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Image Processing and Acquisition using Python
Ravishankar Chityala
University of Minnesota at Minneapolis USA
SriRav Scientific Solutions
Minneapolis, Minnesota, USA
Sridevi Pudipeddi
MATLAB® is a trademark of The MathWorks, Inc. and is used with permission. The MathWorks does not warrant the accuracy of the text or exercises in this book. This book’s use or discussion of MATLAB® software or related products does not constitute endorsement or sponsorship by The MathWorks of a particular pedagogical approach or particular use of the MATLAB® software.
CRC Press
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© 2014 by Taylor & Francis Group, LLC
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Toourparentsandsiblings
6.3.1FastFourierTransformusingPython......
6.5.1IdealLowpassFilter...............
6.5.2ButterworthLowpassFilter...........
6.5.3GaussianLowpassFilter.............
6.5.4IdealHighpassFilter...............
6.5.5ButterworthHighpassFilter...........
7.2.3AdaptiveThresholding..............
B.5.1Point-to-PointCommunication.........
ListofFigures
1.1PythonXYcommandpromptwithouttheIDE.....7
2.1Exampleofaplotgeneratedusingmatplotlib......32
3.1Imageprocessingworkflow................37
3.2Widthandheightofpixelinphysicalspace.......40
3.3Anexampleofvolumerendering.............41
3.4Anexampleofahistogram................42
3.5Windowandlevel.....................43
3.6Anexampleof4and8pixelconnectivity........43
4.1Anexampleofdifferentpaddingoptions.........61
4.2Exampleofmeanfilter...................64
4.3Exampleofmedianfilter..................67
4.4Exampleofmaxfilter...................68
4.5Exampleofminfilter...................69
4.6Anexampleofzero-crossing................71
4.7ExampleforSobelandPrewitt..............75
4.8Outputfromvertical,horizontalandregularSobeland Prewittfilters........................77
4.9ExampleofCannyfilter..................80
4.10ExampleoftheLaplacianfilter..............82
4.11AnotherexampleofLaplacianfilter...........83
4.12ExampleofLoG......................86
5.1Illustrationoftransformation T (x)= x2.........90
5.2Exampleoftransformation T (x)= x +50........91
5.3Exampleofimageinversetransformation........93
5.4Graphofpowerlawtransformationfordifferent γ. ..94
5.5Anexampleofpowerlawtransformation........96
5.6Graphoflogandinverselogtransformations......98
5.7Exampleoflogtransformation..............99
5.8Anexampleofa5-by-5image...............101
5.9Probabilities,CDF,histogramequalizationtransformation............................102
5.10Exampleofhistogramequalization............104
5.11Anexampleofcontraststretchingwherethepixelvalue rangeissignificantlydifferentfrom[0, 255]........106
5.12Anexampleofcontraststretchingwheretheinputpixel valuerangeissameas[0, 255]...............106
6.1Anexampleof2DFastFouriertransform........117
6.2Anexampleoflowpassfilters.Theinputimageandall theoutputimagesaredisplayedinspatialdomain...128
6.3Anexampleofhighpassfilters.Theinputimageand alltheoutputimagesaredisplayedinspatialdomain.134
6.4AnexampleofIBPF.Theinputandtheoutputare displayedinspatialdomain................137
7.1Thresholddividesthepixelsintoforegroundandbackground............................140
7.2AnexampleofOtsu’smethod...............143
7.3AnotherexampleofOtsu’smethod............144
7.4AnexampleofRenyientropy...............148
7.5Anexampleofthresholdingwithadaptivevs.Otsu’s..151
7.6Anexampleofanimageforregion-basedsegmentation.152
7.7Anexampleofwatershedsegmentation.........160
8.1Anexampleofbinarydilation...............167
8.2Anexampleofbinarydilation...............171
8.3Anexampleofbinaryerosion...............172
8.4Anexampleofbinaryerosion...............175
8.5Anexampleofbinaryopeningwith5iterations.....178
8.6Anexampleofbinaryclosingwith5iterations.....179
8.7Anexampleofhit-or-misstransformation........181
8.8Anexampleofhit-or-misstransformationonabinary image............................183
8.9Anexampleofskeletonization...............187
9.1Anexampleofregionprops................194
9.2AnexampleofHoughlinetransform...........197
9.3AnexampleofHoughcircletransform..........201
9.4Anexampleoftemplatematching............204
10.1Componentsofanx-raytube...............211
10.2X-rayspectrumillustratingcharacteristicandBremsstrahlung spectrum..........................213
10.3ProductionofBremsstrahlungorbrakingspectrum...214
10.4Productionofcharacteristicradiation..........215
10.5LambertBeerlawformonochromaticradiationandfor asinglematerial......................217
10.6LambertBeerlawformultiplematerials.........219
10.7Ionizationdetector.....................220
10.8Componentsofanimageintensifier............222
10.9Flatpaneldetectorschematic...............223
10.10Fluoroscopymachine....................225
10.11Parallelbeamgeometry..................228
10.12Centralslicetheorem....................229
10.13Fanbeamgeometry....................232
10.14AxialCTslice.......................233
10.15MontageofalltheCTslicesofthehumankidneyregion.............................233
10.163Dobjectcreatedusingtheaxialslicesshowninthe montage.The3Dobjectingreenissuperimposedon thesliceinformationforclarity..............234
10.17Conebeamgeometry....................235
10.18Parametersdefiningaconebeamsystem.........239
10.19Scatterradiation......................240
10.20Effectofmetalartifact...................243
11.1IllustrationofFaraday’slaw................249
11.2Precessingofnucleusinamagneticfield.........250
11.3Blochequationasa3Dplot................251
11.4 T1 magnetization......................254
11.5Plotof T1 magnetization..................254
11.6Plotof T2 de-magnetization................255
11.7NetmagnetizationandeffectofRFpulse........257
11.8Freeinductiondecay....................257
11.9Sliceselectiongradient...................258
11.10ClosedmagnetMRImachine...............260
11.11OpenmagnetMRImachine................261
11.12Headcoil..........................262
11.13k-spaceimage........................263
11.14k-spacereconstructionofMRIimages..........264
11.15 T1, T2 andprotondensityimage.............265
11.16Spinechopulsesequence.................266
11.17Inversionrecoverypulsesequence.............267
11.18Gradientechopulsesequence...............268
11.19EffectofmotionartifactonMRIreconstruction.....270
11.20Metalartifactformation..................271
12.1Lightmicroscope......................277
12.2Schematicofthelightmicroscope.............278
12.3Markingsontheobjectivelens..............279
12.4RayleighCriterion.....................280
12.5Jablonskidiagram.....................285
12.6Nipkowdiskdesign.....................290
12.7Nipkowdisksetup.....................290
12.8PhotographofNipkowdiskmicroscope.........291
13.1Intensitydistributions...................299
13.2Thermionicgun.......................302
13.3Fieldemissiongun.....................303
13.4Electromagneticlens....................304
13.5Everhart-Thornleysecondaryelectrondetector.....305
13.6Back-scatteredelectrondetector.............306
13.7Comparisonofopticalmicroscope,TEMandSEM...308
13.8TEMsliceanditsiso-surfacerendering.........308
13.9AnSEMmachine......................309
13.10BSEimageobtainedusinganSEM............310
A.1Specifyingthetypeofinstall...............314
A.2TheWindowsmenuitemtostartPythonXYunder Spyder............................315
A.3TheSpyderinterface....................315
A.4SpecifyingaPythondistributionforinstallation....316
A.5Installationofskimagemodule..............317
A.6Specifyingtheinterpreterversionandlocation.....317
A.7InstallingEnthoughtPythondistributiononMac....319
A.8LoadingEnthoughtPythondistributiononMacand skimagemodule......................319
A.9Installingcythonmoduleusingeasy install.Thismoduleisrequiredtouseskimagemodule..........320
A.10Installingskimagemoduleusingeasy install.......320
A.11Loadingskimagemodule..................321
A.12StepsforinstallingpydicomonWindows........321
C.1ImageJmainscreen....................334
C.2ImageJwithanMRIimage................335
C.3AdjustingwindoworlevelonanMRIimage......335
C.4Performingmedianfilter..................336
C.5Obtaininghistogramoftheimage............336
ListofTables
4.1A3-by-3filter........................58
4.2A3-by-3sub-image.....................59
4.3Sobelmasksforhorizontalandverticaledges......72
4.4A3-by-3subimage.....................72
4.5Outputaftermultiplyingthesub-imagewithSobel masks............................73
4.6Prewittmasksforhorizontalandverticaledges.....73
4.7Sobelmasksfordiagonaledges..............75
4.8Prewittmasksfordiagonaledges.............76
4.9Laplacianmasks......................80
4.10LaplacianofGaussianmask...............83
8.1Hit-or-missstructuringelement.............180
8.2Variationofallstructuringelementsusedtofindcorners.............................180
10.1RelationshipbetweenkVpandHVL...........218
11.1AnabbreviatedlistofthenucleiofinteresttoNMR andMRIimagingandtheirgyromagneticratios....252
11.2Listofbiologicalmaterialsandtheirprotonorspin density............................253
11.3Listofbiologicalmaterialsandtheir T1 and T2 values forfieldstrengthof1.0T.................255
11.4TRandTEsettingsforvariousweightedimages....268
12.1Listofthecommonlyusedmediaandtheirrefractive indexes...........................281
12.2Listofthefluorophoresofinteresttofluorescenceimaging..............................286
Foreword
Ifirstmetoneoftheauthors,Dr.Ravishankar(Ravi)Chityala,in2006 whenhewasaPhDstudentattheToshibaStrokeResearchCenter, SUNY-Buffalo.Ravi’sPhDworkinmedicalimagingwasfruitfuland influential,andIhavebeenfollowinghispost-PhDcareereversince. Inreadingthisbook,Iwasimpressedbythefactthat,despiteRavi’s currentfocusoncomputingandvisualization,hisknowledgeofmedical imaginghasonlydeepenedandexpanded,whichhasenabledhim,along withhisco-author,Dr.SrideviPudipeddi,towriteaverycompetent treatmentofthesubjectofmedicalimaging.Thus,itisapleasurefor metowriteaforewordtothisverygoodbook.
Thisisabookthateveryimagingscientistshouldhaveonhis orherdeskbecauseimageacquisitionandprocessingisbecominga standardmethodforqualifyingandquantifyingexperimentalmeasurements.Moreover,Ibelievestudentsandresearchersneedacourseora booktolearnbothimageacquisitionandimageprocessingusingasinglesource,andthisbook,asawell-roundedintroductiontobothtopics, servesthatpurposeverywell.Thetopicstreatedarecomplex,butthe authorshavedoneagreatjobofcoveringthemostcommonlyused imageacquisitionmodalities,suchasx-rayandcomputedtomography, magneticresonanceimaging,andmicroscopes,conciselyandeffectively, providingahandycompendiumofthemostusefulinformation.
AsConfuciussaid,“IseeandIremember,IdoandIunderstand;” thisbookaimstoprovidehands-onlearningthatenablesthereaderto understandtheconceptsexplainedinthebookbymeansofapplying thevariousexampleswritteninthePythoncode.ButdonotbediscouragedifyouhaveneverusedPythonoranyotherscriptlanguage
xxvi Foreword sincelearningitisverystraightforward.Asalong-timePerluser,Ihad noprobleminstallingPythonandtryingseveralusefulexamplesfrom thebook.Mostoftheequationsprovidedinthebookareaccompanied bycodesthatcanbequicklyrunandmodifiedforthereadertotest newideasandapplytohisorherownresearch.
Beingamedicalimagingscientistmyself,Ireallyenjoyedreading thesectionsonx-ray,computedtomographyandmagneticresonance imaging.Theauthorsprovideawell-balancedintroductiontothese modalitiesandcoveralltheimportantaspectsofimageacquisition, aswellasimagereconstructionandartifactscorrection.Theauthors alsoprovidealargenumberofreferencestootherbooksandpapersfor readersinterestedinlearningmoredetails.
Insummary,thestrengthsofthebookare:
1.ItteachesimageprocessingusingPython,oneoftheeasiestand mostpowerfulprogramminglanguages
2.Itcoverscommonlyusedimageacquisitionandprocessingtechniques
3.Itcementsreaders’understandingwithnumerousclearexamples.
Preface
Imageacquisitionandprocessinghavebecomeastandardmethodfor qualifyingandquantifyingexperimentalmeasurementsinvariousScience,Technology,Engineering,andMathematics(STEM)disciplines. Discoverieshavebeenmadepossibleinmedicalsciencesbyadvances indiagnosticimagingsuchasx-raybasedcomputedtomography(CT) andmagneticresonanceimaging(MRI).Biologicalandcellularfunctionshavebeenrevealedwithnewimagingtechniquesinlightbased microscopy.Advancementsinmaterialscienceshavebeenaidedbyelectronmicroscopy.Alltheseexamplesandmanymorerequireknowledge ofboththephysicalmethodsofobtainingimagesandtheanalytical processingmethodstounderstandthesciencebehindtheimages.ImagingtechnologycontinuestoadvancewithnewmodalitiesandmethodsavailabletostudentsandresearchersinSTEMdisciplines.Thus, acourseinimageacquisitionandprocessinghasbroadappealacross theSTEMdisciplinesandisusefulfortransformingundergraduateand graduatecurriculumtobetterpreparestudentsfortheirfuture.
Thisbookcoversbothimageacquisitionandimageprocessing.Existingbooksdiscusseitherimageacquisitionorimageprocessing,leavingastudenttorelyontwodifferentbookscontainingdifferentnotationsandstructurestoobtainacompletepicture.Integrationofthe twoislefttothereaders.
Duringtheauthors’combinedexperiencesinimageprocessing,we havelearnedtheneedforimageprocessingeducation.Wehopethis bookwillprovidesufficientbackgroundmaterialinbothimageacquisitionandprocessing. xxvii
Audience
Thebookisintendedprimarilyforadvancedundergraduateand graduatestudentsinappliedmathematics,scientificcomputing,medicalimaging,cellbiology,bioengineering,computervision,computer science,engineeringandrelatedfields,aswellastoengineers,professionalsfromacademia,andtheindustry.Thebookcanbeusedasa textbookforanadvancedundergraduateorgraduatecourse,asummerseminarcourse,orcanbeusedforself-learning.Itservesasa self-containedhandbookandprovidesanoverviewoftherelevantimageacquisitiontechniquesandcorrespondingimageprocessing.The bookalsocontainspracticeexercisesandtipsthatstudentscanuseto rememberkeyinformation.
Acknowledgments
Weareextremelythankfultostudents,colleagues,andfriendswho gavevaluableinputduringtheprocessofwritingthisbook.Weare thankfultotheMinnesotaSupercomputingInstitute(MSI)attheUniversityofMinnesota.AtMSI,RaviChityalahaddiscussionswithstudents,staffandfacultyonimageprocessing.Thesediscussionshelped himrecognizetheneedforatextbookthatcombinesbothimageprocessingandacquisition.
WewanttospeciallythankDr.NicholasLabello,Universityof Chicago;Dr.WeiZhang,UniversityofMinnesota;Dr.GuillermoMarques,UniversityImagingCenter,UniversityofMinnesota;Dr.Greg Metzger,UniversityofMinnesota;Mr.WilliamHellriegel,Universityof Minnesota;Dr.AndrewGustafson,UniversityofMinnesota;Mr.AbhijeetMore,Amazon;Mr.ArunBalaji;andMr.KarthikBharathwaj forproofreadingthemanuscriptandforprovidingfeedback.
WethankCarlZeissMicroscopy;VisibleHumanProject;Siemens AG;Dr.UmaValeti,UniversityofMinnesota;Dr.SusantaHui,UniversityofMinnesota;Dr.RobertJones,UniversityofMinnesota;Dr.Wei Zhang,UniversityofMinnesota;Mr.KarthikBharathwajforproviding uswithimagesthatwereusedinthisbook.
WealsothankoureditorSunilNairandeditorialassistantSarah Gelson;projectcoordinatorLaurieSchlags;projecteditorAmyRodriguezatTaylorandFrancis/CRCPressforhelpingusduringthe proofreadingandpublicationprocess.
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