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.

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells…

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Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer

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Determining the bacterial cell biology of planctomycetes

Determining the bacterial cell biology of planctomycetes

Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools…

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Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C. F. van Teeseling et al.

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3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons

Macroautophagy is morphologically characterized by autophagosome formation. Autophagosomes are double-membraned vesicles that sequester cytoplasmic components for further degradation in the lysosome. Basal autophagy is paramount for intracellular quality control in post-mitotic cells but, surprisingly, the number of autophagosomes in post-mitotic neurons is very low, suggesting that alternative degradative structures could exist in neurons…

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Maria Rosario Fernandez-Fernandez, Desire Ruiz-Garcia, Eva Martin-Solana, Francisco Javier Chichon, Jose L. Carrascosa, Jose-Jesus Fernandez

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Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells

Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells

The orchestration of intercellular communication is essential for multicellular organisms. One mechanism by which cells communicate is through long, actin-rich membranous protrusions called tunneling nanotubes (TNTs), which allow the intercellular transport of various cargoes, between the cytoplasm of distant cells in vitro and in vivo. Here, we use correlative FIB-SEM, light- and cryo-electron microscopy approaches to elucidate the structural organization of neuronal TNTs. Our data indicate ... Read more

Anna Sartori-Rupp, Diégo Cordero Cervantes, Anna Pepe, Karine Gousset, Elise Delage, Simon Corroyer-Dulmont, Christine Schmitt, Jacomina Krijnse-Locker & Chiara Zurzolo

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Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons

Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons

The tissue inhibitor of metalloproteinases-1 (TIMP-1) exerts inhibitory activity against matrix metalloproteinases and cytokine-like effects. We previously showed that TIMP-1 reduces neurite outgrowth in mouse cortical neurons and that this cytokine-like effect depends on TIMP-1 endocytosis mediated by the low-density lipoprotein receptor-related protein-1 (LRP-1). To gain insight into the interaction between TIMP-1 and LRP-1, we considered conformational changes that occur when a ligand bind... Read more

Laurie Verzeaux, Nicolas Belloy, Jessica Thevenard-Devy, Jérôme Devy, Géraldine Ferracci, Laurent Martiny, Stéphane Dedieu, Manuel Dauchez, Hervé Emonard, Nicolas Etique & Emmanuelle Devarenne-Charpentier

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Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images

Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images

Immunofluorescence tomography is a high-resolution 3-D reconstruction method based on methacrylate embedding and serial-sectioning, where 2-D images of immuno-stained serial-sections are computationally aligned into image stacks, and the 3-D volume rendered. Butyl-Methyl Methacrylate (BMMA) plastic was adopted as it preserves excellent tissue morphology and can be de-plasticized easily using an organic solvent, which enables immuno-staining of serial-sections without antibody penetration issu... Read more

Parfitt, Geraint J

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