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Amira Software: Essential for biological image analysis
Thermo Scientific Amira Software is highly valued by scientists and researchers worldwide for its exceptional capabilities in biological image analysis. Testimonials from leading institutions such as the University of Glasgow, the University of Washington, and the Max Planck Institute of Neurobiology highlight its role in advancing research across diverse fields. Users praise its intuitive design, ability to handle large datasets, and versatile optical controls, which greatly enhance the research and discovery process. Whether it's analyzing vascular structures, understanding mummification processes, or aiding cancer pathology, Amira Software proves to be an indispensable tool in modern scientific research.
Amira Software supports mitochondria research at Vanderbilt University
Dr. Antentor Hinton, Jr. uses Amira Software
Dr. Antentor Hinton Jr, has made extensive use of Amira Software as part of his lab’s work in mitochondrial research.
"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."
Dr. Antentor Hinton, Jr.
Department of Molecular Physiology and Biophysics, Vanderbilt University
Correlative microscopy: using Amira Software to understand the spread of cancer
Matthia A. Karreman, MSc, PhD uses Amira Software
Matthia A. Karreman at EMBL and DKFZ, Heidelberg, Germany, uses Amira Software.
“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 and DKFZ, Heidelberg, Germany
Amira Software accelerates veterinary research with 3D visualization and analysis
Stephan Handschuch, PhD uses Amira Software
"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
Amira Software characterizing the replication cycle of SARS-CoV-2 inside host cells
Steffen Klein, Heidelburg, uses Amira Software for 3D cell imaging and analysis
"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."
Steffen Klein
Chlanda lab, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
Leveraging Amira Software to unveil mammalian olfactory evolution
Leveraging Amira Software to unveil mammalian olfactory evolution
“To understand the evolution of olfaction in amphibious mammals, I scan skulls or heads of museum specimens, sometimes collected more than a hundred years ago. This method allows me to access internal structures such as olfactory organs without damaging the museum specimens. I use Amira Software to visualize, segment and quantify the olfactory organs.”
Dr. Quentin Martinez
State Museum of Natural History in Stuttgart (SMNS), Germany
Researchers at Guangzhou Medical University have discovered an intercellular organelle reservoir in the epididymal epithelium using FIB-SEM imaging
Intercellular organelle reservoir in the epididymal epithelium using FIB-SEM imaging
“Amira [Software] is a great tool for 3D reconstruction, and it is easy to use.” The impressive 3D models created using Amira Software were showcased in a paper published in the Nature Communications journal.”
Prof. Hao Chen
Guangzhou Medical University, Guangdong, CN
UZ Leuven uses Amira Software for postoperative evaluation of orthognathic patients
3D orthognathic visualization created by UZ Leuven using Amira Software
"We will focus on postoperative evaluation of orthognathic patients to quantify the accuracy of the surgical outcome of bimaxillary surgeries by comparing it to the 3D virtual preoperative planning."
The Max Planck Institute of Neurobiology uses Amira Software for axon tracing from head to toe
Axon tracing performed with Amira Software at the Max Planck Institute of Neurobiology
“As a long-term Amira Software user, Ertürk trusted the system, with its filament tracing and visualization features, to be the tool of choice. Using Amira Software's skeletonization modules and filament editing tools, he succeeded in tracing axons from the spinal cord lesion site to their dorsal root ganglions, thereby validating that they were derived from neurons whose peripheral axon had been cut. The tracing of axons up to their tip shows the great potential of 3D imaging to clearly distinguish regenerated axons from unharmed axons, all at a resolution of traditional histology methods.”
University of Washington Researchers use Amira Software towards aiding the pathology of pancreatic cancer
Pancreatic cancer analysis workflow in Amira Software
"Amira Software permits our original optical dataset to be completely loaded into its software package at full resolution, where object manipulation is easy and rapid for initial tissue interrogation studies. The software additionally renders the entire volume of the biopsy and allows our team to threshold the reconstructed data for specific investigations involving whole tissue staining."
University of Glasgow uses Amira Software to analyze vascular structures
3D vascular structure analysis with Amira Software at the University of Glasgow
"Amira Software permits our original optical dataset to be completely loaded into its software package at full resolution, where object manipulation is easy and rapid for initial tissue interrogation studies. The software additionally renders the entire volume of the biopsy and allows our team to threshold the reconstructed data for specific investigations involving whole tissue staining."
AMSC Research, LLC uses Amira Software to understand processes and rituals of Egyptian mummification
3D scan of an Egyptian mummy visualized with Amira Software at AMSC Research
"Elias uses Amira Software to analyze scan data. Mummies are biological entities, so apart from the usual forensic side of things (features having to do with skin and bone), they also have cultural elements that relate to their chronology and social significance. [...] Elias has come to favor the Amira [Software] system because of its intuitive design. It accepts large data sets quite easily, and furnishes a wide range of optical controls which are versatile and sensitive. These features greatly speed up the discovery process. It makes research so much more colorful and interesting, which translates into powerful teaching media."
The Oriental Institute of the University of Chicago uses Amira software to visualize and analyze Egyptian mummified birds
3D scan of a mummified bird, created with Amira Software at the Oriental Institute of the University of Chicago
"With this specimen, careful segmentation in Amira Software was the essential key for visualization of the mummy's interior and identification of the bird. Here, the low calcification proved challenging during the segmentation process. Once the segmentation was completed, Amira Software's crisp surface rendering allowed further analysis and identification."
For Research Use Only. Not for use in diagnostic procedures.