Jan. 2017

EDT/Collect

for DigitalMicrograph

Data Collection for Electron Diffraction Tomography

EDT/Collect Manual 1.0

HREM Research Inc.

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IntroductionThe EDT/Collect software has been developed by HREM Research Inc. in collaboration with the

AnaliteXcompany(www.analitex.com).

The EDT/Collect DigitalMicrograph plugin allows the user to Collect beam-tilt Electron DiffractionTomography3Ddatasets.

GeneralenquiriesontheEDT/CollectforDigitalMicropraphshouldbesentto:

HREMResearchInc.14-48MatsukazedaiHigashimatsuyamaSaitama355-0055Japan

email: support@hremresearch.comwebsite: www.hremresearch.com

EnquiriesonEDT/Collectofatechnicalnatureshouldbedirectedto:

AnaliteXcompanyemail: support@analitex.comwebsite: www.analitex.com

TheproperreferencetothedatacollectionmethodasofJanuary2013is

M. Gemmi and P. Oleynikov. Scanning reciprocal space for solving unknown structures: energy

filtered diffraction tomography and rotation diffraction tomography methods. Zeitschrift fürKristallographie-CrystallineMaterials:Vol.228,No.1,pp.51-58(2013).

CopyrightStatements

©Copyright2016HREMResearchInc.andAnaliteX

All rights reserved. This manual is protected by international copyright laws and treaties.Unauthorizedreproductionanddistributionofthismanual,oranyportionofit,willbeprosecutedtothemaximumextentpossibleandmayresultinseverecivilandcriminalpenalties.

PortionsofthisdocumentwerepreparedbyHREMResearchInc.byeditingthematerialssuppliedbyAnaliteX.

DigitalMicrographisatrademarkofGatanInc.

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WhatdoesEDT/Collectprogramdo?

Figure1illustrateshowdoesEDT/CollectDigitalMicrographpluginworkinanexperiment.

Fig.1RaypathdiagramofEDT/Collectexperiment

EDT/Collectprogramdeflectstheincidentelectronbeambychangingdeflectorlenscurrent,andtheprogramtakesaseriesofdiffractionpatternswithvariousdiffractionconditions.

Afterthetakingonetiltseriesofdiffractionpatterns,theprogramtiltsthesampleholderslightly.

Thenagaintheprogramstartstotakeanewtiltseriesofelectrondiffractionpatterns.

By continueing this operation EDT/Collect program allows user to collect beam-tilt electron 3Ddiffraction tomography data, in a range say from -70 degrees to + 70 degrees, if awide angle tiltspecimenholderisused.

-Inthisoperationthebeamtiltdirectionbybeamdeflectorsmustbeperpendiculartothe

sampleholdertiltaxis.

-Incidentelectronbeammustillumineatthesameandsmallpositiononacrystalsampleduringthisexperiment.

-Transmitted000electronbeammustbefixedatasamepositiononaCCDcamera.

UsingEDT/Collectprogramthesecomplicatedexperimentscanbeperformedeasily.

TechnicalReferences[1]P.Oleynikov.AutomatedQuantitative3DElectronDiffractionRotationTomography.In:UnitingElectronCrystallographyandPowderDiffraction,NATOSeriesB:PhysicsandBiophysics.2012,p327.[2]MayenceA,NavarroJRG,MaY,TerasakiO,BergStromL,OleynikovP:PhaseIdentificationandStructureSolutionbyThree-DimensionalElectronDiffractionTomography:Gd-PhosphateNanorods,Inorg.Chem.,2014,53,5067.[3]SunQ,MaY,WangN,LiX,LiD,XuJ,DengF,YoonKB,OleynikovP,TerasakiO,YuJ:Highperformancenanosheet-likesilicoaluminophosphatemolecularsieves:synthesis,3DEDTstructuralanalysisandMTOcatalyticstudies,J.Mater.Chem.A,2014,2,17828.

Beam%&lt%by%%Deflector%coil%

Descan%by%%Projector%%shi6%coil%

Incident%beam%must%be%fix%at%a%same%%posi&on%on%a%sample%under%the%&lted%incident%

Incident%beam%must%be%fix%at%the%same%%posi&on%on%the%CCD%under%the%&lted%condi&on%

crystal%sample%

Electron%beam%

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Installingtheprogram

EDT/CollectisavailableasaplugintoDigitalMicrographoftheGatanmicroscopySuite(GMS).Asof2016thefollowingGMSversionsaresupported:

• 32bit:GMS1.xandGMS2.x;

• 64bit:GMS2.xandGMS3.x;

TheEDT/Collectsoftwarecontainsonlyproprietarylibrariessuchas,forexample,Intel®MKL.

SoftwarerequirementsThefollowingisalistofthesoftwarerequirementsnecessarytoruntheEDT/Collectplug-in:

- DigitalMicrograph(GATANTM)- USBKeyDriver- IPUPlug-in(Free-waredownloadablefromwww.hremresearch.com)- GatanEMControlPlug-in(aplug-insupportedbyGatantocommunicatewithamicroscope

thismustbeinstalledbeforehand)- AnaliteXTEMServer(pleaseconsultthemanualfortheTEMserver)

SoftwareInstallationInstallation ofEDT/Collect is almost same to that ofEDT-test programexcept for the license key.PleaseconsultthemanualofEDT-test.ToexaminethatEDT/Collectprogramcanworkcorrectlyonuser’sTEM,itisrecommendedtoinstalltheEDT-testatfirst,andpleasecheckthattheprogramEDT-testworks correctly. EDT-test is a free program. After the check by EDT-test program users candecidethattheyaregoingtouseEDT/Collectornot.OnceEDT-testprogramisonuser’sTEM,onlythelicencekey isnecessarytouseEDT/Collect.ProcedurebelowisthecasethatEDT-test isnot inuser’sTEM.InstallingUSBKeyDriver

Theuserkeydrivershouldbeinstalledbyfollowingtheinstructionsgivenbythekeydriverinstaller.ThekeydriverinstallercomeswithEDT/Collect,oryoucanfinditonourwebsite.

InstallingEDT/CollectPlug-in

Theplug-incanbeinstalledbydrag-and-dropcopytothefolder“PlugIns”(ThePlugInsfoldershouldexistunderanormalinstallationoftheDigitalMicrograph.)

WhentheDigitalMicrographislaunchedafterplacingtheplug-insintothePlugInsfolder,EDT/Collectmenucommandswillappearunder“EDT/Collect”menu.

InstallingIPUPlug-in

EDT/CollectusessomefunctionsbasedontheIntel’MKL(MathKernelLibrary)providedbytheIPUplug-in.All the files relating the IPUplug-incanbe installedbydrag-and-dropcopy.PleaseconsulttheReadMefilethatcomeswiththeIPUplug-in.InstallingAnaliteXTEMServer

PleaseconsulttheinstallationmanualfortheAnaliteXTEMserver.Ifyouneedanyhelptoinstall/usetheAnaliteXTEMServer,pleasecontacttoHREMresearchInc.

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AccessingthepluginfromtheDMmenu

EachmoduleisaccessiblethroughthemainDigitalMicrographmenu,andEDT/CollecthasauniquenamethatrepresentsthecontentofthecorrespondingmoduleasshowninFig.2.

Fig.2Pull-downmenuofEDT/CollectinDigitalMicrograph.

Theavailablecommandsthroughthemainmenuare:

Calibration…–theTEMbeamtiltcoilscalibration;

CollectData…–themaindatacollectionmodule;

CheckDataSet…–viewingthecollecteddataafteraseriesofexperiment;

Settings…–changingtheprogramsettings(forserviceoperators,notrecommendedtouse);

EDT-test…–testprogramtocheckwhethertheEDT/Collectworkscorrectlyforuser’sTEMornot.ThisprogrampartworkswithouttheUSBlicensekey;

Help–gettinghelpontheplugin;

About…–displaysdialogwiththeplugininformation.

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Pluginsettings

After the installationof the EDT/Collect plugin in theDigitalMicrograph users should set up someparameters so that thepluginknowswhatCCDcameras canbeused, thediffractionpattern scalebars(pixelsize)foraccessiblecameralengths,availablespecimenholdersandetc.

InordertoaccessthepluginsettingspleasechoosetheSettings…menuitemfromtheEDT/CollectDMmainmenu.ThedialogboxshowninFig.3willappear.

Fig.3Settingdialogbox.ThestatethatCCDtabischosen.

CCDsettings

ThepluginwillautomaticallyidentifyallcamerasavailabletoDigitalMicrographthatcanbeaccessedthroughtheCurrentcamerapulldownlist.

ForeachcameratheusercansettheOversaturationLevel(willbeusedbytheEDT/Processsoftwarepackagetocountoversaturatedpixels).

Itemsinthepull-downmenuandscaleinthegroupboxofCalibrationareblankunlesstheTEMcoils

calibrationisperformed.

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SampleholderSettingsThistabwillhelpyoutomaintainthelistofsampleholdersthatcanbeusedonyourTEM.Theuserscanadd/remove(usingAddandRemovebuttonsrespectively)sampleholdersfromthelist:

Fig.4Settingdialogbox.ThestatethatSampleHoldertabischosen.

Currently selected sample holder will be removed from the list by pressing the Remove button.WhenpressingtheAddbuttonthefollowingdialogwillappear:

Fig.5SampleHolderdialogboxtoregistrantanewholder

Hereuserscanspecify:

• nameoftheholder(Nameeditbox);

• tiltinglimitoftheholderindegrees(Limitoftiltangleeditbox);

Usersmustinputtheanglealphainthe“AlphaTiltAxis”boxintheSampleHolderSettingtabinFig.

4.Thealpha is theanglebetweeny-direction,namelyverticaldirection,andthetiltaxisofsampleholder in user’s camera screen. If users have already known the angle alpha user can input,otherwisetheanglealphamustbeestimatedusing“CheckAlphaTiltAxis”.Detaileddescriptionon

using“CheckAlphaTiltAxis”buttonwillbedescribedlater.

“TestBeamTilt”buttonisusedtotestwhetherthedirectionofbeamtiltissettobeperpendicularto the sampleholder tilt axis,ornot.Thisbuttonmustbeusedafter inputof theanglealphaand

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afterthe“Temcoilscalibration”process.Detaileddescriptiononhowtouse“TestBeamTilt”button

willbedescribedafterthe“Temcoilscalibration.”

SettingparametersTheParameterstabisusedforswitchof“InvertBeamTiltdirection”.

Fig.6Settingdialogbox.Parameterstabischosen.

Ifthedirectionofbeamtiltisthesametothatofthesampleholdertiltinauser’sTEM,userneedtoput a checkmark in theboxof Invert beam tilt direction.User can seewhether theyare sameor

oposit by checking the collectedexperimental data. Theprocedure to seewill bedescribed in thesectionof“CheckDataSet”.

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TEMcoilscalibration

Sinceonsomeelectronmicroscopes(forexampleJEOL)thechangesofelectroncurrentforcoilsaredoneusinginternalunits,thecalibrationofthesecoilsisneededinorderto:

• Converttheinternalunitsintophysicalunits(e.g.nmordegrees);

• Compensatethebeamshiftinducesbyonelensusingtheother.

Thecalibrationofeachcoil isdonein2dimensions:alongX-andY-axesofthecorrespondingcoil.ThecalibrationmustbeperformedinthestandardDIFF-modeorNanoBeamDIFF-mode.IncaseofthestandardDIFF-modeinserttheSA(SelectedArea)apertureandfocusthebeamintoasmallspot.IncasetheNanoBeamDIFF-modeselect thesizeandthebrightnessof thebeam(sameaswillbeusedlaterforthedatacollection)andfocusthebeamintoasmallspot.

PleaseselecttheCalibrationfromtheEDT/Collectpull-downmenuinFig.2.Thefollowingdialogwillbeshown:

Fig.7Calibrationdialogbox.

Forthecalibration:

1. Set theobjective lens currentat the standard currentposition. This current is for the zerodeforcusposition,otherwisefortheeucentricspecimenposition.

2. In the image-modethe incidentbeammustbe fixedat thecentralpositionevenwhentheincidentbemaistilted.Tofixthebeamposition,adjustthebeamtiltcompensatororadjustthebeampositionusingthebeamtiltwobbler.

3. Selectanemptyareaonyourgrid.4. InsertasmallSAaperture.5. Spreadthebeam.6. Switch into Diff-mode. Select an appropriate camera length; e.g. 300mm; and focus the

incidentelectronbeamintoasmallspot.

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CAUTION! Be careful for the direct exposure of the CCD camera to the electronbeam!Useminimumintensitybeam(spreadthebeamusingtheBrightnessknobofthe JEOL TEM; use small spot size, for example 5; use small condenser aperture;insertsmallSAapertureinImagemode).RemovetheCCDcamerafromtheelectronbeampathwhennotinusetoavoidunnecessaryexposure.

7. BringtheincidentspottothecentreofCCDcamera.

8. ChecktheRecalculateangleontheCalibrationdialog.

9. Setsomevalue,or0inChangevalueboxfortheBeamtilt.AninitialvalueforJEOLTEMcanbe1000unitsforthestart.

Note:If0issetinthebox,theautomaticcalibrationwillstart.Ifanon-zerovalueisset,

thesemi-automaticcalibrationwillstart.10. PressCalibratebuttonandwaitwhilethecalibrationisfinished.11. Repeatthesteps9-10forthecalibrationoftheprojectorshiftcoils.

CalibrationofIS1coilisnotnecessaryunlessNanoBeamDiffractionmodeisused.

Note:Onceyouhavesettheobjectivelenscurrent,donotchangeit.

Note:Onceyouhavechosenacameralengthincalibrationyoushouldnotchangethelengthinthefollowingtest.

Note:IfthebeamgoesoutfromtheSA-apertureduringthecalibration,thecalibrationmayfail.Pleaseadjustthebeamtiltcompensatorasmentionedabovebeforehand.

Incaseofautomaticcalibration,thecalibrationchartasshowninFig.8willappearatthe end. If in case of failure the chart is not linear. Please try semi-automaticcalibrationincaseoffailure.

Fig.8Arelationbetweenaparameterforcoilcurrent,CV-value,andtiltedelectronbeampositioninlogvs.logaxis.

Thecalibrationoftheselectedcoilisdoneautomaticallyaccordingtothefollowingsteps,whenyoupressCalibratebutton.Thecalibrationprogram

1. readstheuser-suppliedChangevaluefromthepanel(let’scallitCVvalue);

2. readscurrentcoilvaluesforx-andy-axes(let’scallthemasX0andY0values);3. recordsthediffractionpattern(originalpattern);4. changesthex-axisvalueofthecoilbytheCVvalue(soitbecomesX0+CV);

5. recordsthediffractionpattern(X-modifiedpattern);

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6. changesthex-axisbacktotheoriginalX0valueandchangesy-axisvalueofthecoilbythe

CVvalue(soitbecomesY0+CV);7. recordsthediffractionpattern(Y-modifiedpattern);8. restoresthecoily-axisvaluebacktoY0;

9. calculatestheshiftsofthespotusingnormalizedcross-correlation;10. iftheshiftsissmallandthecheckboxforAutomaticChangevalueisselected,theCVvalue

isautomaticallydoubledandgotothestep4;

11. savesthecalibrationmatrix(thedirectionofthecoilx-andy-axesandthemeasureddeviationsalongx-andy-axes).

Thecorrectcoilcalibrationimagesshouldlooksimilartothefollowing:

Current Shifted Cross-correlation

Fig.9Coilcalibrationimagesappearafterthecalibrationprocess.

TheCurrentpatterninFig.9isasumof3recordeddiffractionpatterns–theoriginaland2withinducedchangesalongx-andy-axesofthecoil.The3spotsseenintheCurrentpatterninFig.9isexplainedinFig.10:

Fig.10ExplanationontheCurrentpatterninFig.9.

Y

The original spot

The spot after Y-axis change

The spot after X-axis change

X

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NOTE: the calibrationwill bemoreprecise if the2 spots obtained from the inducedchangesofx-andy-axesofthecoilarewellseparated(closetotheedgeoftheCCDframe).ThesepositionsdependontheChangevalueforthecorrespondinglens.Thex-andy-axes inthis imagearethatforthebeamtiltcoil,butnotforthecoordinate inthisCCDimage.

TheShiftedpatterninFig.9showsthelastpatternwiththedeviationofthey-axisof

thecoil.

The Cross-correlation pattern in Fig. 9 is the sum of 2 individual cross-correlationpatterns:(1)theoriginalpatternandthepatternwherethex-axishasbeenchanged;(2) theoriginalpatternand thepatternwhere they-axishasbeenchanged. Since in

each case the cross-correlation shows a single peak then the sum of the 2 cross-correlationfunctionsmustshow2well-separatedpeaks.

Note: If the calibration of a camera length for a selected CCD camera and for aselected nominal camera length has not been carried out beforehand for

DigitalMicrograph, the warning message appears and TEM coil calibration stops. Insuch case please calibrate beforehand the camera length consulting the manual ofDigitalMicrograph.

If the calibration of TEM coils is performed for a new camera length and for a new

selected camera, as seen in the CCD setting dialog box, a new item with a new IDnumber appear in the pull down menu. Recalibrate for the same experimentalconditionwilloverwritethedata.

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CheckAlphatiltaxisandBeamTilttest

1. EstimationofangleAlphaandsettheangle

InFig.4wehaveabox“Alpha tiltaxis”to inputtheangleAlpha. IfuserdoesnotknowtheangleAlpha,itcanbedeterminedusing“CheckAlphaTiltAxis”.Byclickingthisbuttontheprogramtakes

oneseriesofdiffration-patternsbychangingthesample-holder-tiltangle.Theremaybesomewaystoestimate theanglealphausing thisbutton. Twoexamples aredescribed inAppendix.After theestimationoftheanglealphausersmustinputtheanglealphaintothebox“AlphaTiltAxis”inFig.4.

2.Beamtilttest

Aftertheinputoftheanglealpha,usersshouldtestwhetherthebeam-tilt-directionisperpendicularto the sample-holder-tilt-axis, namely whether the beam-tilt-direction and the sample-holder-tilt-

directionareparallel(oranti-parallel)toeachotherornot.“TestBeamTilt”buttoninFig.4isusedtocheckthese.

InDiff-modewithoutspecimen inthebeampath,byclicking“TestBeamTilt”button, the incidentbeam is tiltedwithout compensationbydescan,namelybyPL-shift.Users canchose the tilt rangeandtiltstepsfollowingthesuggestionindialogbox.Theresultsofthebeamtilttestarerecordedby

CCDcamera.Theprogramcratesone imagestack.The imagestackcanbeseenusingslice toolofDigitalMicrograph(DM).IfusersarenotfamilarwiththeDMslicetool,pleaseconsulttothemanualofDM.Figure11istheresultofsummingupoftherecordedpicturesusingtheDMslicetool.Itcan

be seen that the beams are tilted in the same distance, and along the same direction. It can beconfirm that thisbeam-tilt-direction isperpendicular to the sample-holder-tilt-axis,namelyparallelto the sample-holder-tilt-direction in this case. The procedure to obtain the sample-holder-tilt-

direction isshown inFig16and17 inAppendix.Thebeam-tilt-direction isset tobeparallel tothesample-holder-tilt-direction,sothatitisconcludedthatthebeam-tilt-directionissetcorrectlybytheinputoftheestimatedanglealpha.

Fig.11Resultofthebeamtilttest.

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Collecting3DEDTdatasets

NOTE:ItisstronglyrecommendedtoruntheTEMcoilsCalibrationmodulebeforethedatacollection.Thedatacollectionof3DElectronDiffractionTomographydatacanbeperformedusingthe“Collect

Data…”modulefromthemain“EDT/Collect”menu.TheDataCollectiondialogboxisshowninFig.12.

Fig.12Datacollectiondialogboxthatappearsafterchoosing“CollectData….”inthepull-downmenuofEDT/CollectinFig.2.

Thegroupbox“SampleHolder”canbeusedtoselecttheappropriatesampleholderthatiscurrentlyinuse(seesection“Sampleholdersettings”onhowtomanagealistofsampleholders).Itisrequired

to choose the sampleholderprior to thedata collection. Theactual limit of the tilt angleswill beshownbelowtheselectedsampleholdertype(“Limit(deg):70”onthefigureabove).

Thegroupbox“CollectData”shouldbeusedforthedatacollection.

Thesettingsthatwillbeusedforthedatacollectionare:

• Collection type can be chosen from the Collect pull-down box (currently “Rotation 3D

(manual)”).

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• Thefolderwheretheacquiredframeswillbestoredcanbechosenusingthebrowsebutton(“Folder…”). The selected folder will be shown next to the button, for example,

(“C:\Users\user_name\Desktop\Test\” on the figure).When the data folder is specified,thegreyoutStartbuttonwillbecomeactive.

• TheBeamtilt range (indegrees)correspondstothe fullanglethatwillbecoveredbythebeamtiltofTEM.Incaseof3°thebeamtiltwillvaryfrom–1.5°to+1.5°.TheBeamtiltstep(indegrees)specifiesthebeamtiltstepthatwillbeusedinordertocovertherangeofthebeamtiltanglesspecifiedinBeamtilt range. Inthisexampletheprogramwillchangethebeam tilt in the range from –1.5° to +1.5° (covering 3°) with a step of 0.1°, andautomaticallyacquire31frames;

• TheSeriesoverlap(indegrees)definestheoverlapbetweenconsequentgoniometertilts.This value is in order to compensate themechanical imperfections of the stage. In idealcasethegoniometershouldtiltbythesamevalueasthe“Beamtiltrange”(3°inthiscase).However, if thevalueof“Seriesoverlap” isdifferentfrom0thentherealgoniometertiltwill be “Beam tilt range”minus “Series overlap” (3.0°–0.2°=2.8° inourexample). The“Seriesoverlap”valuecanbekeptas0.2°formostdatacollections;

• TheDelayforthefirstFramewillbeappliedtothefirstframeofthebeamtiltseriesafterthestagetilt.ForthestagetiltthemicroscopemodeisswitchedbetweenDIFFandImaging

modes (or SAMAGmode in JEOL microscope), and this delay will be effective for somemicroscopetostabilizethelenssettings.

• TheDelayonconsequentframes(milliseconds)andtheBeamblankcheckboxareusedforsometypesofCCDsthataresensitive forthebeampositionchanges.SomeCCDcameras(suchasGatanES500W)usea fluorescentscreenso that therecanbea trace leftby thestrongbeamwhile itmovesduring thebeamtiltorshift. ItmaydecayslowlyandcanbenoticedontheCCD.InordertocompensatefortheseeffectspleasechecktheBeamblankandputsomedelay(500-1000msshouldbegenerallyenough)fortheConsequentFrames.

NOTE:Thecollecteddatasetmustoccupyan individualfolder.Everynewdatacollectionmustbe pointed into a new folder otherwise all-previous data will be overwritten with the newdataset!

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Datacollectionstep-by-stepThedatacollectionwillstartbypressingtheStartbuttonatthebottomofthepanel.

Thedatacollectioncontainsthefollowingsteps:

1. Checkthesamplepositionandheight(usingTestWobblerbuttons).2. Collectthebeamtiltdata(usingtheCollectDatabutton).

3. Tiltthestage(usingtheTiltstagebutton).4. ManuallytrackbackandcorrectX-Yposition,andcorrecttheZpositionusingCCDcamera

(usingTestWobbler)

5. PressingStopviewingbuttonandswitchintotheDIFFmode.6. Gobackto2andrepeatthesameprocedure.7. FinishthedatacollectionbypressingtheCancelorFinishbutton.

1.CheckingthesampleheightThere are twoways to check the crystal height in imagingmode (SAMAGmode): (i) the dynamicwobbleofthebeambytiltingand(ii)subtracttwoframesrecorderwithoppositebeamtilts.

Theproceduretousedynamicwobbleisasfollows.ByPresstheTestWobblerbutton,thedynamicwobble test starts, this button is similar to the (JEOL) X-WOBBLE. In this case the data collection

programinduces2oppositebeamtilts(+/–0.5°inourcase)andswitchestheCCDintotheviewmodefortheobservations.Thecorrectsampleheightwillbetheonewhenthecrystalrelativemovementwillbeminimum.

Figure 13 shows the subtraction procedure to correct the crystal height. The frame subtraction

producesthefollowingimagesinthecaseofFig.13athecorrectsampleheight–noticetheaveragegrayleveloftheinnerpartoftheSAaperturewithminimumnumberofdistinguishablefeaturesandinFig.13bthesampleheightiswrong–thereare2shadowsofthecrystalcorner.

Fig.13ImageswithSAaperturesforthecorrectionofthesampleheightusingsubtractionprocedure.a:correctsampleheightcase.b:wrongheightcase.

Twoshadowsofthecrystalduetothesamplemovementcausedbythebeamtilt

(a) (b)

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BypressingtheStopViewerbuttontheviewmodewillstop,andtheCollectDatabuttonbecomes

active.TheStopViewerbuttonbecomesTilt Stage,but the Tilt Stagebuttonbecomesactiveonlyafterthedatacollectionprocess.

2.CollectingdataBypressingtheCollectDatabutton,datawillbecollectedautomaticallywiththebeamtiltseries.AlltheframeswillbesavedtodiskintheDM3/DM4format.Thetypicalstatusofthedatacollectionis

showninFig.14below:

Fig.14Typicalstatusofdisplayduringdatacollection.

NOTE:Duringthedatacollectionofthebeamtiltseriesallbuttons(exceptCancel)willbedisabled.BypressingtheCancelbutton,youcanstopthecurrentdataacquisition.Aftertheonesequenceof

datacollection,theCancelbuttonbecomesFinishbutton.Ifuserswanttofinishthedatacollection,presstheFinishbutton.Ifuserswanttocontinuethedatacollectionatanincreasedstage-angleofthespecimen,pleasepresstheTiltStagebuttontoincreasethetiltangleofthespecimenstage.

3.TiltingthestageBypressingtheTiltStagebuttonthespecimenstagewillbetiltedfromthecurrentstage-angle.Asitwasmentionedpreviously, the stagewill be tiltedby the angle that is calculated as theBeam tilt

angleminustheSeriesoverlap.Inthecasethatispresentedinthismanualthestagetiltwillbe2.8°(3.0°–0.2°).

TheTiltStagebuttonbecomestheCanceltiltbuttonduringthistiltingstageaction.Ifuserswanttostopthestagetiltingaction,presstheCancelTiltbutton.

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WhentheTiltStagebuttonispressed,thedatacollectionprogramwillswitchtheCCDintotheview

mode for the crystal tracking.When the stage tilt action finishes, theCancel Tilt button becomesStopViewer.

4.CorrectionofX,Y,ZpositionofspecimenAfterthespecimenstagetilt,thespecimenmaymove.Trackbackthespecimenmanuallyisacrucialstep during the data collection. The user must move the crystal back so that it will occupy the

appropriate position. The crystal tracking can be easily achievedwith the X-Y stage control of themicroscope. Then, the specimen height must be checked and corrected, by pressing the Testwobblerbutton.AfterthecorrectionofZ,pleasepresstheStopwobblerbutton.

5.Stopviewingmode

IfX,Y,Zpositionsofthespecimenareappropriate,pleasepresstheStopViewerbutton.Then,theviewmodewill stop, and theCollect Data buttonbecomesactive. YourTEMgoes intoDIFFmode

automatically.

6.RepeatingtheCollectDataThen,byclickingCollectDatabutton,wegobacktotheprocess“2.Collectingdata”.

7.Finish/Cancelthedatacollection

The data collection starts from the stage tilt angle that users set initially. Repeating the datacollectionprocedurewillincreasethestagetiltangle.PresstheFinishorCancelbuttonatanytimetofinishorstopthedatacollection.

NOTE,inthisdialogboxvariousbuttonswillchangeasfollows

• Start/CollectData

• TiltStage/CancelTilt/StopViewer

• Cancel/Finish

• TestWobbler/StopWobbler.

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CheckDataSet

Fig.15Dialogboxthatappearsbyselecting“CheckDataSet…”inthepull-downmenu

ofEDT/Collect.

Byselecting“CheckDataSet”fromthepulldownmenu,filesselectionmenuwindowasseeninFig.15 will appear. The files were saved with names “Rotate-n-m.dm3/dm4”, n is an index for thespecimenstagetilt,misanindexforbeamtiltinoneseries.

Ifusersselectasingledata inoneseriesofthebeamtilt, theprogrammakesadatastackfromall

collecteddatainoneseriesofbeamtilt.ThecreateddatastackcanbeviewedbyusingSlicetoolinDM.

Ifusersselectmultipledata,theprogrammakesadatastackfromtheselecteddata,anduserscan

view through the data stack using Slice tool similarly. The selected data is sorted. This may beconvenienttoseethecontinuityofdifferentseriesofcollecteddata.

Ifthebeam-tilt-directionisanti-paralleltothespecimen-holder-tilt-direction,dataattheendpartofaseriesofbeamtiltwillcontinuetothebeginningpartofthenextbeamtiltseries.Ifthebeam-tilt-

direction is parallel to the specimen-holder-tilt-direction, data at the beginning part of beam tiltseriesissimilartothatattheendpartofthenextbeamtiltseries.InthiscasepleasechecktheboxofinvertbeamtiltdirectioninparametersettingdialogseeninFig.6.

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Dataprocessing

All therecordedframesandthedatacollection logfilewillbestored intheselectedfolder forthecurrent data collection. Do not change/erase/modify the files in the folder! The whole folderhowevercanbemovedtoanyotherlocation.

ThecollecteddatasetcanbefurtherprocessedwiththedataprocessingprogramEDT/Processfrom

AnaliteX.

Bugreporting

Therearelogfilescreatedbytheprogramduringeveryrun.TheselogsarestoredinaspecialfolderthatdependsontheWindowsversion.

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Appendix

EstimationofangleAlphausingcrossingpointsofKikuchi-lines

TheeasyproceduretoestimatetheanglealphaistouseKikuchi-lines.Setarelativelythickspecimentoseekikuchi-lines.PleaseswitchintoDiff-mode,thecameralengthmustbethesametothatusedincalibration.Byclicking“CheckalphaTiltAxis”buttonintheSampleHolderdialogboxseeninFig.4,theprogramtakesoneseriesofdiffration-patternsbychangingthespecimenstagetiltangle.Userscansetthetiltrangeandtiltstepsbyfollowingthesuggestioninthedialogboxwhichwillappeareafterclicking“CheckalphaTiltAxis”button.

Fig.16a,b,c,d,diffraction-patternfromacrystalspecimenatrelativelythickposition.aanddshowtheKikuchi-patternbeforethesampleholdertilt,bandcshowthepatternaftertheholdertilt.

YoucansavethesetofdiffractionpattersdatawithyourconveinetnameandlookthroughusingDMslicetool.

ChosetwoKikuchi-lineswithacrossinginadiff-patterntaknebeforethesampleholdertilt.RedlinesinFig.16aindicatethetwoKikuchi-lines.Fig.16bshowstheresultafterthesampleholdertiltbyafewdegrees.Moveof theKikuchi-lines canbe seen. ThemovedKikuchi-lines are indicatedby redbrocken lines. Themovingdirectionof the crossingpoint is shownbya redarrow in Fig. 16c. ThedirectioncanbemeasuredusingDMlinetool.

Youcan findmanycrossingpointsofKikuchi-linesmove towoards the samedirection, so that youmaymeasure the direction frommany crossing points as shown in Fig. 16d. Different color linesindicat different Kikuchi-lineswith different crossings.Themoving direction can be obtained as anavaragedresult.Themovingdirectioncanbethesample-holder-tilt-direction.

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Sampleholdertiltaxisisdeterminedasaperpendiculartothesample-holder-tilt-direction.Thealphaisdefinedfromthey-axisdirectiontotheholdertiltaxisinthecounterclockwiserotationintheCCDcamera images, thus the alpha is obtained as +178.1 +1.0 degrees in the Fig. 16 case. Tolelrancewithin+2digreesforthemeasuredalphaisaccurateenoug.

EstimationofangleAlphausingLauecircles

If users do not have a specimen with clear Kikuchi-lines, users can measure the angle alpha byobservingLaue-circles.Ifuserstiltaspecimenslightlyfromanexactzoneaxisdirection,userscanseeanexcitationofBragg reflectionswith circular formas seenbelowFig17a. This circle, Laue circle,appearsatintersectionbetweenEwaldsphereandthezerothorderLauezoneplane.Fig.17ashowsastatethatsampleholderistiltedslightlytowards(-)directionfromanexactzoneaxis.Lauecircle“A”canbeseen.Fig.17bistakenunderaconditionslightlytiltedtowards(+)direction.Lauecircle“B”canbeseen.

Fig17cindicatesLauecircles“A”and“B”onthesamepicture.Ifusersdeterminecentresofcircles,userscandeterminethemovingdirectionofthecentres.AredarrowinFig.17cindicatesthemovingdirection.Thismovingdirectionissampleholder-tiltdirection,anditisperpendiculartothesampleholdertiltaxis.Aspecimenwithalargeunit-cell,sothatusercanseeaclearLauecirclebecauseofmanyBraggreflections,ispreferableforthisestimation.

Fig.17a:Sampleholderisslightlytiltedtowardsthe(-)directionfromanexactzoneaxis.Lauecircle“A”canbeseen.b:Sampleholderistiltedtowardsthe(+)directionslightly.Lauecircle“B”isseen.c:indicatesLauecircles“A”and“B”onasamepicture.

Pleaseinputtheestimatedanglealphaatthe“AlphaTiltAngle”intheSampleHolderdialogboxinFig.4.

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Relationsbetweensample-holder-tilt-axisandsample-holder-tilt-directioninaCCDcameraimge

Fig.18Relationbetweensample-holder-tilt-axisandsample-holder-tilt-direction

Figure18illustratesatipofsampleholderanditshowstherelationbetweensample-holder-tilt-axisand sample-holder-tilt-diretion. Sample-holder-tilt-direction is the direction that Kikuchi-patternsandLaue-circlesmovealongbythetiltofsampleholder.Sample-holder-tilt-axis istheaxisthattheholder moves respecting to. Sample-holder-tilt axis and sample-holder-tilt-direction areperpendiculartoeachothers.InanactualCCDimagethesetwoaxesareseentoberotatedinsomeanglesrespectingtoz-axis,thougthesetwoaxesarestillperpendiculartoeachothers.

sample'holder',,,,-lt'axis�

sample'holder',,,,-lt'direc-on�

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crystal,sample�

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24

Quick Reference Guide The EDT-Collect Main Menu

The commands in the EDT-Collect menu are described below.

Command Description Calibration… (see Dialog)

Opens the dialog for calibration.

Collect Data… (see Dialog)

Opens the dialog for data collection.

Settings… (see sub menus)

Opens the dialog for parameter setup.

TED-TEST Test program to check whether the EDT/Collect works for user’s TEM

Help Opens Help document

About...

Opens About dialog

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Calibration Dialog

The components of the dialog are described below.

Dialog

Component Description Illumination Displays the current illumination mode TEM Mode Displays the current imaging/diffraction mode Camera length Displays the current camera length (or magnification) Update Updates above three parameters Beam Tilt Displays the current beam in DAC Recalculate angle When checked, the beam tilt angle for the “Change

value” is displayed at “BT angle” as a mean value for x and y-tilts. The CCD should be calibrated beforehand.

Change value Suggested DAC value to shift the beam (zero (0) means an automatic search for this value)

Calibrate Executes a calibration IS1 Displays the current image shift 1 in DAC Change value Suggested DAC value to shift the beam (zero (0)

means an automatic search for this value) Calibrate Executes a calibration Projector Displays the current projector alignment (PLA) angles Change value Suggested DAC value to shift the beam (zero (0)

means an automatic search for this value) Calibrate Executes a calibration

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Collect Data Dialog

The components of the dialog are described below.

Dialog

Component Description Sample Holder Sample Holder Sample holder selector Limit Displays the maximum tilt angle Collect Data Collect Data collection mode selector Folder Browse for a folder to save the data Mode Displays the current microscope modes Mag Displays the current mag/camera length Stage Displays the current stage position Update Updates the microscope and stage parameters Beam Tilt (deg) Maximum rotation angle using the beam tilt Frame Step (deg) Rotation step for the beam tilt series Series overlap (deg) Overlap rotation angle between two series of the

beam tilt frames. Delay on First Frame (ms)

If checked, the specified delay is applied for the first frame of the beam tilt series.

Delay on Consequent Frames (ms)

If checked, the specified delay is applied for the consequent frames of the beam tilt series.

Beam blank When checked, the beam will be blanked between exposure frames.

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Data Collection Buttons Start / Collect Data Starts the whole data collection or the frame series. Tilt Stage Starts manual stage rotation. The View window will

open. Cancel / Finish / Stop Viewer

Cancels or Finishes data collection, or stops the Viewer.

Test Wobbler / Stop Wobbler

Starts or Stops wobbling the beam wobbler for sample height adjustment.

Test Focus Not-implemented.

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Settings Dialog

The components of the dialog are described below.

CCD Tab

Component Description Current Camera Camera selection Oversaturation Level CCD saturation level Calibrations Calibration ID etc. Calibration selector Scale CCD pixel calibration for this mode

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Sample Holder Tab

Component Description Sample Holder Sample holder selection Limit Maximum tilt angle Add... Opens a dialog to add the stage information Remove Removes the stage entry Check Alpha Tilt Axis For experimental measurement of the angle Alpha Alpha Tilt Axis (deg) Angle between an axis of tilt stage for specimen and

Y-direction in CCD Test Beam Tilt Use to check beam tilt direction Sample Holder Add Dialog

Component Description Name Stage name Limit (deg) Maximum tilt angle

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Parameters Tab

Component Description Invert Beam Tilt Direction

If checked, the beam tilt direction of the frame series is inverted during the data processing. This parameter has no effect on data acquisition.