysis of the neurites of a neurospheroid. Data courtesy of Dr. Stefan Masjosthusmann, IUF – Leibniz Research Institute for Environmental Medicine.
Visualization of the results of a Diffusion Tensor Imaging study of the human head
Visualization of the results of a Diffusion Tensor Imaging study of the human head. Courtesy of Prof. Dr. Alexander Brawanski, University Hospital of Regensburg.
Volume rendering of cleared spinal cord as imaged with 2-photon microscopy
Volume rendering of cleared spinal cord as imaged with 2-photon microscopy. Data courtesy of Ali Ertürk, Max Planck Institute of Neurobiology.
Tube rendering of traced axons colorized according to axon thickness.
Tube rendering of traced axons colorized according to axon thickness. Data courtesy of Ali Ertürk, Max Planck Institute of Neurobiology.
Paired Helical Filaments (PHF)
Paired Helical Filaments (PHF). Data courtesy of The Medical Research Council Laboratory of Molecular Biology. Fitzpatrick et al., 2017.Data courtesy of The Medical Research Council Laboratory of Molecular Biology. Fitzpatrick et al., 2017.

Visualization of the results of a Diffusion Tensor Imaging study of the human head Courtesy of Prof. Dr. Alexander Brawanski, University Hospital of Regensburg1001.

Visualization of a brain of Mus musculus.

Fertilizers effects on neuronal outgrowth and synapse expression by IUF – Leibniz Research Institute for Environmental Medicine.

Analysis of the neurites of a neurospheroid
Analysis of the neurites of a neurospheroid. Data courtesy of Dr. Stefan Masjosthusmann, IUF – Leibniz Research Institute for Environmental Medicine.
Visualization of the results of a Diffusion Tensor Imaging study of the human head
Visualization of the results of a Diffusion Tensor Imaging study of the human head. Courtesy of Prof. Dr. Alexander Brawanski, University Hospital of Regensburg.
Volume rendering of cleared spinal cord as imaged with 2-photon microscopy
Volume rendering of cleared spinal cord as imaged with 2-photon microscopy. Data courtesy of Ali Ertürk, Max Planck Institute of Neurobiology.
Tube rendering of traced axons colorized according to axon thickness.
Tube rendering of traced axons colorized according to axon thickness. Data courtesy of Ali Ertürk, Max Planck Institute of Neurobiology.
Paired Helical Filaments (PHF)
Paired Helical Filaments (PHF). Data courtesy of The Medical Research Council Laboratory of Molecular Biology. Fitzpatrick et al., 2017.Data courtesy of The Medical Research Council Laboratory of Molecular Biology. Fitzpatrick et al., 2017.

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

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