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.

Use the Domain selector to filter by main application area, and use the Search box to enter keywords related to specific topics you are interested in.

Microbial-tubeworm associations in a 440 million year old hydrothermal vent community

Microbial-tubeworm associations in a 440 million year old hydrothermal vent community

Microorganisms are the chief primary producers within present-day deep-sea hydrothermal vent ecosystems, and play a fundamental role in shaping the ecology of these environments. (…) The oldest known hydrothermal vent community that includes metazoans is preserved within the Ordovician to early Silurian Yaman Kasy massive sulfide deposit, Ural Mountains, Russia. (…) A re-examination of these fossils using a range of microscopy, chemical analysis and nano-tomography techniques re... Read more

Magdalena N. Georgieva , Crispin T. S. Little , Russell J. Bailey , Alexander D. Ball and Adrian G. Glover

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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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Spiny fruits revealed by nano-CT scanning: Pseudoanacardium peruvianum (Berry) gen. et comb. nov. from the early Oligocene Belén flora of Peru

Spiny fruits revealed by nano-CT scanning: Pseudoanacardium peruvianum (Berry) gen. et comb. nov. from the early Oligocene Belén flora of Peru

Fossil fruits formerly described as cashews from the Oligocene of Peru are reinvestigated based on the original specimens and newly collected materials. The recovery of an outer spiny layer, preserved in the sedimentary molds surrounding the locule casts, indicates that these disseminules do not represent Anacardium. Imagery from nano-CT scans of the specimens documents a distinctive morphology which does not resemble any fruits or seeds of Anacardiaceae. We describe the morphology in more de... Read more

STEVEN R. MANCHESTER, BEHNAZ BALMAKI

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3D virtual reconstruction of the Kebara 2 Neandertal thorax

3D virtual reconstruction of the Kebara 2 Neandertal thorax

The size and shape of the Neandertal thorax has been debated since the first discovery of Neandertal ribs more than 150 years ago, with workers proposing different interpretations ranging from a Neandertal thoracic morphology that is indistinguishable from modern humans, to one that was significantly different from them. Here, we provide a virtual 3D reconstruction of the thorax of the adult male Kebara 2 Neandertal. Our analyses reveal that the Kebara 2 thorax is significantly different but ... Read more

Asier Gomez-Olivencia, Alon Barash, Daniel Garcia-Martinez, Mikel Arlegi, Patricia Kramer, Markus Bastir, Ella Been

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Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group

Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group

Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that fl... Read more

Isaac Casanovas-Vilar, Joan Garcia-Porta, Josep Fortuny, Oscar Sanisidro, Jerome Prieto, Marina Querejeta, Sergio Llacer, Josep M Robles, Federico Bernardini, David M Alba

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New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)

New omomyoids (Euprimates, Mammalia) from the late Uintan of southern California, USA, and the question of the extinction of the Paromomyidae (Plesiadapiformes, Primates)

Paromomyidae has been thought to represent the longest-lived group of stem primates (plesiadapiforms), extending from the early Paleocene to late Eocene. We analyzed primate material from the late-middle Eocene of southern California that had initially been ascribed to cf. Phenacolemur shifrae. This material falls at the lowest end of the size range for the family. The Californian specimens also exhibit several dental features that are atypical for paromomyids, such as a strong paraconid on t... Read more

Sergi López-Torres, Mary T. Silcox, and Patricia A. Holroyd

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Allometry and integration do not strongly constrain beak shape evolution in large-billed (Corvus macrorhynchos) and carrion crows (Corvus corone)

Allometry and integration do not strongly constrain beak shape evolution in large-billed (Corvus macrorhynchos) and carrion crows (Corvus corone)

Here, to evaluate the intensity of evolutionary constraints on avian beak shape more appropriately, we selected large billed (Corvus macrorhynchos) and carrion crows (Corvus corone) as study objects. These landbird species seem to experience selection pressures favoring a departure from an allometric trajectory. A landmark based geometric morphometric approach using three dimensional reconstructions of CT scan images revealed that only 45.4% of the total shape variation was explained by allom... Read more

Takeshi Yamasaki, Sou Aoki, Masayoshi Tokita

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Digitizing extant bat diversity: An open-access repository of 3D μCT-scanned skulls for research and education

Digitizing extant bat diversity: An open-access repository of 3D μCT-scanned skulls for research and education

Biological specimens are primary records of organismal ecology and history. As such, museum collections are invaluable repositories for testing ecological and evolutionary hypotheses across the tree of life. Digitizing and broadly sharing the phenotypic data from these collections serves to expand the traditional reach of museums, enabling widespread data sharing, collaboration, and education at an unprecedented scale. In recent years, μCT-scanning has been adopted as one way for efficiently... Read more

Jeff J. Shi, Erin P. Westeen, Daniel L. Rabosky

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Over the rainbow? Micro-CT scanning to non-destructively study Roman and early medieval glass bead manufacture

Over the rainbow? Micro-CT scanning to non-destructively study Roman and early medieval glass bead manufacture

The usefulness of desktop Micro-CT scanners for the study of archaeological artefacts is demonstrated in a non-destructive study of manufacturing methods of Roman and Early Medieval monochrome and polychrome glass beads. Differences in glass colours show up in these scans as differences in attenuation. The presence and distribution of bubbles and various inclusions (metal, opacifier) are also well visible. Shaft shapes and patterns of bubbles inside the glass make it possible in most cases to... Read more

D.J.M.Ngan-Tillard, D.J.Huisman, F.Corbella, A.Van Nass

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A high-throughput, fully automated morphometric method to discover the genes controlling shape differences in the Faroese mice

A high-throughput, fully automated morphometric method to discover the genes controlling shape differences in the Faroese mice

The Faroe Islands are a group of islands in the North Atlantic that are known for its natural beauty, Viking culture and a special population of house mouse. The Faroese house mouse from the most remote island of the Faroese, Mykines (population: 10 people), looked so distinct when it was discovered that it was declared a subspecies, Mus musculus faeroenesis. These mice are large-bodied and showed an extreme form of left-right asymmetry in its skull. Our research group has... Read more

Yingguang Frank Chan, William H. Beluch, Rémi Blanc

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A method for deducing neck mobility in plesiosaurs, using the exceptionally preserved Nichollssaura borealis

A method for deducing neck mobility in plesiosaurs, using the exceptionally preserved Nichollssaura borealis

The elongate-necked aquatic plesiosaurs existed for 135 Myr during the Mesozoic. The function of this elongate neck is a point of debate. Using computed tomography and three-dimensional (3D) modelling, the range of motion (ROM) of the plesiosaur Nichollssaura borealis neck was assessed. To quantify the ROM, the intervertebral mobility was measured along the cervical vertebral column. This was done by manipulating the 3D models in the lateral and dorsoventral directions during two tri... Read more

Ramon S. Nagesan, Donald M. Henderson, Jason S. Anderson

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Convergent evolution of a mobile bony tongue in flighted dinosaurs and pterosaurs

Convergent evolution of a mobile bony tongue in flighted dinosaurs and pterosaurs

The tongue, with fleshy, muscular, and bony components, is an innovation of the earliest land-dwelling vertebrates with key functions in both feeding and respiration. Here, we bring together evidence from preserved hyoid elements from dinosaurs and outgroup archosaurs, including pterosaurs, with enhanced contrast x-ray computed tomography data from extant taxa. Midline ossification is a key component of the origin of an avian hyoid. The elaboration of the avian tongue includes the evolution o... Read more

Zhiheng Li, Zhonghe Zhou, Julia A. Clarke

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Under the armor: X-ray computed tomographic reconstruction of the internal skeleton of Coahomasuchus chathamensis (Archosauria: Aetosauria) from the Upper Triassic of North Carolina, USA, and a phylogenetic analysis of Aetosauria

Under the armor: X-ray computed tomographic reconstruction of the internal skeleton of Coahomasuchus chathamensis (Archosauria: Aetosauria) from the Upper Triassic of North Carolina, USA, and a phylogenetic analysis of Aetosauria

Aetosauria is a clade of heavily armored, quadrupedal omnivorous to herbivorous archosaurs known from the Late Triassic across what was the supercontinent of Pangea. Their abundance in many deposits relative to the paucity of other Triassic herbivores indicates that they were key components of Late Triassic ecosystems. However, their evolutionary relationships remain contentious due, in large part, to their extensive dermal armor, which often obstructs observation of internal skeletal anatomy... Read more

Devin K. Hoffman​, Andrew B. Heckert, Lindsay E. Zanno

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Sea shell measurements and visualization

Sea shell measurements and visualization

Naturalis uses Avizo to obtain quantitative measurements on sea shells to quantify the process of shell development and compare different specimens.

After extracting the surface of the shell, defining its axis, and interactively tracing a path spiraling around the shell, quantitative measurements are extracted to characterize the specimen and compare it with others.

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Zac bin Khalik – Naturalis Biodiversity Center, The Netherlands

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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A multianalytic investigation of weapon-related injuries in a Late Antiquity necropolis, Mutina, Italy

A multianalytic investigation of weapon-related injuries in a Late Antiquity necropolis, Mutina, Italy

Human skeletal remains from archaeological contexts occasionally present signs of traumatic injuries from weapons, revealing, for example, the degree of interpersonal violence, the type of weapon and the sequence of events of a specific historical context.

Traumatic lesions are generally analyzed using macroscopic and microscopic methods, which are not necessarily integrated in the same study. In this study, we employed a multi-analytical approach to determine i... Read more

Antonino Vazzana, Lucia Martina Scalise, Mirko Traversari, Carla Figus, Salvatore Andrea Apicella, Laura Buti, Gregorio Oxilia, Rita Sorrentino, Silvia Pellegrini, Chiara Matteucci, Lucio Calcagnile, Raffaele Savigni, Robin N.M.Feeney, Giorgio Gruppioni, Stefano Benazziah

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A Middle Triassic pachypleurosaur (Diapsida: Eosauropterygia) from a restricted carbonate ramp in the Western Carpathia

A Middle Triassic pachypleurosaur (Diapsida: Eosauropterygia) from a restricted carbonate ramp in the Western Carpathia

An eosauropterygian skeleton found in the Middle Triassic (upper Anisian) Gutenstein Formation of the Fatric Unit (Demänovská dolina Valley, Low Tatra Mountains, Slovakia) represents the earliest known occurrence of marine tetrapods in the Western Carpathians. The specimen represents a partly articulated portion of the postcranial skeleton (nine dorsal vertebrae, coracoid, ribs, gastral ribs, pelvic girdle, femur and one zeugopodial element). It is assigned to the Pachypleurosauria, more pr... Read more

ANDREJ ČERŇANSKÝ, NICOLE KLEIN, JÁN SOTÁK, MÁRIO OLŠAVSKÝ, JURAJ ŠURKA, and PAVEL HERICH

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Scientists discover the oldest Homo sapiens fossils at Jebel Irhoud, Morocco

Scientists discover the oldest Homo sapiens fossils at Jebel Irhoud, Morocco

New finds of fossils and stone tools from the archaeological site of Jebel Irhoud, Morocco, push back the origins of our species by one hundred thousand years and show that by about 300 thousand years ago important changes in our biology and behaviour had taken place across most of Africa.

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Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany)

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Revealing the skeleton of polar dinosaur using synchrotron computed tomography

Revealing the skeleton of polar dinosaur using synchrotron computed tomography

Leaellynasaura amicagraphica was a small, bipedal, herbivorous dinosaur from the Early Cretaceous (~106 million years ago) of Australia within the Antarctic Circle of that time.

Synchrotron scans, and the resulting 3D reconstruction of the skull and post-cranial skeleton, provide a unique view of the morphology of Leaellynasaura, and allows this material to be 3D printed for display.

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1University College London, UK; Monash University, Melbourne, Australia; Museum Victoria, Melbourne, Australia

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