WIXLIB

Appendix AList of Computational SoftwareA.1DICOM ViewersThe listed DICOM viewers have similar functionalityAcculiteMicroDicomDICOM WorksSante DICOM ViewerMangoOsiriX ceforge.netwww.irfanview.comwww.xnview.comOpen Source Medical Imaging and SegmentationCVIPToolsFiji/ImageJGemIdentITK-SNAPA UNIX/Win32-based package and contains a collection of Cand C computer imaging tools that includes edge/line detection, segmentation, and many other functions(www.ee.siue.edu/CVIPtools)A Java-based image processing package that uses additionalplugins for a variety of functionalities including segmentationalgorithms (pacific.mpi-cbg.de/wiki/index.php/Fiji)An interactive program that is designed for colour segmentationin images with few colours, and the objects of interest look alikewith small variation (www.gemident.com)An interactive software application that allows users to navigate three-dimensional medical images, manually delineateanatomical regions of interest, and perform automatic imagesegmentation(www.itksnap.org)J. Tu et al., Computational Fluid and Particle Dynamics in the Human Respiratory System,Biological and Medical Physics, Biomedical EngineeringDOI 10.1007/978-94-007-4488-2, Springer Science Business Media Dordrecht 2013339

340Appendix AList of Computational SoftwareMegawave 2Made up of C library modules, that contains original algorithmswritten 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 processing, segmentation, and registration algorithms(www.mitk.net/download.htm)SlicerHas a GUI that allows manual and automatic segmentation, registration, and three-dimensional visualization. It is a modularplatform which means that it allows addition of new modules(www.slicer.org)VXLA collection of C libraries designed for computer vision research and implementation(vxl.sourceforge.net)A.3Commercial Medical Imaging and Segmentation3D DoctorAn image processing and measurement software for MRI, CT,PET, microscopy, scientific, and industrial imaging s custom modules through C . There is also a researchversion called ZIBAmira (http://amira.zib.de) which provide licenses for joint research lyseA software package for multi-dimensional display and segmentation(www.analyzedirect.com)MimicsAn interactive tool for the visualization, 3D rendering, and segmentation of CT/MRI images. It also has a built in mesh programfor CFD and structural analysis models(www.materialise.com)SliceOmaticTargeted at imaging of soft-tissue and for this, the use of MRIimages 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.4Open Source Computer Aided Design SoftwareFreeCAD3D computer assisted design program(sourceforge.net/projects/free-cad)

A.6 CFD Packages341Open CASCADE Allows for 3D surface and solid modeling, visualization, dataexchange and rapid application development(www.opencascade.org)BRL CADHas interactive editing for 3D solid modeling. Can also use forimage processing and analysis(brlcad.org)OpenSCADUsed for creating solid 3D CAD objects(www.openscad.org)A.5Commercial Computer Aided Design SoftwareThe listed CAD software have similar functionality in their ability to create 3D solidmodels ready for importing into a CFD meshing D PackagesOpenFOAMANSYSCD-AdapcoCFDesignFlow 3DNumecaOpen source CFD software package built using C and compiledunder UNIX. The code is open and therefore allows full customisation and extensions to its standard capability(www.openfoam.com)Includes ICEM meshing, CFX and Fluent CFD solvers, and CFDPost for post processing. Also includes multi-physics for structuraland FSI (www.ansys.com)Includes STAR-CD and STAR-CCM for simulations involving flowof fluids and solids, heat transfer and stress analysis(www.cd-adapco.co)Part of the Autodesk Simulation portfolio, it provides fluid flow simulation and thermal simulation(www.cfdesign.com)Modelling for liquids and gases in a wide range of industrial applications and physical processes(www.flow3d.com)Provides for fluid dynamics simulations for industrial applications(www.numeca.be)

342PhoenicsAppendix AList of Computational SoftwareHandles CFD simulations for fluid flow, heat or mass transfer,chemical reaction and combustion in engineering equipment and theenvironment(www.cham.co.uk)A.7 Third Party Post Processing SoftwareParaViewGNU PlotOpenDXEnsightTecplotPlot3DAn open-source, multi-platform data analysis and visualization application(www.paraview.org)An open source portable command-line graphing utility(www.gnuplot.info)Uses IBM’s visualisation data explorer interface for data input andoutput(www.opendx.org)Visualisation for most CFD data file formats(www.ensight.com)Visualisation for most CFD data file formats(www.tecplot.com)Interactive graphics program for visualizing CFD results(www.openchannelfoundation.org)

Appendix BGlossaryAn aim of this book is to bring together the two streams of biomedicine with classicalmechanical engineering. A student from one field is likely to encounter specialisedterminology from the other. Therefore this glossary is collated in order to providea quick reference to explain the terminology to allow the reader to understand thework they are reading.B.1CFPD and Engineering TerminologyAdverse spect RatioBernoulli’s equationBoundary conditionsBoundary layerBuoyancyCapillaryCavitationCell ReWhen the static pressure increases in the direction of the flowflow i.e. when the rate of change in pressure is positive(compare with favourable pressure gradient)The study of flow of gasesWhere the turbulent fluctuations (u, v, w) are equalA type of descriptor for the quality and shape of a meshcell describing its maximum dimension to its minimumdimensionDescribes the behaviour of moving fluids along a streamlineSpecification of the dynamic fluid state or properties at thecomputational domain boundariesA layer of fluid in the immediate vicinity of a surfaceIs the vertical force that a completely submerged body experiences which is equal to the weight of the displacedfluidA narrow tube or confined flow channelOccurs when a liquid is subjected to rapid changes of pressure causing the formation of cavities in the lower pressureregions of the liquidLocal Reynolds number based on the cell velocity and celllength scaleJ. Tu et al., Computational Fluid and Particle Dynamics in the Human Respiratory System,Biological and Medical Physics, Biomedical EngineeringDOI 10.1007/978-94-007-4488-2, Springer Science Business Media Dordrecht 2013343

344CFLCoanda effectCompressible ag coefficientDynamic pressureEddyEuler equationsEulerian descriptionFavourable pressuregradientFinite difference(FD)Finite elementFinite volume (FV)Flow separationGauss divergencetheoremAppendix BGlossaryCourant–Friedrichs–Lewy is a value or condition used to determine the convergence condition for solving hyperbolicpartial differential equations. The CFL number should always be checked when dealing with transient simulations(i.e. explicit time marching schemes)Is the tendency for a stream of fluid to remain attached to asurfaceFluid flow is considered compressible if there is variation inits density within the flow domain. This is important whensetting up a CFPD problem so that the density changes areaccounted forIs the name given to the mass conservation equation, (e.g.describes how mass in mass out)When the solution being iterated does not change with eachsuccessive iterationThe mass of fluid per unit volume (kg/m3 )The process whereby random motion of molecules movefrom regions of higher concentration to regions of lowerconcentrationThe entire region where the mesh encompassesAn opposing force in the flow direction exerted on an object by the fluid flowing around it, normalised by dynamicpressure and frontal areaThe pressure relative to a velocity referenceSee vortexSimplified equations of fluid motion which describe the flowof a compressible inviscid fluidDescribes fluid motion by following an individual fluid particle as it moves through space and time (compare withEulerian description)When the static pressure decreases in the direction of the flowi.e. when the rate of change in pressure is negative (comparewith favourable pressure gradient)A numerical technique to solve differential and integralequations (see Sect. 7.21 of book)A numerical technique to solve differential and integralequations. An alternative to the finite difference and finitevolumeA numerical technique to solve differential and integralequations (see Sect. 7.22)The fluid boundary layer detaches from a surface when anadverse pressure gradient dominates the flowFrom vector calculus, which states that the outward fluxthrough a closed surface (how much fluid flows out of a volume through its surface) is equal to the volume integral of thedivergence of the vector field inside the volume (total sourcesinside the volume minus any sinks)

B.1 CFPD and Engineering TerminologyHagen-PoiseuilleflowHomogeneous fluidHomogenousmultiphase flowHydrostatic pressureHydrostaticsIdeal gasIncompressible flowInhomogenousmultiphase flowInvisicid flowIrrotational flowKinetic energyLagrangiandescriptionLaminarLift coefficientMeshMesh independenceNewtonianNodesNon-Newtonian345Flow is laminar viscous and incompressible and the flow isthrough a constant circular cross-section that is substantiallylonger than its diameterFluid having constant densityThe assumption whereby each phase shares a common flowfield as well as other relevant fields such as temperature andturbulenceThe forces from a fluid acting on the submerged surface ofan objectThe study of liquids at restIs a concept that allows a simplified state for analysis. Itis a theoretical gas composed of randomly moving noninteracting particlesFluid flow is considered incompressible when its densityremains constant within the flow domain. This is importantwhen setting up a CFPD problem so that simpler models canbe used for a constant densityA more complex representation of multiphase flows whereeach phase has its own flow (includeing temperature andturbulence) fieldFlow without viscous effects, also known as potentialflow. The viscous terms in the momentum equation areneglectedFlow where the streamlines ever loop back on itself, typicallyfound in invisicid flowsIs the energy which the fluid possesses due to its motion, andis also usually defined as the dynamic pressure, determinedby 1/2 ρu2Describes fluid motion by focussing on a fixed location inspace through which the fluid flows as time passes (comparewith Lagrangian description)An organized flow field where fluid particles flow in layersand do not readily mix.A perpendicular force to the flow direction exerted on anobject by the fluid flowing around it, normalised by dynamicpressure and frontal areaRegions of the computational domain where the mathematical equations are applied toThe method implemented to ensure that any further refinements to increase the number of mesh cells does not affectthe resultsDescribes a fluid or flow that exhibits a constant viscosityand there is a linear stress versus strain rate curvePoints in the mesh where data is storedDescribes a fluid or flow where the viscosity is not constantand there is a non-linear relationship between the shear andstrain rates