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List of Computational Software

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List of Computational Software Appendix A List of Computational Software A.1 DICOM Viewers The listed DICOM viewers have similar functionality Acculite www.accuimage.com MicroDicom www.microdicom.com DICOM Works www.dicomworks.com Sante DICOM Viewer www.santesoft.com Mango ric.uthscsa.edu/mango OsiriX (MAC) www.osirix-viewer.com AMIDE amide.sourceforge.net Irfanview www.irfanview.com XNView www.xnview.com A.2 Open Source Medical Imaging and Segmentation CVIPTools A UNIX/Win32-based package and contains a collection of C and C++computer imaging tools that includes edge/line detec- tion, segmentation, and many other functions (www.ee.siue.edu/CVIPtools) Fiji/ImageJ A Java-based image processing package that uses additional plugins for a variety of functionalities including segmentation algorithms (pacific.mpi-cbg.de/wiki/index.php/Fiji) GemIdent An interactive program that is designed for colour segmentation in images with few colours, and the objects of interest look alike with small variation (www.gemident.com) ITK-SNAP An interactive software application that allows users to nav- igate three-dimensional medical images, manually delineate anatomical regions of interest, and perform automatic image segmentation (www.itksnap.org) J. Tu et al., Computational Fluid and Particle Dynamics in the Human Respiratory System, 339 Biological and Medical Physics, Biomedical Engineering DOI 10.1007/978-94-007-4488-2, © Springer Science+Business Media Dordrecht 2013 340 Appendix A List of Computational Software Megawave 2 Made up of C library modules, that contains original algorithms written by researchers and is run using Unix/Linux (megawave.cmla.ens-cachan.fr) MITK and 3Dmed Made up of C++ library for integrated medical image process- ing, segmentation, and registration algorithms (www.mitk.net/download.htm) Slicer Has a GUI that allows manual and automatic segmentation, reg- istration, and three-dimensional visualization. It is a modular platform which means that it allows addition of new modules (www.slicer.org) VXL A collection of C++ libraries designed for computer vision re- search and implementation (vxl.sourceforge.net) A.3 Commercial Medical Imaging and Segmentation 3D Doctor An image processing and measurement software for MRI, CT, PET, microscopy, scientific, and industrial imaging applications (www.ablesw.com/3d-doctor) Amira Includes custom modules through C++ . There is also a research version called ZIBAmira (http://amira.zib.de) which provide li- censes for joint research collaboration (www.visageimaging.com/amira.html) Analyse A software package for multi-dimensional display and segmen- tation (www.analyzedirect.com) Mimics An interactive tool for the visualization, 3D rendering, and seg- mentation of CT/MRI images. It also has a built in mesh program for CFD and structural analysis models (www.materialise.com) SliceOmatic Targeted at imaging of soft-tissue and for this, the use of MRI images is an advantage, however it can be used with CT (www.tomovision.com) Vida Diagnostics A lung analysis tool for Chronic Obstructive Pulmonary Disease, emphysema and asthma (www.vidadiagnostics.com) A.4 Open Source Computer Aided Design Software FreeCAD 3D computer assisted design program (sourceforge.net/projects/free-cad) A.6 CFD Packages 341 Open CASCADE Allows for 3D surface and solid modeling, visualization, data exchange and rapid application development (www.opencascade.org) BRL CAD Has interactive editing for 3D solid modeling. Can also use for image processing and analysis (brlcad.org) OpenSCAD Used for creating solid 3D CAD objects (www.openscad.org) A.5 Commercial Computer Aided Design Software The listed CAD software have similar functionality in their ability to create 3D solid models ready for importing into a CFD meshing program. Geomagic www.geomagic.com CATIA www.3ds.com Autodesk www.autodesk.com Solidworks www.solidworks.com PRO/Engineer www.ptc.com IronCAD www.ironcad.com A.6 CFD Packages OpenFOAM Open source CFD software package built using C++and compiled under UNIX. The code is open and therefore allows full customisa- tion and extensions to its standard capability (www.openfoam.com) ANSYS Includes ICEM meshing, CFX and Fluent CFD solvers, and CFD- Post for post processing. Also includes multi-physics for structural and FSI (www.ansys.com) CD-Adapco Includes STAR-CD and STAR-CCM for simulations involving flow of fluids and solids, heat transfer and stress analysis (www.cd-adapco.co) CFDesign Part of the Autodesk Simulation portfolio, it provides fluid flow sim- ulation and thermal simulation (www.cfdesign.com) Flow 3D Modelling for liquids and gases in a wide range of industrial appli- cations and physical processes (www.flow3d.com) Numeca Provides for fluid dynamics simulations for industrial applications (www.numeca.be) 342 Appendix A List of Computational Software Phoenics Handles CFD simulations for fluid flow, heat or mass transfer, chemical reaction and combustion in engineering equipment and the environment (www.cham.co.uk) A.7 Third Party Post Processing Software ParaView An open-source, multi-platform data analysis and visualization appli- cation (www.paraview.org) GNU Plot An open source portable command-line graphing utility (www.gnuplot.info) OpenDX Uses IBM’s visualisation data explorer interface for data input and output (www.opendx.org) Ensight Visualisation for most CFD data file formats (www.ensight.com) Tecplot Visualisation for most CFD data file formats (www.tecplot.com) Plot3D Interactive graphics program for visualizing CFD results (www.openchannelfoundation.org) Appendix B Glossary An aim of this book is to bring together the two streams of biomedicine with classical mechanical engineering. A student from one field is likely to encounter specialised terminology from the other. Therefore this glossary is collated in order to provide a quick reference to explain the terminology to allow the reader to understand the work they are reading. B.1 CFPD and Engineering Terminology Adverse pressure When the static pressure increases in the direction of the flow gradient flow i.e. when the rate of change in pressure is positive (compare with favourable pressure gradient) Aerodynamics The study of flow of gases Anisotropic Where the turbulent fluctuations (u, v, w) are equal turbulence Aspect Ratio A type of descriptor for the quality and shape of a mesh cell describing its maximum dimension to its minimum dimension Bernoulli’s equation Describes the behaviour of moving fluids along a streamline Boundary conditions Specification of the dynamic fluid state or properties at the computational domain boundaries Boundary layer A layer of fluid in the immediate vicinity of a surface Buoyancy Is the vertical force that a completely submerged body ex- periences which is equal to the weight of the displaced fluid Capillary A narrow tube or confined flow channel Cavitation Occurs when a liquid is subjected to rapid changes of pres- sure causing the formation of cavities in the lower pressure regions of the liquid Cell Re Local Reynolds number based on the cell velocity and cell length scale J. Tu et al., Computational Fluid and Particle Dynamics in the Human Respiratory System, 343 Biological and Medical Physics, Biomedical Engineering DOI 10.1007/978-94-007-4488-2, © Springer Science+Business Media Dordrecht 2013 344 Appendix B Glossary CFL Courant–Friedrichs–Lewy is a value or condition used to de- termine the convergence condition for solving hyperbolic partial differential equations. The CFL number should al- ways be checked when dealing with transient simulations (i.e. explicit time marching schemes) Coanda effect Is the tendency for a stream of fluid to remain attached to a surface Compressible flow Fluid flow is considered compressible if there is variation in its density within the flow domain. This is important when setting up a CFPD problem so that the density changes are accounted for Continuity Is the name given to the mass conservation equation, (e.g. describes how mass in = mass out) Convergence When the solution being iterated does not change with each successive iteration Density The mass of fluid per unit volume (kg/m3) Diffussion The process whereby random motion of molecules move from regions of higher concentration to regions of lower concentration Domain The entire region where the mesh encompasses Drag coefficient An opposing force in the flow direction exerted on an ob- ject by the fluid flowing around it, normalised by dynamic pressure and frontal area Dynamic pressure The pressure relative to a velocity reference Eddy See vortex Euler equations Simplified equations of fluid motion which describe the flow of a compressible inviscid fluid Eulerian description Describes fluid motion by following an individual fluid par- ticle as it moves through space and time (compare with Eulerian description) Favourable pressure When the static pressure decreases in the direction of the flow gradient i.e. when the rate of change in pressure is negative (compare with favourable pressure gradient) Finite difference A numerical technique to solve differential and integral (FD) equations (see Sect. 7.21 of book) Finite element A numerical technique to solve differential and integral equations. An alternative to the finite difference and finite volume Finite volume (FV) A numerical technique to solve differential and integral equations (see Sect. 7.22) Flow separation The fluid boundary layer detaches from a surface when an adverse pressure gradient dominates the flow Gauss divergence From vector calculus, which states that the outward flux theorem through a closed surface (how
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