Avizo (software)

Software for scientific and industrial data visualization and analysis

Avizo

Developer(s)| Thermo Fisher Scientific
Stable release|

2020.3 / February 2021; 4 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 (pronounce: ‘a-VEE-zo’) is a general-purpose commercial software application for scientific and industrial data visualization and analysis.

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

[edit]

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

[edit]

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

[edit]

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 Open Inventor 3D graphics toolkits (FEI Visualization Sciences Group).

## References

[edit]

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67. ^ Visual and Spatial Technology Center (VISTA) (University of Birmingham, UK)"Visual and Spatial Technology Centre". Archived from the original on 2009-07-15. Retrieved 2010-01-29.
68. ^ INTERACTIVE 3D VISUALIZATION IN EARTH SYSTEM RESEARCH, by The German Climate Computing Center (Deutsches Klimarechenzentrum, DKRZ)"3D Visualization 2008 with Avizo". Archived from the original on 2008-12-17. Retrieved 2010-01-29.
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71. ^ Volume Edit and Thresholding – By Elise Orellana (LSU Honors Class 3035, Spring'11, Student Project Showcase) The Use of Metal Markers In 3D Imaging – By Caroline Blevins (LSU Honors Class 3035, Spring'11, Student Project Showcase) Using 3D Reconstruction to Illustrate the Cranio-cervical Envelope in the Alligator – By Brooke Hopkins (LSU Honors Class 3035, Spring'11, Student Project Showcase) Visualization and Analysis of the Human Shoulder Suspensory Apparatus – By Michelle Osborn (LSU Honors Class 3035, Spring'11, Student Project Showcase)"CCT - Advanced Visualization Serive Laboratory". Archived from the original on 2011-09-27. Retrieved 2011-06-30.
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86. ^ Ohta, Keisuke; Sadayama, Shoji; Togo, Akinobu; Higashi, Ryuhei; Tanoue, Ryuichiro; Nakamura, Kei-Ichiro (2012). "Beam deceleration for block-face scanning electron microscopy of embedded biological tissue". Micron. 43 (5): 612–620\. doi:10.1016/j.micron.2011.11.001. PMID 22285616.
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99. ^ Spitting behaviour and fang morphology of spitting cobras, by RA Berthé – 2011 [20]
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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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\. Bibcode:2012Aquac.324..281A. doi:10.1016/j.aquaculture.2011.11.006.
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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 "Archived copy" (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 "Archived copy" (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.2010.03.031.1–2&rft.pages=53-64&rft.date=2010&rft_id=info:doi/10.1016/j.jhydrol.2010.03.031&rft_id=info:bibcode/2010JHyd..393...53L&rft.aulast=Luo&rft.aufirst=Lifang&rft.au=Lin,+Henry&rft.au=Li,+Shuangcai&rft_id=https://www.ars.usda.gov/ARSUserFiles/43576/lluo_pub06.pdf&rfr_id=info:sid/en.wikipedia.org:Avizo+(software)" class="Z3988">
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123. ^ Porter, Mark L.; Wildenschild, Dorthe; Grant, Gavin; Gerhard, Jason I. (2010). "Measurement and prediction of the relationship between capillary pressure, saturation, and interfacial area in a NAPL-water-glass bead system" (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) "Archived copy" (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)"Meteorologisches Institut: One month simulated Planet Simulator circulation". Archived from the original on 2011-07-19. Retrieved 2010-01-31.
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