Avizo (software)

Avizo (pronounce: ‘a-VEE-zo’) is a general-purpose commercial software application for scientific and industrial data visualization and analysis.

Avizo

Developer(s)	Thermo Fisher Scientific
Stable release	2020.3 / February 2021; 3 years ago (2021-02)
Operating system	Linux, Mac OS X, Microsoft Windows
Type	Visualization and analysis software
License	Proprietary
Website	www.thermofisher.com/de/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software.html

Avizo is developed by Thermo Fisher Scientific and was originally designed and developed by the Visualization and Data Analysis Group^[1] at Zuse Institute Berlin (ZIB) under the name Amira. Avizo was commercially released in November 2007. For the history of its development, see the Wikipedia article about Amira.

Overview

 

Metallic foam quantification

 

Virtual permeameter for absolute permeability computation

 

3D image-based meshing for CFD/FEA analysis of a mechanical part

 

Geosciences data visualization

Avizo is a software application which enables users to perform interactive visualization and computation on 3D data sets. The Avizo interface is modelled on the visual programming. Users manipulate data and module components, organized in an interactive graph representation (called Pool), or in a Tree view. Data and modules can be interactively connected together, and controlled with several parameters, creating a visual processing network whose output is displayed in a 3D viewer.

With this interface, complex data can be interactively explored and analyzed by applying a controlled sequence of computation and display processes resulting in a meaningful visual representation and associated derived data.

Application areas

Avizo has been designed to support different types of applications and workflows from 2D and 3D image data processing to simulations. It is a versatile and customizable visualization tool used in many fields:

• Scientific visualization^[2]
• Materials Research^{[3][4][5][6][7][8][9]}
• Tomography,^[10][11][12]Microscopy,^[13][14] etc.
• Nondestructive testing,^[15] Industrial Inspection,^[16][17] and Visual Inspection
• Computer-aided Engineering^[18][19] and simulation data post-processing
• Porous medium analysis^{[20][21][22][23][24][25][26]}
• Civil Engineering^[27]
• Seismic Exploration, Reservoir Engineering, Microseismic Monitoring, Borehole Imaging^[28]
• Geology,^[29][30][31] Digital Rock Physics (DRP),^[32][33][34] Earth Sciences^{[35][36][37][38][39]}
• Archaeology^[40][41]
• Food technology and agricultural science^{[42][43][44][45]}
• Physics, Chemistry^[46]
• Climatology,^{[47][48][49][50]} Oceanography, Environmental Studies ^[51]
• Astrophysics

Features

Data import:

• 2D and 3D image stack and volume data: from microscopes (electron, optical),^{[52][53][54][55][56][57]} X-ray tomography (CT, micro-/nano-CT, synchrotron),^[58][59][60] neutron tomography^[61] and other acquisition devices (MRI, radiography, GPR)
• Geometric models (such as point sets, line sets, surfaces, grids)
• Numerical simulation data ^{[62][63][64][65]} (such as Computational fluid dynamics or Finite element analysis data)
• Molecular data
• Time series and animations ^[66]
• Seismic data^[67]
• Well logs
• 4D Multivariate Climate Models ^[68][69]

2D/3D data visualization: ^[70][71][72]

• Volume rendering^{[73][74][75][76]}
• Digital Volume Correlation
• Visualization of sections, through various slicing and clipping methods ^[77]
• Isosurface rendering^{[78][79][80][81]}
• Polygonal meshes
• Scalar fields, Vector fields, Tensor representations, Flow visualization (Illuminated Streamlines, Stream Ribbons) ^[82]

Image processing:^{[83][84][85][86][87][88]}

• 2D/3D Alignment of image slices,^[89] Image registration^[90]
• Image filtering
• Mathematical Morphology (erode, dilate, open, close, tophat)
• Watershed Transform, Distance Transform
• Image segmentation^{[91][92][93][94][95][96][97][98]}

3D models reconstruction:^{[99][100][101][102][103][104][105]}

• Polygonal surface generation from segmented objects^[106]
• Generation of tetrahedral grids^[107]
• Surface reconstruction from point clouds
• Skeletonization (reconstruction of dendritic, porous or fracture network)^{[108][109][110]}
• Surface model simplification

Quantification and analysis:^{[111][112][113][114][115][116][117][118][119]}

• Measurements and statistics^{[120][121][122][123][124]}
• Analysis spreadsheet and charting

Material properties computation, based on 3D images:

• Absolute permeability
• Thermal conductivity
• Molecular diffusivity
• Electrical resistivity/formation factor

3D image-based meshing for CFD and FEA:^[125]

• From 3D imaging modalities (CT, micro-CT, MRI, etc.) ^[126][127]
• Surface and volume meshes generation ^[128]
• Export to FEA and CFD solvers for simulation
• Post-processing for simulation analysis

Presentation, automation:

• MovieMaker,^[129] Multiscreen, Video wall, collaboration, and VR^[130] support
• TCL Scripting, C++ extension API

Avizo is based on 3D graphics toolkits (FEI Visualization Sciences Group).

External links

• Official website
• Avizo videos

References

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90. Trtik, Pavel; Kaufmann, Josef; Volz, Udo (2012). "On the use of peak-force tapping atomic force microscopy for quantification of the local elastic modulus in hardened cement paste". Cement and Concrete Research. 42: 215–221. doi:10.1016/j.cemconres.2011.08.009.
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97. Ho, Quang Tri; Verboven, Pieter; Verlinden, Bert E.; Herremans, Els; Wevers, Martine; Carmeliet, Jan; Nicolaï, Bart M. (2011). "A Three-Dimensional Multiscale Model for Gas Exchange in Fruit". Plant Physiology. 155 (3): 1158–1168. doi:10.1104/pp.110.169391. PMC 3046576. PMID 21224337. S2CID 9700180.
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100. Radionuclide Retention in Concrete Wasteforms, By CC Bovaird, DM Wellman, DP Jansik, MI Wood – US Department Energy [21]
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105. Jiao, Zhenjun; Shikazono, Naoki; Kasagi, Nobuhide (2010). "Comparison of ultra-fast microwave sintering and conventional thermal sintering in manufacturing of anode support solid oxide fuel cell" (PDF). Journal of Power Sources. 195 (24): 8019–8027. Bibcode:2010JPS...195.8019J. doi:10.1016/j.jpowsour.2010.06.072.
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108. Zhu, Wenlu; Gaetani, Glenn A.; Fusseis, Florian; Montési, Laurent G. J.; De Carlo, Francesco (2011). "Microtomography of Partially Molten Rocks: Three-Dimensional Melt Distribution in Mantle Peridotite". Science. 332 (6025): 88–91. Bibcode:2011Sci...332...88Z. doi:10.1126/science.1202221. JSTOR 29783979. PMID 21454786. S2CID 7963547.
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110. Lück, S.; Sailer, M.; Schmidt, V.; Walther, P. (2010). (PDF). Journal of Microscopy. 239 (1): 1–16. doi:10.1111/j.1365-2818.2009.03348.x. PMID 20579265. S2CID 42230871. Archived from the original (PDF) on 2012-10-03.
111. Kanitpanyacharoen, Waruntorn; Parkinson, Dilworth Y.; De Carlo, Francesco; Marone, Federica; Stampanoni, Marco; Mokso, Rajmund; MacDowell, Alastair; Wenk, Hans-Rudolf (2013). "A comparative study of X-ray tomographic microscopy on shales at different synchrotron facilities: ALS, APS and SLS". Journal of Synchrotron Radiation. 20 (Pt 1): 172–180. doi:10.1107/S0909049512044354. PMC 3943535. PMID 23254671.
112. Abdul Wahab, M.A.; De Nys, R.; Whalan, S. (2012). "Closing the lifecycle for the sustainable aquaculture of the bath sponge Coscinoderma matthewsi". Aquaculture. 324–325: 281–289. doi:10.1016/j.aquaculture.2011.11.006.
113. Lee, Joung-Hyun; Gu, Yexin; Wang, Hongjun; Lee, Woo Y. (2012). "Microfluidic 3D bone tissue model for high-throughput evaluation of wound-healing and infection-preventing biomaterials". Biomaterials. 33 (4): 999–1006. doi:10.1016/j.biomaterials.2011.10.036. PMID 22061488.
114. Verboven, Pieter; Pedersen, Ole; Herremans, Els; Ho, Quang Tri; Nicolaï, Bart M.; Colmer, Timothy David; Teakle, Natasha (2012). "Root aeration via aerenchymatous phellem: Three-dimensional micro-imaging and radial O2 profiles in Melilotus siculus". New Phytologist. 193 (2): 420–431. doi:10.1111/j.1469-8137.2011.03934.x. PMID 22029709.
115. Enhancing Appalachian Coalbed Methane Extraction by Microwave-Induced Fractures, by Jonathan P. Mathews – The Pennsylvania State University (PDF). Archived from the original (PDF) on 2012-03-31. Retrieved 2011-09-05.{{cite web}}: CS1 maint: archived copy as title (link)
116. FRACTURING CONTROLLED PRIMARY MIGRATION OF HYDROCARBONS FLUIDS DURING HEATING OF ORGANIC-RICH SHALES, by Maya Kobchenko (1), Hamed Panahi (1)(2), François Renard (1)(3), Dag K. Dysthe (1), Anders Malthe-Sørenssen (1), Adriano Mazzini (1), Julien Scheibert (1), Bjørn Jamtveit (1) and Paul Meakin (1) (4) (5) – (1) Physics of Geological Processes, University of Oslo, Norway; (2) Statoil ASA, Norway; (3) Institut des Sciences de la Terre, Université Joseph Fourier-CNRS, Grenoble, France; (4) Idaho National Laboratory, Idaho Falls, USA; (5) Institute for Energy Technology, Kjeller, Norway [22]
117. VISUALIZATION AND QUANTIFICATION OF BIOFILM ARCHITECTURE WITHIN POROUS MEDIA USING SYNCHROTRON BASED X-RAY COMPUTED MICROTOMOGRAPHY, by Gabriel Iltis, Ryan Armstrong, and Dorthe Wildenschild – Dpt of Chemical, Biological and Environmental Engineering, Oregon State University, USA (PDF). Archived from the original (PDF) on 2011-09-27. Retrieved 2010-12-17.{{cite web}}: CS1 maint: archived copy as title (link)
118. Luo, Lifang; Lin, Henry; Li, Shuangcai (2010). "Quantification of 3-D soil macropore networks in different soil types and land uses using computed tomography" (PDF). Journal of Hydrology. 393 (1–2): 53–64. Bibcode:2010JHyd..393...53L. doi:10.1016/j.jhydrol.2010.03.031.
119. Haubrich, Sarah Shiley (2009). "Experimental observations and simulations of the mechanical deformation of amorphous metallic foam" (PDF). doi:10.31274/etd-180810-1434. {{cite journal}}: Cite journal requires |journal= (help)
120. Liu, Zhao; Scott Cronin, J.; Chen-Wiegart, Yu-Chen K.; Wilson, James R.; Yakal-Kremski, Kyle J.; Wang, Jun; Faber, Katherine T.; Barnett, Scott A. (2013). "Three-Dimensional Morphological Measurements of LiCoO₂ and LiCoO₂/Li(Ni_1/3Mn_1/3Co_1/3)O₂ Lithium-ion Battery Cathodes". Journal of Power Sources. 227: 267–274. doi:10.1016/j.jpowsour.2012.11.043.
121. Al-Mutairi, S. H.; Al-Obied, M. A.; Al-Yami, I. S.; Shebatalhamd, A. M.; Al-Shehri, D. A. (2012). "Wormhole Propagation in Tar During Matrix Acidizing of Carbonate Formation". All Days. doi:10.2118/151560-MS.
122. Brodersen, C. R.; McElrone, A. J.; Choat, B.; Matthews, M. A.; Shackel, K. A. (2010). "The Dynamics of Embolism Repair in Xylem: In Vivo Visualizations Using High-Resolution Computed Tomography". Plant Physiology. 154 (3): 1088–1095. doi:10.1104/pp.110.162396. PMC 2971590. PMID 20841451.
123. Porter, Mark L.; Wildenschild, Dorthe; Grant, Gavin; Gerhard, Jason I. (2010). (PDF). Water Resources Research. 46 (8). Bibcode:2010WRR....46.8512P. doi:10.1029/2009WR007786. S2CID 55863065. Archived from the original (PDF) on 2011-07-16.
124. Xin, Huolin L.; Ercius, Peter; Hughes, Kevin J.; Engstrom, James R.; Muller, David A. (2010). "Three-dimensional imaging of pore structures inside low-κ dielectrics". Applied Physics Letters. 96 (22): 223108. Bibcode:2010ApPhL..96v3108X. doi:10.1063/1.3442496.
125. SIMULATIONS ET ANALYSES 2D-3D DE LA POROSITE DE DEPOTS PLASMA D'ALUMINE POUR LA CARACTERISATION DE PROPRIETES MECANIQUES ET PHYSIQUES by Vincent Guipont, Centre des Matériaux, CNRS (France) (PDF). Archived from the original (PDF) on 2011-07-20. Retrieved 2010-07-21.{{cite web}}: CS1 maint: archived copy as title (link)
126. Identification des propriétés des tissus mous de la jambe sous compression élastique, by L. Dubuis (1), S. Avril (1), P. Badel (1), J. Debayle (2) – (1) LCG, École des Mines de Saint-Étienne (France), (2) LPMG, École des Mines de Saint-Étienne (France)[23]
127. Vanderesse, N.; Maire, É.; Chabod, A.; Buffière, J.-Y. (2011). "Microtomographic study and finite element analysis of the porosity harmfulness in a cast aluminium alloy". International Journal of Fatigue. 33 (12): 1514–1525. doi:10.1016/j.ijfatigue.2011.06.010.
128. Transport Phenomena on the Channel-Rib Scale of Polymer Electrolyte Fuel Cells, by Reto Fluckiger – ETH Zurich [24]
129. ONE-MONTH SIMULATED PLANET SIMULATOR CIRCULATION, Meteorologisches Institut, Universität Hamburg (Germany). Archived from the original on 2011-07-19. Retrieved 2010-01-31.
130. VISUALISATION IMMERSIVE ET INTERACTION HAPTIQUE : UNE REVOLUTION POUR LES GEOSCIENCES, by BRGM (Bureau des recherches géologiques et minières, France)[25]