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 * Amira Software for drug discovery



SOFTWARE FOR 2D-5D MICROSCOPY IMAGE VISUALIZATION AND ANALYSIS


AMIRA SOFTWARE


AMIRA SOFTWARE FOR DRUG DISCOVERY


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Applications
Techniques
Services
Testimonials
Features
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POWERFUL, MULTIFACETED 2D–5D SOFTWARE FOR VISUALIZATION, PROCESSING AND ANALYSIS
OF MICROSCOPY IMAGING SERVING DRUG DISCOVERY

Supporting scientists and imaging experts on the challenging path toward drug
discovery need state-of-the-art, repeatable, and automated 2D/3D software
solutions. Thermo Scientific Amira Software reduces manual steps in the drug
discovery process while increasing accuracy, time, and cost-effectiveness. From
target discovery to compound identification, Amira Software is a powerful,
multi-faceted 2D-5D platform for visualizing, manipulating, and understanding
life science research data from many image modalities, including CT (Computed
Tomography), MRI (Magnetic Resonance Imaging), 3D microscopy, and other
techniques. It offers a comprehensive toolbox of image processing methods that
can be automated through custom detection workflows.

Life science researchers continue to drive drug discovery and academic research
down to a structural, sub-cellular level using automated, all-in-one tools and
technologies. In pushing these limits, scientists can better understand how
cells function and respond to disease or genetic variations, using their
findings to advance research and development for breakthrough drug discoveries.

IMAGING DATA



PROCESSING



VISUALIZATION



ANALYSIS





--------------------------------------------------------------------------------

EMPOWER YOUR LAB WITH POWERFUL AND COMPREHENSIVE IMAGING DATA ANALYSIS TOOLBOX

Amira Software offers high-end processing, registration, segmentation,
visualization, animation, and data analysis to support your advanced discovery
workflows in pharmaceutical research areas ranging from structural and cellular
biology to tissue imaging, neuroscience, preclinical imaging, and
bioengineering.



ACCELERATE TIME TO DATA AND TIME TO MARKET

By providing ready-to-use recipes and AI-powered automated processing tools,
Amira Software supports faster image analysis reducing the number of manual
steps. The software has built-in support for deep learning models and includes a
ready-to-use Python environment. By creating automated workflows, Amira Software
supports scientists with faster image analysis and reproducibility, reducing the
learning curve for inexperienced users. Deep learning models accelerate and
improve the segmentation and interpretation of complex or large data sets.





ANALYZE AND CORRELATE DATA FROM ANY IMAGING MODALITY, AT ANY SCALE

Amira Software offers native compatibility and expansive correlative analysis to
help you better understand your 2D-5D imaging data. It is a flexible software
solution that can handle any modality at any scale and size. With a multi-volume
infrastructure, Amira Software is designed to perform image registration on as
many modalities as desired. It can also perform correlative analysis at either
single points in time or as part of longitudinal studies.



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.





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.



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.





--------------------------------------------------------------------------------

Applications


CELL BIOLOGY

Learn more




PRECLINICAL IMAGING

Learn more




NEUROSCIENCE

Learn more





 


REGISTER NOW TO GET EXCLUSIVE CONTENT DELIVERED DIRECTLY TO YOUR INBOX.

Register

Techniques

 * Correlative imaging
 * Membrane detection
 * Cell detection
 * High Content Screening
 * Multi-channel and time-series visualization
 * Filament tracing


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.

 EMPTY HEADING





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.

 EMPTY HEADING





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.

 EMPTY HEADING





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

 EMPTY HEADING





MULTI-CHANNEL AND TIME-SERIES VISUALIZATION

With Amira Software’s new Xplore5D extension, life scientists can easily
visualize, correlate, and process large multi-channel 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

 EMPTY HEADING





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
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.

 EMPTY HEADING



Correlative imaging


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.

 EMPTY HEADING



Membrane detection


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.

 EMPTY HEADING



Cell detection


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.

 EMPTY HEADING



High Content Screening


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

 EMPTY HEADING



Multi-channel and time-series visualization


MULTI-CHANNEL AND TIME-SERIES VISUALIZATION

With Amira Software’s new Xplore5D extension, life scientists can easily
visualize, correlate, and process large multi-channel 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

 EMPTY HEADING



Filament tracing


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
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.

 EMPTY HEADING




Services

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.



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.



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

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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

 



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EMBL AND DKFZ USES AMIRA SOFTWARE

The present 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. Read reference paper.
Video: 6 min




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Features

Import and process imaging data


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


Segmentation


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

 


Presentation


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


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


Analysis and quantification


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

 


Customization


EASILY AND QUICKLY ADAPT AMIRA SOFTWARE TO YOUR SPECIFIC NEEDS

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





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Formatvorlage für das Original der Instrumentenkarten

Products

AMIRA SOFTWARE
LIFE SCIENCES


 * 2D-5D-Biobilddaten untersuchen
 * Strukturen identifizieren und verstehen
 * Statistische Informationen erhalten
 * Berichte und beeindruckende Animationen teilen

Produkt anzeigen

 Datenblatt herunterladen

KRIOS G4 KRYO-TEM



 * Verbesserte Ergonomie
 * Passt leichter in neue und bestehende Labore
 * Maximierte Produktivität und Automatisierung
 * Beste Bildqualität für hochauflösende 3D-Rekonstruktion

Produkt anzeigen

 Datenblatt herunterladen

AQUILOS 2 KRYO-FIB



 * Die Automatisierung ermöglicht die Produktion mehrerer Lamellen
 * Zielauswahl und Extrahierung der gewünschten Struktur mit dem
   Nano-Manipulator zum Herausheben
 * 3D-Visualisierung für hochauflösende Tomographie

Produkt anzeigen

 Datenblatt herunterladen

APREO 2 REM



 * Hochleistungs-REM für eine Allround-Auflösung im Nanometer- oder
   Subnanometer-Bereich
 * T1-Rückstreudetektor in der Säule für empfindlichen Materialkontrast mit
   TV-Rate
 * Hervorragende Leistung bei langen Arbeitsabständen (10 mm)

Produkt anzeigen

 Datenblatt herunterladen




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


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