Welcome to the Amira-Avizo Software Use Case Gallery

Below you will find a collection of use cases of our 3D data visualization and analysis software. These use cases include scientific publications, articles, papers, posters, presentations or even videos that show how Amira-Avizo Software is used to address various scientific and industrial research topics.

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Juvenile Ovine Ex Vivo Larynges: Phonatory, Histologic, and Micro CT Based Anatomic Analyses

Juvenile Ovine Ex Vivo Larynges: Phonatory, Histologic, and Micro CT Based Anatomic Analyses

It is well known that the phonatory process changes during the life span. However, detailed investigations on potential factors concerned are rare. To deal with this issue, we performed extended biomechanical, macro anatomical, and histological analyses of the contributing laryngeal structures in ex vivo juvenile sheep models. Altogether twelve juvenile sheep larynges were analyzed within the phonatory experiments. Three different elongation levels and 16 different flow levels were applied to... Read more

Michael Döllinger, Olaf Wendler, Claus Gerstenberger, Tanja Grossmann, Marion Semmler, Hossein Sadeghi, and Markus Gugatschka

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Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

Computed tomography is an increasingly popular technique for the non-destructive study of fossils. Whilst the science of X-ray computed tomography (CT) has greatly matured since its first fossil applications in the early 1980s, the applications and limitations of neutron tomography (NT) remain relatively unexplored in palaeontology. These highest resolution neutron tomographic scans in palaeontology to date were conducted on a specimen of Austrosequoia novae-zeelandiae (Ettingshausen) Mays an... Read more

Chris Mays, Joseph J. Bevitt, and Jeffrey D. Stilwell

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3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris)

3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris)

Avian flight is achieved through a number of modifications to the body, including the pectoral girdle (…). Muscle architecture is a critical variable in determining the biomechanical function of the vertebrate musculoskeletal system; however, accurate three-dimensional (3D) understanding of muscle architecture has been historically difficult to acquire. Here, we present a musculoskeletal model of a European starling (Sturnus vulgaris) pectoral girdle generated from iodine contr... Read more

S.P. Sullivan, F.R. McGechie, K.M. Middleton, C.M. Holliday

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Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography

Comparative Morphology of the Internal Nasal Skeleton of Adult Marsupials Based on X-ray Computed Tomography

The internal skeleton of the nasal cavity is sporadically and often incompletely described for many marsupial species and mammals in general. Here, I provide an anatomical survey of the ethmoid in the skulls of adult marsupials based on examination of computed tomography (CT) imagery of 29 taxa representing all the major extant groups of marsupials. (…) I compared ecological data with the number of ecto- and endoturbinals as a preliminary test to determine whether some of the interspec... Read more

Thomas E. Macrini

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Preservation of three-dimensional anatomy in phosphatized fossil arthropods enriches evolutionary inference

Preservation of three-dimensional anatomy in phosphatized fossil arthropods enriches evolutionary inference

External and internal morphological characters of extant and fossil organisms are crucial to establishing their systematic position, ecological role and evolutionary trends. (…) We found well-preserved three-dimensional anatomy in mineralized arthropods from Paleogene fissure fillings and demonstrate the value of these fossils by utilizing digitally reconstructed anatomical structure of a hister beetle. The new anatomical data facilitate a refinement of the species diagnosis and allowed... Read more

Achim H Schwermann, Tomy dos Santos Rolo, Michael S Caterino, Gunter Bechly, Heiko Schmied, Tilo Baumbach, Thomas van de Kamp

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University of York student wins Anatomical Society Best Image Prize using Amira-Avizo Software

University of York student wins Anatomical Society Best Image Prize using Amira-Avizo Software

PhD student Jesse Hennekam wins for his reconstruction of the skull of a giant dormouse.

A York PhD student has won a prestigious award for his work reconstructing the skull of a giant rodent.

Jesse Hennekam, from the Centre for Anatomical and Human Sciences at the Hull York Medical School, created a digital reconstruction of the skull of a gigantic dormouse (Leithia melitensis), which roamed on the island of Sicily during the Pleistocene, roughly 2 million years ago... Read more

Jesse Hennekam

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Hyperpolarized 13C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model

Hyperpolarized 13C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model

Proinflammatory mononuclear phagocytes (MPs) play a crucial role in the progression of multiple sclerosis (MS) and other neurodegenerative diseases. Despite advances in neuroimaging, there are currently limited available methods enabling noninvasive detection of MPs in vivo. Interestingly, upon activation and subsequent differentiation toward a proinflammatory phenotype MPs undergo metabolic reprogramming that results in increased glycolysis and production of lactate. Hyperpolarized (HP) Read more

Caroline Guglielmetti, Chloé Najac, Alessandro Didonna, Annemie Van der Linden, Sabrina M. Ronen, and Myriam M. Chaumeil

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Operative Anatomy of the Human Skull: A Virtual Reality Expedition

Operative Anatomy of the Human Skull: A Virtual Reality Expedition

The human cranial vault possesses an incredible, complex anatomical intricacy. Bridging the divide between 2-dimensional (2D) learning resources and the 3-dimensional (3D) world in which the anatomy becomes clinically relevant poses an intellectual challenge. Advances in computer graphics and modelling technologies have allowed increasingly accurate and representative resources to supplement cadaveric dissection specimens. To create accurate v... Read more

Benjamin K Hendricks, MD Akash J Patel, MD Jerome Hartman Mark F Seifert, PhD Aaron Cohen-Gadol, MD, MSc, MBA

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Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

Patient-specific anatomical model for deep brain stimulation based on 7 Tesla MRI

Deep brain stimulation (DBS) requires accurate localization of the anatomical target structure, and the precise placement of the DBS electrode within it. Ultra-high field 7 Tesla (T) MR images can be utilized to create patient-specific anatomical 3D models of the subthalamic nuclei (STN) to enhance pre-surgical DBS targeting as well as post-surgical visualization of the DBS lead position and orientation. We validated the accuracy of the 7T imaging-based patient-specific model of the STN and m... Read more

Yuval Duchin, Reuben R. Shamir, Remi Patriat, Jinyoung Kim, Jerrold L. Vitek, Guillermo Sapiro, Noam Harel

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Secure corridor for infraacetabular screws in acetabular fracture fixation—a 3-D radiomorphometric analysis of 124 pelvic CT datasets

Secure corridor for infraacetabular screws in acetabular fracture fixation—a 3-D radiomorphometric analysis of 124 pelvic CT datasets

Acetabular fracture surgery is directed toward anatomical reduction and stable fixation to allow for the early functional rehabilitation of an injured hip joint. Recent biomechanical investigations have shown the superiority of using an additional screw in the infraacetabular (IA) region, thereby transfixing the separated columns to strengthen the construct by closing the periacetabular fixation frame. However, the inter-individual existence and variance concerning secure IA screw corridors a... Read more

Stephan Arlt, Hansrudi Noser, Andreas Wienke, Florian Radetzki, Gunther Olaf Hofmann, Thomas Mendel

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Resurrecting Darwin’s Niata - anatomical, biomechanical, genetic, and morphometric studies of morphological novelty in cattle

Resurrecting Darwin’s Niata - anatomical, biomechanical, genetic, and morphometric studies of morphological novelty in cattle

The Niata was a cattle variety from South America that figured prominently in writings on evolution by Charles Darwin. Its shortened head and other aspects of its unusual morphology have been subject of unsettled discussions since Darwin’s time. Here, we examine the anatomy, cranial shape, skull biomechanics, and population genetics of the Niata. Our results show that the Niata was a viable variety of cattle and exhibited anatomical differences to known chondrodysplastic forms. In cranial s... Read more

Kristof Veitschegger, Laura A. B. Wilson, Beatrice Nussberger, Glauco Camenisch, Lukas F. Keller, Stephen Wroe, Marcelo R. Sánchez-Villagra

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Mechanical adaptation of trabecular bone morphology in the mammalian mandible

Mechanical adaptation of trabecular bone morphology in the mammalian mandible

Alveolar bone, together with the underlying trabecular bone, fulfils an important role in providing structural support against masticatory forces. Diseases such as osteoporosis or periodontitis cause alveolar bone resorption which weakens this structural support and is a major cause of tooth loss. However, the functional relationship between alveolar bone remodelling within the molar region and masticatory forces is not well understood. This study investigated this relationship by comparing m... Read more

Peter J. Watson, Laura C. Fitton, Carlo Meloro, Michael J. Fagan, Flora Gröning

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Reinvestigating an enigmatic Late Cretaceous monocot: morphology, taxonomy, and biogeography of Viracarpon

Reinvestigating an enigmatic Late Cretaceous monocot: morphology, taxonomy, and biogeography of Viracarpon

Angiosperm-dominated floras of the Late Cretaceous are essential for understanding the evolutionary, ecological, and geographic radiation of flowering plants.

The Late Cretaceous–early Paleogene Deccan Intertrappean Beds of India contain angiosperm-dominated plant fossil assemblages known from multiple localities in central India. Numerous monocots have been documented from these assemblages, providing a window into an important but poorly understood time in their diversification. On... Read more

Kelly K.S. Matsunaga, Selena Y. Smith, Steven R. Manchester, Dashrath Kapgate, Deepak Ramteke, Amin Garbout, and Herminso Villarraga-Gómez

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Exploring hominin and non-hominin primate dental fossil remains with neutron microtomography

Exploring hominin and non-hominin primate dental fossil remains with neutron microtomography

Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on Xray microfocus sources (X-µCT) and Synchrotron Radiation (SR-µCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through highresolution “virtual histology”. Nonetheless, depending on the degree of alterations undergone during fossiliza... Read more

Clément Zanolli, Laboratory AMIS, UMR 5288, University of Toulouse III - Paul Sabatier, France, and al.

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The first Neanderthal remains from an open-air Middle Palaeolithic site in the Levant

The first Neanderthal remains from an open-air Middle Palaeolithic site in the Levant

The late Middle Palaeolithic (MP) settlement patterns in the Levant included the repeated use of caves and open landscape sites. The fossil record shows that two types of hominins occupied the region during this period—Neandertals and Homo sapiens. Until recently, diagnostic fossil remains were found only at cave sites. Because the two populations in this region left similar material cultural remains, it was impossible to attribute any open-air site to either species. In this study... Read more

Ella Been, Erella Hovers, Ravid Ekshtain, Ariel Malinski-Buller, Nuha Agha, Alon Barash, Daniella E. Bar-Yosef Mayer, Stefano Benazzi, Jean-Jacques Hublin, Lihi Levin, Noam Greenbaum, Netta Mitki, Gregorio Oxilia, Naomi Porat, Joel Roskin, Michalle Soudack, Reuven Yeshurun, Ruth Shahack-Gross, Nadav Nir, Mareike C. Stahlschmidt, Yoel Rak & Omry Barzilai

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Propagation-based phase-contrast x-ray tomography of cochlea using a compact synchrotron source

Propagation-based phase-contrast x-ray tomography of cochlea using a compact synchrotron source

We demonstrate that phase retrieval and tomographic imaging at the organ level of small animals can be advantageously carried out using the monochromatic radiation emitted by a compact x-ray light source, without further optical elements apart from source and detector. This approach allows to carry out microtomography experiments which – due to the large performance gap with respect to conventional laboratory instruments – so far were usually limited to synchrotron sources. We dem... Read more

Mareike Töpperwien, Regine Gradl, Daniel Keppeler, Malte Vassholz, Alexander Meyer, Roland Hessler, Klaus Achterhold, Bernhard Gleich, Martin Dierolf, Franz Pfeiffer, Tobias Moser & Tim Salditt

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