Avizo (software)
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]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]
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]- ^ "Visual and Data-centric Computing". www.zib.de. Zuse Institute Berlin (ZIB).
- ^ Maiolino, Stephanie; Boyer, Doug M.; Bloch, Jonathan I.; Gilbert, Christopher C.; Groenke, Joseph (2012). "Evidence for a Grooming Claw in a North American Adapiform Primate: Implications for Anthropoid Origins". PLOS ONE. 7 (1): e29135. Bibcode:2012PLoSO...729135M. doi:10.1371/journal.pone.0029135. PMC 3254620. PMID 22253707.
- ^ Morris, Robert A.; Wang, Billie; Butts, Daniel; Thompson, Gregory B. (2013). "Variations in Tantalum Carbide Microstructures with Changing Carbon Content". International Journal of Applied Ceramic Technology. 10 (3): 540–551. doi:10.1111/j.1744-7402.2012.02761.x.
- ^ Rask, Morten; Madsen, Bo; Sørensen, Bent F.; Fife, Julie L.; Martyniuk, Karolina; Lauridsen, Erik M. (2012). "In situ observations of microscale damage evolution in unidirectional natural fibre composites" (PDF). Composites Part A: Applied Science and Manufacturing. 43 (10): 1639–1649. doi:10.1016/j.compositesa.2012.02.007. S2CID 55380600.
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- ^ Nazari, Amir; Sadr, Alireza; Saghiri, Mohammad Ali; Campillo-Funollet, Marc; Hamba, Hidenori; Shimada, Yasushi; Tagami, Junji; Sumi, Yasunori (2013). "Non-destructive characterization of voids in six flowable composites using swept-source optical coherence tomography". Dental Materials. 29 (3): 278–286. doi:10.1016/j.dental.2012.11.004. PMID 23182792.
- ^ Lozano-Perez, Sergio; Kruska, Karen; Iyengar, Ilya; Terachi, Takumi; Yamada, Takuyo (2012). "The role of cold work and applied stress on surface oxidation of 304 stainless steel". Corrosion Science. 56: 78–85. Bibcode:2012Corro..56...78L. doi:10.1016/j.corsci.2011.11.021.
- ^ Proulx, T. (2011). Optical Measurements, Modeling, and Metrology, Volume 5: Proceedings of the 2011 Annual Conference on Experimental and Applied Mechanics. Conference Proceedings of the Society for Experimental Mechanics Series. Springer New York. p. 55. ISBN 978-1-4614-0228-2.
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- ^ DATA ACQUISITION FOR A BRIDGE COLLAPSE TEST, by Kurt Veggeberg (National Instruments) – Bridge Model Validation visualization with Avizo "Archived copy" (PDF). Archived from the original (PDF) on 2011-07-20. Retrieved 2010-09-17.
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- ^ Wu, Xiaomin; Schlangen, Erik; Van Der Zwaag, Sybrand (2012). "Linking Porosity to Rolling Reduction and Fatigue Lifetime of Hot Rolled AA7xxx Alloys by 3D X-Ray Computed Tomography". Advanced Engineering Materials. 14 (7): 457–463. doi:10.1002/adem.201200087. S2CID 137507957.
- ^ Evaluation of Asphalt Field Cores with Simple Performance Tester and X-ray Computed Tomography, by Florentina Angela Farca – Division of Highway and Railway Engineering, Department of Transport Science School of Architecture and the Built Environment, Royal Institute of Technology Stockholm (Sweden)[2]
- ^ Meidani, H.; Desbiolles, J.-L.; Jacot, A.; Rappaz, M. (2012). "Three-dimensional phase-field simulation of micropore formation during solidification: Morphological analysis and pinching effect". Acta Materialia. 60 (6–7): 2518–2527. Bibcode:2012AcMat..60.2518M. doi:10.1016/j.actamat.2011.12.049.
- ^ Kishimoto, Masashi; Iwai, Hiroshi; Saito, Motohiro; Yoshida, Hideo (2012). "Three-Dimensional Simulation of SOFC Anode Polarization Characteristics Based on Sub-Grid Scale Modeling of Microstructure". Journal of the Electrochemical Society. 159 (3): B315–B323. doi:10.1149/2.086203jes. hdl:2433/154853. S2CID 93265233.
- ^ 3D Quantitative Characterization of Nickel-Yttria-stabilized zirconia Solid Oxide Fuel Cell anode Microstructure in Discharge, by Z Jiao, N Shikazono…[3]
- ^ Poromechanics Investigation at Pore-scale Using Digital Rock Physics Laboratory, by S Zhang, N Saxena, P Barthelemy, M Marsh… – 2011 "Archived copy" (PDF). Archived from the original (PDF) on 2012-04-26. Retrieved 2011-12-20.
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: CS1 maint: archived copy as title (link) - ^ You, Taesun; Abu Al-Rub, Rashid K.; Darabi, Masoud K.; Masad, Eyad A.; Little, Dallas N. (2012). "Three-dimensional microstructural modeling of asphalt concrete using a unified viscoelastic–viscoplastic–viscodamage model". Construction and Building Materials. 28: 531–548. doi:10.1016/j.conbuildmat.2011.08.061.
- ^ CHARACTERIZATION OF HETEROGENEITIES FROM CORE X-RAY SCANS AND BOREHOLE WALL IMAGES IN A REEFAL CARBONATE RESERVOIR: INFLUENCE ON THE POROSITY STRUCTURE, by V. Hebert, C. Garing, P.A. Pezard, P. Gouze, and Y. Maria-Sube (Geosciences Montpellier, CNRS, University of Montpellier 2, Montpellier, France), G. Camoin (CEREGE, CNRS, Aix-en-Provence, France), and P. Lapointe (TOTAL – CSTJF, Pau, France)[4]
- ^ Kobchenko, Maya; Panahi, Hamed; Renard, François; Dysthe, Dag K.; Malthe-Sørenssen, Anders; Mazzini, Adriano; Scheibert, Julien; Jamtveit, Bjørn; Meakin, Paul (2011). "4D imaging of fracturing in organic-rich shales during heating". Journal of Geophysical Research. 116 (B12). arXiv:1101.2295. Bibcode:2011JGRB..11612201K. doi:10.1029/2011JB008565.
- ^ Ivarsson, M.; Bengtson, S.; Belivanova, V.; Stampanoni, M.; Marone, F.; Tehler, A. (2012). "Fossilized fungi in subseafloor Eocene basalts". Geology. 40 (2): 163–166. Bibcode:2012Geo....40..163I. doi:10.1130/G32590.1.
- ^ Fusseis, F.; Schrank, C.; Liu, J.; Karrech, A.; Llana-Fúnez, S.; Xiao, X.; Regenauer-Lieb, K. (2011). "Pore formation during dehydration of polycrystalline gypsum observed and quantified in a time-series synchrotron radiation based X-ray micro-tomography experiment". Solid Earth Discussions. 3 (2): 857. Bibcode:2011SolED...3..857F. doi:10.5194/sed-3-857-2011.
- ^ Shulakova, Valeriya; Pervukhina, Marina; Müller, Tobias M.; Lebedev, Maxim; Mayo, Sherry; Schmid, Susanne; Golodoniuc, Pavel; De Paula, Osni Bastos; Clennell, Michael B.; Gurevich, Boris (2013). "Computational elastic up-scaling of sandstone on the basis of X-ray micro-tomographic images". Geophysical Prospecting. 61 (2): 287–301. Bibcode:2013GeopP..61..287S. doi:10.1111/j.1365-2478.2012.01082.x. S2CID 129619766.
- ^ QUANTITATIVE CHARACTERIZATION OF 3D MELT DISTRIBUTION IN PARTIALLY MOLTEN OLIVINE6BASALT AGGREGATES USING X-RAY SYNCHROTRON MICROTOMOGRAPHY, by Zhu W., Gaetani G. A., Fusseis F. – American Geophysical Union, Fall Meeting 2009, abstract #V33A-2029 [5]
- ^ IMPROVED METHODOLOGY FOR THE CHARACTERIZATION OF COMPLEX VUGGY CARBONATE, by A. Bersani, B.B. Bam, F. Radaelli and E. Rossi (ENI E&P)"Archived copy" (PDF). Archived from the original (PDF) on 2011-07-28. Retrieved 2010-01-29.
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: CS1 maint: archived copy as title (link) - ^ 3-D imaging and quantification of graupel porosity by synchrotron-based micro-tomography, by F. Enzmann (1), M. M. Miedaner (1), M. Kersten (1), N. von Blohn (1), K. Diehl (1), S. Borrmann (1), M. Stampanoni (2), M. Ammann (2), and T. Huthwelker (2) – (1) Earth System Science Research Centre, Johannes Gutenberg-University, Mainz (Germany), (2) Paul Scherrer Institut, Villigen-PSI, Villigen (Switzerland)[6]
- ^ X-Ray Microtomography for Studying 3D Textures of Speleothems Developed inside Historic Walls, by JAVIER MARTÍNEZ-MARTÍNEZ (1,2,*), NICOLETTA FUSI (3), VALENTINA BARBERINI (3), JUAN CARLOS CAÑAVERAS(1,2), GIOVANNI BATTISTA CROSTA (3) – (1) Laboratorio de Petrología Aplicada. Universidad de Alicante (Spain), (2) Dep. Ciencias de la Tierra y del Medio Ambiente. Universidad de Alicante (Spain), (3) Dip. Scienze Geologiche e Geotecnologie. Università degli Studi di Milano–Bicocca (Italia)[7]
- ^ PHYSICAL AND MECHANICAL CHARACTERIZATION OF ALTERED VOLCANIC ROCKS FOR THE STABILITY OF VOLCANIC EDIFICES, by Dr. Antonio Pola Villaseñor – Università degli Studi di Milano-Bicocca (Facoltà di Scienze Matematiche, Fisiche, Naturali Dipartimento di Scienze Geologiche e Geotecnologie)[8]
- ^ DISCRETE 3D DIGITAL IMAGE CORRELATION (DIC) USING PARTICLE RECONNAISSANCE, by Rutger C.A. Smit, January 7, 2010 [9] Archived 2011-07-18 at the Wayback Machine
- ^ Bengtson, S.; Belivanova, V.; Rasmussen, B.; Whitehouse, M. (2009). "The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older". Proceedings of the National Academy of Sciences of the United States of America. 106 (19): 7729–7734. Bibcode:2009PNAS..106.7729B. doi:10.1073/pnas.0812460106. PMC 2683128. PMID 19416859.
- ^ VISTA Center, Institute of Archaeology and Antiquity, University of Birmingham, UK "Visual and Spatial Technology Centre". Archived from the original on 2009-07-15. Retrieved 2010-01-29.
- ^ MAPPING DOGGERLAND: The Mesolithic Landscapes of the Southern North Sea. Archaeopress. Oxford. Gaffney V., Thomson K. and Fitch S. (Eds.) 2007 [10]
- ^ Perez, Jonathan H.; Tanaka, Fumihiko; Uchino, Toshitaka (2012). "Modeling of mass transfer and initiation of hygroscopically induced cracks in rice grains in a thermally controlled soaking condition: With dependency of diffusion coefficient to moisture content and temperature – A 3D finite element approach". Journal of Food Engineering. 111 (3): 519–527. doi:10.1016/j.jfoodeng.2012.02.029.
- ^ DIFFERENCES IN THREE-DIMENSIONAL STRUCTURE REVEALED BY HIGH RESOLUTION MICRO X-RAY TOMOGRAPHY ARE RELATED TO FRESH AND COOKED MEAT TENDERNESS, by VLAD BRUMFELD* AND DAVID E. GERRARD – Electron Microscopy Unit, The Weizmann Institute of Science Rehovot, ISRAEL AND Department of Animal & Poultry Sciences Virginia Tech USA [11]
- ^ Viscoelastic stress-development during drying of corn kernels: a multiscale porous media study from cellular to tissue scales, P S. Takhar, Department of Animal and Food Sciences, International Center for Food Industry Excellence, Texas Tech University, Lubbock, TX (USA) "Archived copy" (PDF). Archived from the original (PDF) on 2012-04-25. Retrieved 2011-11-02.
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- ^ Shearing, P.R.; Bradley, R.S.; Gelb, J.; Tariq, F.; Withers, P.J.; Brandon, N.P. (2012). "Exploring microstructural changes associated with oxidation in Ni–YSZ SOFC electrodes using high resolution X-ray computed tomography". Solid State Ionics. 216: 69–72. doi:10.1016/j.ssi.2011.10.015.
- ^ Neset, T-S S., Johansson, J. and Linnér, B-O. (eds.) (2009). STATE OF CLIMATE VISUALISATION, CSPR Report N:o 09:04, Centre for Climate Science and Policy Research, Norrköping, Sweden [12]
- ^ 2008 Geoinformatics Conference – AVIZO – 3D VISUALIZATION FRAMEWORK -, by Peter Westenberger [13]
- ^ INTERACTIVE DATA VISUALIZATION WITH FOCUS ON EARTH SYSTEM RESEARCH, by Michael Böttinger (DKRZ, German Climate Computing Centre)[14] Archived 2011-07-19 at the Wayback Machine
- ^ Simulation of typhoon Morakot (2009), Chinese winter storms (2008) and hurricane Katrina (2005), By Taiwan Typhoon and Flood Research Institute (TTFRI). Youtube
- ^ Nachshon, Uri; Shahraeeni, Ebrahim; Or, Dani; Dragila, Maria; Weisbrod, Noam (2011). "Infrared thermography of evaporative fluxes and dynamics of salt deposition on heterogeneous porous surfaces". Water Resources Research. 47 (12). Bibcode:2011WRR....4712519N. doi:10.1029/2011WR010776. S2CID 129426750.
- ^ TOPOLOGY OF SPHEROIDIZED PEARLITE, by Yoshitaka Adachi (1) and Yuan Tsung Wang (1) – (1) National Institute for Materials Science, Tsukuba, Japan [15][permanent dead link ]
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- ^ POROSITY AND PERMEABILITY ANALYSIS ON NANOSCALE FIB-SEM 3D IMAGING OF SHALE ROCK, By Shawn Zhang (1), Robert E. Klimentidis (2), Patrick Barthelemy (1) – (1) Visualization Sciences Group (VSG), (2) ExxonMobil Upstream Research Co."Archived copy" (PDF). Archived from the original (PDF) on 2012-04-25. Retrieved 2011-11-02.
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- ^ Vivet, N.; Chupin, S.; Estrade, E.; Piquero, T.; Pommier, P.L.; Rochais, D.; Bruneton, E. (2011). "3D Microstructural characterization of a solid oxide fuel cell anode reconstructed by focused ion beam tomography" (PDF). Journal of Power Sources. 196 (18): 7541–7549. Bibcode:2011JPS...196.7541V. doi:10.1016/j.jpowsour.2011.03.060. Archived from the original (PDF) on 2012-03-26. Retrieved 2011-06-30.
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: CS1 maint: archived copy as title (link) - ^ Smith, S. Y.; Collinson, M. E.; Rudall, P. J.; Simpson, D. A.; Marone, F.; Stampanoni, M. (2009). "Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants". Proceedings of the National Academy of Sciences. 106 (29): 12013–12018. Bibcode:2009PNAS..10612013S. doi:10.1073/pnas.0901468106. PMC 2715531. PMID 19574457.
- ^ Ferreira, Ester S. B.; Boon, Jaap J.; Van Der Horst, Jerre; Scherrer, Nadim C.; Marone, Federica; Stampanoni, Marco (2009). "3D synchrotron x-ray microtomography of paint samples". In Pezzati, Luca; Salimbeni, Renzo (eds.). O3A: Optics for Arts, Architecture, and Archaeology II. Vol. 7391. pp. 73910L. doi:10.1117/12.827511. S2CID 97960642.
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- ^ VISUALIZATION AND ANALYSIS OF THE GREAT SPHINX EROSION, by the VISTA team of Bibliotheca Alexandrina (Cairo, Egypt)"VISTA". Archived from the original on July 25, 2011. Retrieved 2010-01-29.
- ^ COMSOLConference 2009: Drying of Corn Kernels: From Experimental Images to Multiscale Multiphysics Modeling, by Pawan S. Takhar (Texas Tech University) and Shuang Zhang (Visualization Sciences Group), 2009 [16]
- ^ ETUDE DU REFROIDISSEMENT POSTCOULEE DE REFRACTAIRES ELECTROFONDUS RICHES EN ZIRCONE : OPTIMISATION DES PROCEDES ET DES MICROSTRUCTURES, by L. Laurence, Y. Ding, M. Boussuge, D. Ryckelynck, S. Forest, 8th Sept 2009 "Archived copy" (PDF). Archived from the original (PDF) on 2011-07-20. Retrieved 2010-01-29.
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- ^ ONE-YEAR ANIMATED PLANET SIMULATOR CIRCULATION, by Meteorologisches Institut Universität Hamburg (Germany)"Meteorologisches Institut: One year animated Planet Simulator circulation (C)". Archived from the original on 2011-07-19. Retrieved 2010-02-01.
- ^ 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.
- ^ 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.
- ^ 3D-VISUALISIERING VON DATEN AUS KLIMAMODELLEN, by Carmen Ulmen, Dipl.-Geografin, Akad. Geoinformatikerin KlimaCampus Hamburg, Climate System Analysis and Prediction (CliSAP)[18][permanent dead link ]
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