Advanced image analysis capabilities compatible with multiple biological imaging techniques

Thermo Scientific Amira Software provides advanced tools (including AI) for comprehensive data analysis across multiple scales and imaging modalities. It seamlessly integrates data from various techniques, enabling detailed multi-scale investigations. This versatility allows precise

analysis of complex structures and relationships, enhancing the depth and accuracy of scientific insights.


Cryo-electron tomography

Cryo-TEM and cryo-electron tomography (cryo-ET) are cutting-edge cryogenic imaging techniques that provide high-resolution insights into cellular structures and protein complexes in their native states. Amira Software is a powerful, multifaceted platform designed for the visualization, manipulation, and analysis of 3D-image data for cryo-ET and cryo-TEM. It offers a comprehensive toolbox that includes AI-based image denoising, precise segmentation, and rapid filament analysis, enabling researchers to transform complex imaging data into insights. Amira Software leverages AI for semi-automated analysis of cryo-TEM images of viral particles and nanocarriers, significantly accelerating the drug development process while ensuring reliable and standardized analysis. With features like ergonomic manual annotation and cross-correlation-based cylindric template matching, Amira Software significantly reduces the time required for data analysis, making it an essential tool for cell biologists and pharmaceutical researchers aiming to understand cellular structures and functions at a deeper level.

Golgi Chlamydomonas – cryo-ET. Data courtesy of Dr. Benjamin Engel, Dept. of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany.

Volume electron microscopy

Volume electron microscopy (volume EM) is a transformative imaging technique that enables researchers to visualize and analyze the intricate 3D ultrastructure of cells and tissues at nanometer resolution. Amira Software offers user-friendly and precise tools dedicated for volume EM data quality enhancement and analysis for all common modalities: array tomography, SBF-SEM, and FIB-SEM. Furthermore, the Thermo Scientific Volumescope 2 SEM and Amira Software offer a powerful combination for this approach. The fully integrated workflow from acquisition to image analysis seamlessly transforms images into quantitative information. Amira Live Tracker allows visualization and navigation of 3D images data during acquisition, optimizing imaging outcomes and automating 3D volume reconstructions. The imported 3D images can be further processed and analyzed within Amira Software using AI-based automated workflows.

 

Experience faster, more accurate insights with Amira Software, offering streamlined workflows, enhanced data analysis, and optimized research outcomes for your volume EM data.

Volume electron microscopy of cells infected with cowpox virus, visualized with Amira Software. Sample courtesy of Robert Koch Institute, Berlin, Germany

"Amira Software is crucial for visualizing SBF-SEM (serial block-face SEM) and FIB-SEM images, so we can analyze the 3D morphology of organelles. The label analysis option allows us to quantify parameters such as area, volume, perimeter, and length. Additionally, MatLab allows for other custom quantifications to be determined, such as the mitochondrial complexity index or sphericity.”

Dr. Antentor Hinton

Jr.

Department of Molecular Physiology and Biophysics, Vanderbilt University


Correlative electron microscopy

Amira Software, with its robust architecture for multi-volume data processing and visualization, is a preferred tool for researchers integrating data from diverse imaging modalities. It offers seamless integration of structural and functional information across multiple scales, supported by flexible and precise automatic registration tools in the Multi-Planar Workroom. This enables researchers to conduct correlative studies using proven intermodal registration methods, enhancing workflows across numerous fields in the life sciences.

CLEM of mice mesenchymal stem cells. Data courtesy Jaromíra Kovářová from Laboratory of Molecular Therapy, Institute of Biotechnology, the Czech Academy of Sciences. Data were acquired in Imaging Methods Core Facility at BIOCEV, Faculty of Science, Charles University, by Marie Olšinová and Markéta Dalecká.

Light microscopy

Amira Software's advanced visualization capabilities enable the generation of detailed 3D reconstructions from 2D light microscopy images, offering deeper insights into the structure and function of biological specimens. The software includes sophisticated image processing techniques such as deconvolution, segmentation, and quantitative analysis, allowing researchers to extract meaningful information from their data.

 

Amira Software supports a wide range of file formats commonly used in light microscopy, ensuring seamless integration with various imaging systems.

Plasma membranes and endomembranes within the eye of a zebrafish embryo. Data courtesy of Tsung-Li Liu, Janelia Research Campus, Howard Hughes Medical Institute, 2018, 'Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms', Science, vol. 360, issue 6386.

“It’s very powerful software [that’s] good for both electron microscopy and fluorescence microscopy, which is quite extraordinary, because typically software is focusing on either one of those. You can do so much with the software—I would really recommend Amira [Software].”

Matthia A. Karreman

MSc, PhD

EMBL, Heidelberg, Germany


MRI

Amira Software addresses MRI challenges such as complex data interpretation, high noise levels, and the need for precise anatomical differentiation with advanced imaging, detailed separation, and comprehensive examination tools. It facilitates the creation of intricate 3D reconstructions, allowing researchers to explore anatomical structures with precision. Amira Software supports quantitative analysis, including volumetric measurements and statistical evaluations, enhancing MRI dataset interpretation. Its user-friendly interface and customizable workflows streamline MRI data analysis, making it an ideal tool in both clinical and research settings.

Visualization of the results of a diffusion tensor imaging study of the human head. Data courtesy of Prof. Dr. Alexander Brawanski, University Hospital of Regensburg.

CT and PET

Amira Software is an ideal choice for bioengineers and preclinical researchers, offering advanced tools for bone segmentation, separation, and detailed measurement in 3D models. Its robust, semi-automated workflows, including specialized cortical and trabecular bone segmentation, save time and effort. Amira Software's performance-optimized registration tools and multi-volume architecture enable automatic co-registration of image data, facilitating in vivo distribution studies of therapeutic agents tagged with radioactive nuclei. Its comprehensive toolbox allows for precise anatomical segmentation and quantification of radiotracer uptake in functional images.

CT-imaged puppy segmentation with 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 support 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 Handschuh

PhD

VetCore, University of Veterinary Medicine, Vienna


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