AFM image artefacts

Page 1 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

UniversityPressScholarshipOnline

OxfordScholarshipOnline

AtomicForceMicroscopyPeterEatonandPaulWest

Printpublicationdate:2010PrintISBN-13:9780199570454PublishedtoOxfordScholarshipOnline:May2010DOI:10.1093/acprof:oso/9780199570454.001.0001

AFMimageartefacts

PeterEaton

PaulWest

DOI:10.1093/acprof:oso/9780199570454.003.0006

AbstractandKeywords

AFM,likeanyothermeasurementtechnique,ispronetoartefacts.ThesecanariseduetotheAFMprobe,thescanner,theinstrumentelectronics,fromthelaboratoryenvironment,orfrommanyoutersources.Someartefactsareobvioustoexperiencedusers,whileothersaremoresubtle.IdentifyingtheartefactssothattheycanbeexplainedandexcludedfromanalysisisoneofthemostdifficulttasksfacingnewAFMusers.ThischapterexplainstheoriginsoftheartefactsthatoccurinAFMimages,andexplainswhatcanbedonetoavoidthem.

Keywords:AFM,artefacts,imageartefacts,probeconvolution,scanners

Allmeasurementsandmeasurementtechniquesarepronetoartefacts.InAFMimaging,theseartefactsaresometimeseasytospotandsometimesverydifficult.Someartefacts

AFM image artefacts

Page 2 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

canbeeasilyavoided,iftheuserknowswhattolookforandknowsthesourceoftheerror.Afewartefactsareunavoidable,butknowingthattheyexistinanimagehelpstoavoidmisinterpretingthemasgenuineimagefeatures.ThismeansthatrecognizingimageartefactsisveryimportantfortheAFMuser.However,whenusersbegintouseAFMforthefirsttime,itisverydifficulttosorttherealfeaturesfromtheartefactual.ExperiencedAFMusersaswellasnovicescanbenefitfromconsideringthesourcesofAFMartefacts,assomeartefactualfeaturesareverysubtle,andcanonlybeclearlyseenwhenmakingparticularmeasurementsfromanimage(forexamplewhenmeasuringlineprofiles,orFourierfiltering).ThischaptercontainsexamplesofcommonAFMartefacts,explainsthesourceofthefeatures,andshowswhatcanbedonetoavoidthem.

6.1ProbeartefactsProbablythemostcommonlyseenAFMartefactsarisefromtheprobeusedtoscanthesample.AsexplainedinChapter2,allAFMimagesareaconvolutionofthetopographyofthesamplewiththeshapeofthetipoftheprobe(andsometimeswiththesidesoftheprobe)[54].WheninterpretingAFMimages,weoftenassumethatthetipradiusisfinerthanthedetailsimaged,andthattheopeningangleoftheprobeissmallerthantheangleofthefeaturesinthesample.Thismeansthattheinfluenceofthetip‐shapeontheimageobtainedwillbesmall(butfinite).However,evenifthisisthecase,continualusemaydulltheprobetiporitcanbreakorbecomecontaminated[46].Often,iftheuserhasmanysamplestoimage,theprobewillbeuseduntiloneofthesephenomenaoccurs,andtheprobebecomesunusable.Ineithercase,theusermustknowwhattolookforwhenthetipdegrades,inordertoknowwhentoreplacetheprobe.

Commoneffectsseenwhenimagingwithaninadequateprobeinclude:

•Thefeaturesonasurfaceappeartoolarge.•Thefeatures,especiallyholes,appeartoosmall.•Strangelyshapedobjectsappear.•Repeatingpatternsappearintheimage.•Theimageappearsnormalonthetopoffeatures,butnotontheirsides.

Thebestadviceiftheuserisunsureistouseatip‐checksample.Thiscanbeanysamplethattheuseriscertainofthetopographyof,andwhichhasrelativelyfinefeatures,suchthattheradiusofthetipcanbedetermined.Inpractice,certaintypesofsamplesareparticularlyusefulforthisoperation,andsomeofthemostcommononesaredescribedin(p.122) AppendixA.Inthischapter,imagesoftip‐checksamplesthatwereacquiredwithfaultyprobesareshown,alongwithimagesmeasuredwithanewprobe,toillustratetheeffectthatprobedamagehasontheimagesobtained.

6.1.1Bluntprobes

Typically,bluntprobeswillleadtoimageswithfeatureslargerthanexpected,withaflattenedprofile,duetotheeffectshownbelow.Notethatholesinaflatsurfacewillshowtheoppositeeffect,appearingsmallerwithbluntprobesthanwithsharpones(seethelowerpartofFigure6.1).

AFM image artefacts

Page 3 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

ThedilationduetotheprobeshapeasshowninFigure6.1isanormalfeatureofAFMimaging.Forexample,whenmeasuringglobularfeatureswithaknowndiameterof2nmitwouldbenormaltofindthefeatureintheAFMimagehas2nmheightbut10–20nmwidth[279,375,376].However,whenitoccurstoalargeextentitisaproblem,becauseitmaysignificantlyaltertheapparentsizeofthefeatures,andcanreallychangetheirappearance.AnexampleisshowninFigure6.2.Ifthiseffectisnoticed,theusershouldchangetheprobe.Ifthefeaturecannotbeimagedcorrectlyevenwithnewerprobes,thenanothertypeofprobe(e.g.super‐sharpprobesorhigh‐aspect‐ratioprobes)mayberequired[377].However,someextremelyhigh‐aspect‐ratiofeaturescanbeextremelychallengingtoimagebyAFM,nomatterwhichprobeischosen.

ThefinedetailsoftheBOPPsamplewhenimagedwithasharpprobeareseenintheleftimageinFigure6.2.Whenimagedwithablunt,wornprobe,asshownintherightimage,theydisappear,andthesamplebecomesalmostunrecognizable.AnexampleoftheeffectofpitsinasamplebecomingsmallerwithadullprobeisshowninFigure6.3.

Fig.6.1. Illustrationofprobe‐baseddilation.Convexfeaturessuchasparticlestendtoappearwiderwithblunterprobes,althoughfeatureheightmaybeaccurate.Concavefeaturessuchaspitstendtoappearsmaller(bothlesswideandlessdeep)withblunterprobes.

(p.123)

Fig.6.2. Illustrationoftheeffectofusingabluntprobe.Thesetwoimagesareofthesamesample,andbothare1.5μm×1.5μm×40nm.Theimageontheleftwastakenwithasharpprobe,theimageontherightwithabluntprobe.ThesampleisBOPP,ausefulsampletocharacterizethesharpnessofIC‐AFMprobetips,seeAppendixA9.

AFM image artefacts

Page 4 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.3. Exampleoffeaturesappearingsmallerduetotheuseofabluntprobe.Left:SEMimageofatestpatternofsquares(NT‐MDTgratingTGX,seeAppendixA).Thesidesofthesquaresareallequal.B:AFMimageofthetestpattern.Becausetheprobeisnotsharp,thetestpatternsquaresappearmuchsmallerthantheyshould,andappearasrectanglesinsteadofsquares.

6.1.2Contaminatedorbrokenprobes

ContaminationofAFMprobesisquitecommon,andscanningcertainsamplesleadstodirtyprobesmorequicklythanothers.Inparticular,biologicalorothersoftsamples,oranysamplewithloosematerialatthesurface,tendtocontaminateprobetipsquickly,leadingtoimagedegradation[378].Ontheotherhand,breakingoftheAFMprobeislesscommon,butstilloccurs,mainlywhentheprobeaccidentallytouchesthesampleoutsideoffeedbackcontrol.Thereasonthesetwoproblemsaredescribedtogetheristhantheycangiveverysimilarresults.Whenimagingasamplewithabrokenordirtyprobe,theresultingimagesoftencontainfeatureswithunexpectedshapes,duetoconvolutionofthemisshapentipwiththesamplefeatures.ExamplesareshowninFigure6.4.Anyrepeatingpatternswithintheimages,whicharenotexpectedbasedonwhatisknownofthesample,arelikelytobeduetoabrokenorcontaminatedprobe.

(p.124)

AFM image artefacts

Page 5 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.4. Examplesofhowimagesproducedwithbrokenordirtyprobesshowrepeatingpatternsintheimages.Left:SEMimagesofdamagedanddirtyprobes.Right:AFMimagesproducedusingtheprobesshownontheleft.Imageswithrepeatingpatternsliketheseareusuallyduetobrokenordirtyprobes.

Doubletips

Afurtherexampleofdamageorcontaminationoftipsalteringtheimageisthecreationofmultipletips.Ifthetipbreakssuchthatithassmallspikesattheend,ormorecommonly,hasdebrisattachednearthetip,thesamplemaybeimagedbothbythetruetip,andthedebris.Thisresultsinmultiplecopiesofeachfeatureappearingintheimage[379].It'snotpossibletodistinguishwhichimagefeatureisfromthe‘true’tip,anddouble,ormultiplecopiesofeachfeatureoccurintheimage,asshowninFigure6.5.

Whentheuserdeterminesthattheprobeisblunt,contaminated,orbroken,theymustreplacetheprobe.SomeproceduresforcleaningofAFMprobeshavebeendescribed[380],however,intheauthors'experience,itisusuallysimplerandfarmoreeffectivetoreplacetheprobethantotrytocleanit.

(p.125)

AFM image artefacts

Page 6 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.5. Exampleofdouble‐tipimaging.Left:animageofvesiclesmeasuredwithadirtytip.Right:DNAmoleculesmeasuredwithabrokentip,eachmoleculehasafalse‘twin’nexttoit.Centre:abadlybrokenandcontaminatedtipwhichproduceddouble‐tipimageslikethese.

6.1.3Probe–sampleangle

Whenscanninglargefeatures,artefactscanbeintroducedbyhavingalargeanglebetweentheprobeandthesample,asillustratedinFigure6.6.Ideally,theAFMprobeshouldbeperpendiculartothesamplesurface.

Solvingthisproblemisachievedbyadjustingtheanglebetweentheprobeandthesamplesothattheyareperpendicular.Often,asetofthreeadjustmentscrewsonthemicroscopeallowstheusertoadjustthisangle.Inmanymicroscopestheprobeisdesignedtobeata12°anglewithrespecttothesample,andsomeprobesaredesignedwiththisangleinmind,i.e.suchthatwhenthecantileversubstrateisat12°tothesample,theprobewillbeperpendiculartoit.SomeAFMsdonothavemechanicaladjustmentstocontroltheprobe–sampleangle.Inthiscase,thesamplemustbeadjustedtocorrecttheprobe–sampleangle.

6.1.4Side‐wall/probeimagingCertainsampleswithextremelyhigh‐aspect‐ratiofeaturesareverydifficulttoimagecorrectly,andtheycaninteractwiththeprobeinsuchawaythattheimagecontainsrepeatingimagesoftheprobe,oroftheside‐wallsoftheprobe.Examplesoffeaturesthatproduceside‐wallimagesaresphericalmicro‐organisms,sphericalparticlesorredbloodcells,withtheirtypicaldoughnut‐likeshape,imagesofwhichoftenaregreatonthetopofthecell,butit'snotpossibletoimagethesidesofthecell,andimagesoftheprobeside‐

Fig.6.6. Illustrationofprobe–sampleangleproblems.Withtheprobeatanangletothesample,distortionsareintroduced,andsamplefeaturesappearasymmetric.

(p.126)

AFM image artefacts

Page 7 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.7. Effectofprobeorprobeside‐wallimaging.Top:illustrationsoftheeffectofimagingaspike–animageoftheprobeisproduced–andimagingasphere‐likefeature–onlyatthetopisthesampletopographyreproduced,andtherestoftheimagefeatureshowstheprobe'sside‐walls.Bottom:examplesofprobe–side‐wallimaging.Left:redbloodcells,right:S.aureusbacteria.Inbothcases,onlytheupperpartsofthecellscanbeimagedcorrectly(someexamplesofprobeside‐wallimaginghighlightedbyarrows).

wallappearinstead(seeFigure6.7)[381,382].Sampleswithspike‐likefeatures(includingcertaintip‐checksamples,seeAppendixA)leadtorepeatedcopiesofthetipintheresultingimages[383].

Typically,anyimageshowingsquarepyramid‐shapedfeatureswillbeshowingimagesoftheproberatherthantruesamplefeatures,sotheseimagefeaturescanbediscounted.Inordertoavoidthisproblem,theuserisrecommendedtouseashapertip,specifically,onewithahigheraspectratio.Siliconnitridecontact‐modeprobesareverypronetoproducingimagesoftheprobeside‐wall,astheytypicallyhavemuchwideropeningangles(ca.35–40°versus15–20°formostintermittentcontact‐modeprobes).Ifthisartefactcausesrealproblems,forexampleinmetrologyapplications,super‐high‐aspect‐ratioprobesarealsoavailable(forexample,withopeningangles

AFM image artefacts

Page 8 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.8. Effectofx‐ynon‐linearityinAFMimages.Left:exampleofanAFMimageofatestsample(TGX01,seeAppendixA)whenscannedwithoutcorrectlylinearizingtheAFMscanner.Right:linearizedAFMimageofthesamesample.Thespacingofthesquaresatthetop,bottom,leftandrightsidesshouldbeallthesamedistanceapart.ImagescourtesyofMikromasch.

toproduce,andgivesrapidandverypreciseresponseundermostcircumstances.However,mostAFMscannersdointroducesomeartefactsintotheimagesobtained,thetubescannermorethanmost.Theartefactsdescribedinthissectionalloccurwithpiezoelectrictubescanners.Manyofthemareavoidedwhenusingalinearizedscanner(seeChapter2).

6.2.1X‐Ycalibration/linearityAllatomicforcemicroscopesmustbecalibratedintheX‐Yaxissothattheimagesandmeasurementsobtainedareaccurate.Themotionofthescannersshouldalsobelinearsothatthedistancesmeasuredfromtheimagesareaccurate.Duetothenon‐linearityofpiezoelectricscanners,withoutcorrection,thefeaturesonanimagewilltypicallyappearsmallerononesideoftheimagethanontheother,seeFigure6.8.Oncethescannerisproperlylinearized,itisalsocriticalthatthescannerbecalibrated.Inotherwords,itispossibleforthescannertobelinearbutnotcalibrated.Ifthecalibrationisincorrect,thentheX‐Yvaluesmeasuredfromlineprofileswillbeincorrect.

AcommonmethodforcorrectingtheproblemsofX‐Ynon‐linearityandcalibrationistoaddcalibrationsensorstotheX‐Ypiezoelectricscanners.Thesesensorscanbeusedtocorrectthelinearityandthecalibrationinrealtime;often,suchasystemisdescribedashavinglinearizedscanners.Ifthesearenotavailable,andnon‐linearityisdetectedinimages,thentheinstrumentshouldbere‐linearizedaccordingtothemanufacturer'sinstructions.Typicallythisiscarriedoutwithatestgridasillustratedabove,andinAppendixA.Notethatnon‐linearityatjustoneedgeoftheimagecouldbeduetoothereffects;seetheothersectionsinthischapter.

6.2.2zcalibrationandlinearity

HeightmeasurementsinanAFMrequirethatthepiezoelectricceramicsintheZaxisofthemicroscopearealsobothlinearandcalibrated.Usuallythemicroscopeiscalibratedatonly(p.128)

AFM image artefacts

Page 9 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.9. GraphshowingtherelationshipbetweenanactualzheightandameasuredzheightinanAFM.Usuallyonlyonecalibrationpointismeasuredasshownbythebox,andthezpiezoelectricisassumedtobelinear,asshownbythedashedline.However,asisoftenthecase,thepiezoelectricactuatorisnon‐linear,asshownbythesolidline.Insuchcasesincorrectzheightsaremeasuredunlessthefeaturebeingmeasuredhasdimensionsclosetothoseofthecalibrationspecimen.

oneheight.However,iftherelationshipbetweenthemeasuredzheightandtheactualzheightisnotlinear,thentheheightmeasurementswillnotbecorrect,seeFigure6.9.

Theonlywaytoensureabsolutelyaccuratezheightmeasurementsatarangeofheightsistouseaninstrumentwithasensorforthezpiezoelectric.Analternative,whichonlyworksformeasurementsoffeatureswithinaparticularheightrange,istorecalibratetheinstrumentusingacalibrationspecimenofknownheight,whichissimilarinsizetothefeatureswhichwillbemeasured.TypicallythezaxesofAFMmicroscopesarecalibratedusingsemiconductortestsampleswithfeaturesontheorderof100–200nminheight.So,forexample,measurementsofsmallfeaturesof5–10nmcouldnotbeexpectedtobeveryaccuratelymeasuredunderthesecircumstances.Inthiscase,itwouldbebesttorecalibratetheinstrumentusingatestsampleofknownheightintherange5–10nm.Alternatively,somesamplescanbeusedasaninternalstandard,avoidingtheneedtorecalibratetheAFM[279].SomewidelyavailableZ‐heightcalibrationstandardsaredescribedinAppendixA.

6.2.3Scannerbow

ThescannersusedinAFMinstrumentsoftenmovetheprobeinaslightlycurvedmotionoverthesamplesurface.Thisistypicallythecasefortubescannersfixedtothemicroscopebodyatoneend,andfreetomoveattheother–currentlythemostcommondesigninAFM.AsshowninFigure6.10,thismotiongivesrisetoacurvatureor‘bow’asitismostoftenknown,intheresultingimages.ThistendstogiveasmallvariationinzheightoverarelativelylargeX‐Yarea,soitismostobviouswithflatsamples.

Thisartefactcannotbeavoidedwithinstrumentswhosedesignispronetoit,buttheeffectcanberemovedinprocessing.TheprocedurestocarryoutthisoperationaredescribedinSection5.1.1.

AFM image artefacts

Page 10 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

(p.129)

Fig.6.10. Effectofscannerbow.Left:withtubescannersfixedatoneend,thetrajectoryoftheprobeiscurved.Right:theresultisanapparentcurvatureintheheightofmeasuredsamples,althoughtheheightchangeissmalloveralargearea.

6.2.4EdgeovershootintheZaxis

Hysteresisinthepiezoelectricceramicthatmovesthecantileverintheperpendicularmotiontothesurfacecancauseedgeovershoot.Hysteresisisaninherentpropertyofpiezoelectricmaterials,andmeansthatforwardandbackwardmovementsarenotexactlyequivalent.TheeffectintheZaxisaffectstheAFM'sabilitytotraceaccuratelyoverstepprofiles.ThisproblemismostoftenobservedwhenimagingmicrofabricatedstructuressuchaspatternedSiwafersorcompactdisks,butmaybeobservedinanysamplewithsharp‐edgedfeatures.Theeffectcancausetheimagestoappearvisuallybetterbecausetheedgesappearsharper.However,alineprofileoftheimagestructureshowserrors,asshowninFigure6.11.

Edgeovershootcannotbeavoidedbytheuser.Itwillonlyoccuronmicroscopeswithoutazaxiscalibrationsensor,however.Incaseswherethisoccursstepheightmeasurementsshouldonlyusetheunaffected(flat)portionofthefeatureprofile.

6.2.5Scannercreep

Creepinpiezoelectricsgivesrisetothephenomenonthatwhenaninstantaneousvoltageisappliedtothepiezoelectricandmaintained,theresponseofthematerialdoesnotfollowexactlytheappliedvoltage,butinsteadcontinuestomoveinthesamedirectionastheinitialoffset,evenwhenthevoltageisnolongerchanging.ThisisillustratedinFigure6.12.Thepracticaleffectofthisisthatwhentheusertranslatesthescanningpositiononthesample,movestheprobetothestartofanewscan,orzoomsintoapreviousscan(allofwhicharedonebyrapidlychangingthevoltageappliedtothepiezoelectric),distortionoccursintheimage.Thedurationofthiseffectislimited,andeventuallyitdisappears.Anexampleofthisdistortion(‘scannerdrift’)isshowninFigure6.12.

Thisartefactcanberemovedbysimplywaitingforthepiezopositiontostabilize.Onewayistomakeaninitialscaninanynewregion,beforerecordingasecondscanfreeof(p.130)

AFM image artefacts

Page 11 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.11. Edgeovershootinthezaxis.Top:theprobeisscannedfromlefttorightacrossafeatureonasurface;overshootmaybeobservedinthelineprofileattheleadingandtrailingedgeofthefeatures.Bottom:theAFMimageofatestpatternappearstohavenoartefactsatfirstglance(left),butalineprofileofthetestpatternshowsovershootatthetopofeachofthelines(right,overshootarrowed).

Fig.6.12. Scannerdriftcauseandeffect.Left:creepinpiezoelectricscannerscausesthescannertokeepmovingevenaftertheappliedvoltagestopschanging.Right:theeffectonAFMimagesismostoftenseenasadistortioninthebeginningofthescan(here,scanningfromthetop).

distortion.Alternatively,theinstrumentcanbesettodoacontinuouslinescaninthenewposition.Whentheuserobservesthatthefeaturesinthelinescanarenolongerchanging,thedrifthasstoppedandtheimagescanshouldthenbebegun.

6.2.6Zanglemeasurements

MechanicalcouplingbetweenthepiezoelectricceramicsthatmovetheprobeinthexorYdirectionsandtheZdirectioncancausesubstantialerrorswhentryingtomeasureverticalangleswiththeAFM.Thissortofcrosstalkiscommoninpiezoelectrictubescanners,andmeansthattheaccuracyofanglesintheZaxismeasuredwithmostAFMs(p.131)

AFM image artefacts

Page 12 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.13. IllustrationandexampleoferrorsinZanglemeasurementbyAFMcausedbycrosstalk.Top:illustrationoftheeffect.Thesamplehasaseriesofrepeatingtrianglesatitssurface.Alineprofileofthesampleshowsthatthetrianglesdonotappearsymmetric.Bottom:realAFMimageofasamplehavingatrianglepatternatitssurface,andalineprofileextractedfromtheAFMimage.Althoughtheanglesofthetwofacetsareinrealityequal,theAFMimagesuggeststhatthisisnotso.

areunreliable.Thiserrorcanbestbemeasuredwithasamplethathasrepeatingtrianglestructures.AnexampleofthisisshowninFigure6.13.

Theusercannotcontroltheappearanceofthisartefact.Itoccurswithnon‐linearizedtubescanner‐basedAFMs,andindependentX‐YandZscannersarerequiredforthemeasurementofcorrectZangles.

6.3ImageprocessingartefactsSomeimageprocessingisusuallynecessarybeforeviewingoranalysinganyAFMimage.AsdescribedinChapter5,therearealargenumberofprocessingoperationsthatcanbeappliedtoAFMimages.ThecorrectproceduresweredescribedinChapter5,sohereonlyexamplesoftheartefactsthatmightbeintroducedareshown.

6.3.1Levellingartefacts

LevellingchangestheentireAFMimage,sotheresultingimageisdifferentfromtherawdata.However,itisveryoftenanecessaryprocedurebeforeusefulinformationcanbeextractedfromanimage.Commonly,levellingartefactsareintroducedbypolynomialfittingroutines;Figure6.14showsanexampleofthis.

Thiserroriseasilyavoidedbyexcludingpartsoftheimagefromthefit.ThiswasdescribedinSection5.1.1.Despitetheeasewithwhichthisartefactisavoided,itiscommonlyseeninpublishedAFMimages.

6.3.2Filteringartefacts

Imagefiltering,bydefinition,altersthedataintheimageandthereforealwaysintroducessomesortofartefact.WhenpresentingAFMdata,itisimportanttospecifywhatfilters,if(p.132)

AFM image artefacts

Page 13 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.14. Examplesofline‐by‐line(polynomialfitting)basedlevellingartefacts.Theleftimageofnanoparticlesisunlevelled.Themiddleimageshowsanartefactcausedbypolynomialline‐by‐linelevelling–theparticlesseemtobesittinginlowered‘trenches’inthebackground.Thecorrectlylevelledimageisshownontheright.

Fig.6.15. Exampleofimagedistortionbyfiltering.Theimageofnanoparticlesontheleftshowsconsiderablenoise.Low‐passfiltering(smoothing)producedtheimageontheright.Thelineprofileshowsthatnoisewasreduced,buttheshapesofthetwoparticlesinthelineprofilewerealsochanged.

any,wereappliedtothedata,becausetheresultsfromfilteredimagescanbeverymisleading.Forexample,low‐pass(orsmoothing)filterstendtogreatlyreducenoiseinAFMimages,butcanalsointroduceartefactssuchaschangingtheshapeoffeatures,andincreasingtheapparentsharpnessofsteps.AnexampleoffilteringartefactsisshowninFigure6.15.

(p.133) Inadditiontomatrixfilters,asillustratedabove,Fouriertransform‐basedfilteringcanalsointroduceartefactsintoanimage.ThiswasdescribedinSection5.3.4,andshowninFigure5.12.

6.4VibrationnoiseEnvironmentalvibrationsintheroomwheretheAFMislocatedcancausetheprobeinthemicroscopetovibrateandmakeartefactsinanimage.Typically,theartefactsappearasoscillationsintheimage.BothacousticandfloorvibrationscanexcitevibrationalmodesinanAFMandcauseartefacts.

6.4.1Floorvibrations

Often,thefloorinabuildingcanvibrateupanddownbyasmuchasseveralmicrons,

AFM image artefacts

Page 14 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

typicallyatfrequenciesbelow5Hz.Thefloorvibrations,ifnotproperlyfiltered,cancauseperiodicstructureinanimage.Becauseithaslowamplitude,thistypeofartefactismostoftennoticedwhenimagingveryflatsamples.Sometimesthevibrationscanbestartedbyanexternaleventsuchasmachineryinmotion,atraingoingby,orevenpeoplewalkingoutsidetheAFMlaboratory.However,itisoftenratherdifficulttodiagnosethistypeofnoise.

6.4.2Acousticvibrations

Soundwaves(acousticvibration)cancauseartefactsinAFMimages.Thesourceofthesoundcouldbefromanairplanegoingoverabuildingorfromthetonesinaperson'svoice.Thenoiseofcoolingfansfromotherinstruments,orevenfromtheAFMelectronics,canalsoberegisteredbytheAFM.Figure6.16isanimagethatshowsthenoisederivedfromapersontalkinginthesameroomasthemicroscope.Diagnosingthistypeofinterferenceisrathereasy;theusermustisolatetheAFMfromthesourcesofnoiseorremovethem,andlookforachangeinthesignalsregistered.

Thesolutiontothisnoiseproblem,likethatfromfloorvibrations,isisolationfromthenoisesource.SolutionsforthiswerediscussedinSection2.6.Briefly,buildingvibrationsaregenerallycounteredbymountingtheAFMonasuspendedstagethatisisolatedfromthefloor.Ontheotherhand,acousticisolationisaccomplishedbyenclosingtheAFMinacabinetwithacousticshieldingontheinside.Alternatively,thenoisesourcescanberemoved,andtheAFMplacedinalocationlesspronetobuildingvibrations.Forthis,aroominthebasementofthebuildingwithlittletrafficusuallyservesbest.

6.5NoisefromothersourcesFloorandacousticnoisearethemostcommontroublesomenoisesourcesinAFM,however,othersourcesofnoisesuchaselectronicnoise,whichoccursrarely,ornoisefromavacuumleak,whichislimitedonlytothoseinstrumentsthatuseavacuumsamplemountingsystem,cansometimescauseproblems.TheresultsofpoorfeedbacksettingscanalsoappeartogiverisetonoiseinAFMimages,whenthePIDsettingsaretoohigh.

(p.134)

AFM image artefacts

Page 15 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.16. Effectofacousticnoise.Thishigh‐zresolutionimageofasiliconwafershowstheeffectofacousticnoiseonanimage.Right:imageandlineprofilesmeasuredwhileacousticnoisewaspresentintheroom.Theacousticvibrationsfromapersonspeakingwhiletheimagewasacquiredareclearlyvisibleinthelinescansandtheimage.Left:imagethatwasmeasuredwithouttheacousticnoise.(Acolourversionofthisillustrationcanbefoundintheplatesection.)

Fig.6.17. ExampleofelectronicnoiseinanAFMimage.Thisimageofatestpatternhaselectronicnoiseatthetopandbottomofthescan.Theelectronicnoiseinthiscasewasaresultofnothavingagroundwireattachedtothestage.Theartefactwasidentifiedbytheoscillationfrequency.(Acolourversionofthisillustrationcanbefoundintheplatesection.)

(p.135) 6.5.1ElectronicnoiseImageartefactscanappearinAFMimagesbecauseoffaultyelectronics,oraccidentalelectricconnectionstoapartoftheAFM.Artefactsfromelectronicsmostoftenappearasregularoscillationsorunexplainablerepeatingpatternsinanimage,seeFigure6.17.Electronicgroundloopsandbrokencomponentsareusuallythesourceofelectronicnoise.

6.5.2Vacuumleaks

Atomicforcemicroscopesthataredesignedforimagingwafersanddisksoftenuseavacuumchucktoholdthewafer/diskwhilescanningimages.Aleakinthevacuumbetweenthespecimenholderandthespecimencancauseimageartefacts.Theartefactcausesalossofresolutionintheimage.Cleaningthevacuumchuckandsampleand

AFM image artefacts

Page 16 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

remountingthesampleinthestageofteneliminatesthisproblem.

6.6OtherartefactsInthissectionwegathersomeothereffectsthatgiverisetoproblemsinAFM.Someofthese,suchassampledriftandsurfacecontaminationarethesortofissuesencounteredinallhigh‐resolutionmicroscopytechniques.

6.6.1Feedbacksettingsandscanrate

Ifthefeedback(PID)settingsusedwhilescanningarenotoptimized,thenit'sverylikelythattheresultingimagewillshowconsiderableartefacts.Thisisbecausetheprobeisnottrackingthesurface,andthecantileverisbendingtopassoversurfacefeatures.ThecorrectsettingsforthePIDcircuitsarealsodependentonthescanrate–higherscanratesmayrequirehigherPIDsettings.Thisartefactcanbeidentifiedeasilybymonitoringtheerrorsignal.Iftheerrorsignalislarge,thentheprobeisnotcorrectlytrackingthesurface.AnexampleofthisisshowninFigure6.18,butseealsoChapter4forfurtherdiscussionoffeedbackparameteroptimization.IfthePIDsettingsaretoohigh,‘feedbackoscillation’canoccur,whichlookslikehigh‐frequencynoiseintheimage.

6.6.2Surfacecontamination

AsexplainedinSection4.1,suitablesamplepreparationisvitalforreproducible,artefact‐freeAFMimaging.SubstantialcontaminationatthesurfaceofasamplesuchasafingerprintoroilfilmcancauseAFMimageartefacts.Suchartefactsmayappearasstreaksontheimageespeciallyinlocationswherethereare‘sharp’featuresandedgesonthesample'ssurface.Oftenthestreakingcanbereducedoreliminatedbycleaningthesamplewithahigh‐puritysolvent.AnexampleofthiseffectisshowninFigure6.19.

6.6.3Laserinterferencepatterns

Interferencepatternscanbecreatedbythelaserusedtodetectthebendingoftheprobecantilever.Theinterferenceappearsaslow‐frequencybackgroundoscillationsinimagesandtypicallyhasaperiodthatissimilartothewavelengthofthelaserlightbeingusedin(p.136)

AFM image artefacts

Page 17 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.18. Exampleofanartefactcreatedbynothavingthefeedback(PID)parametersfullyoptimizedwhilescanning.Intheupperimageparametersareoptimized,inthelowerimageparameterarenotoptimizedandtheerrorsignalislarge.Thisalsoleadstolessaccurateheightimage,seethelineprofiles.

Fig.6.19. Theeffectofsurfacecontamination.Left:SEMimageofaheavilycontaminatedcalibrationgridsample.Right:thecontaminationcausesstreakingandpreventstheprobefromproperlyfollowingthesurfacetopographyintheAFMimage.

theAFMscanner(typically0.5–1.5microns).Thisinterferenceoriginatesfromlaserlightspillingoverthecantilever,orpassingthroughit,reflectingfromthesamplesurface,andinterferingwiththelightreflecteddirectlyfromthecantilever.Asimilareffectcanalsobeseeninforce–distancecurves,wheretheinterferenceappearsaswavinessinthebaselineoftheforce–distancecurve,withthesameperiod.ThisisillustratedalongwithatypicalimageshowingtheartefactinFigure6.20.

(p.137)

AFM image artefacts

Page 18 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.20. ExamplesoftheeffectoflaserinterferenceonAFMimagesandforce–distancecurves.Left:animageofareflectivesample,showingtypicallaserinterferencefringes.Right:theeffectonaforcecurve;thebaselineshowssimilaroscillations.Inset:theartefactoriginatesfrominterferencebetweenthelaserbeamsreflectedbythecantileverandthesample.

ThiseffectisreducedinAFMinstrumentswithlowcoherencelasers,whicharefittedinnewerinstruments.Itisalsomorecommonwithpatternedorreflectivesamples.Iftheuserencountersthisproblem,itcansometimesbereducedbyadjustmentoftheopticalalignmentoftheAFM.Theusershouldtrytoensurethelaserispositioneddirectlyinthecentreofthecantileverbeam,andnottooclosetotheend.SeeSection4.2.1foralaserspotpositioningprotocol.

6.6.4Sampledrift

Acommonprobleminhigh‐resolutionmicroscopiesissamplemovement.Ingeneral,AFMsamplesmustbewellfixeddowninordertoenablehigh‐resolutionimaging.Atlowresolutions(scansofsizelargerthan5μm),somesamplesdonotneedtobefixedtothemicroscope,providedtheyhaveastablesubstrate.Atsmallerscansizes,thesampleshouldbegluedtoasamplesupport,whichisheld(usuallymagnetically)inthemicroscope.Evenwhenfirmlyfixeddownsomesamplescanappeartobe‘moving’inthemicroscope.Thereasonforthisisthermalexpansionofthesample;thiscanbeexacerbatedbysourcesofheatinthemicroscope(e.g.thelaserorheatfromtheelectronics),leadingtosamplesmovingbyexpansionathundredsofnanometresperminute,whichtotallyprecludeshigh‐resolutionimaging.Somesamples(e.g.metals)aremorepronethanotherstothiseffectduetohighthermalexpansioncoefficients.

AsshowninFigure6.21,scanningthesamplewiththeslowscanaxisinoppositedirectionscanhelptodiagnosethisproblem.AnothermajorproblemassociatedwithsampledriftisthatifthesampledriftsintheZ‐axis,itcanpreventscanningaltogether.ThiscanbeduetoexpansionintheZaxisorexpansionlaterally,whicheffectivelymovesthesampleinZ,duetosampletilt.Althoughthefeedbacksystemcantakeaccountofsmall(p.138)

AFM image artefacts

Page 19 of 19

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2014.All Rights Reserved. Under the terms of the l icence agreement, an individual user may print out a PDF of a single chapter of amonograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: UC -Berkeley Library; date: 20 February 2015

Fig.6.21. ExampleoftheeffectofsampledriftonAFMimages.ThetwoimagesofaclusterofE.colibacteriaweremeasuredwiththeslowscanaxisinoppositedirections.Thedifferencebetweenthemindicatesthatthesamplewasdriftingwhilescanning.Whenthesampledriftsinthesamedirectionastheslowscanaxis,thesamplewillappearstretched(imageontheleft);ifitdriftsintheoppositedirectionitwillbecompressed(rightimage).Scanningintwodirectionscanhelptodeterminethecauseofimagedistortion.

driftsinZ,thiseffectwilleventuallycauseproblemsinscanningduetothelimitedZscanrangeofmanyscanners.Iftheuserdeterminesthesampleisdrifting,theyshouldattempttofixthesampledownmorefirmly,andremovepossiblesourcesofheat,forexamplethewhitelightusedtoilluminatethesample.Sometimestheonlysolutionistowaitforthermalequilibrium.