Table of Contents - CID Bio-Science, Inc.€¦ · device. Users can choose to enter Longitude and Latitude manually, or use the GPS device in the CI-110, or enter a text based tag

1.1

1.2

1.2.1

1.3

1.4

1.5

1.5.1

1.5.2

1.5.3

1.6

1.7

1.7.1

1.7.2

1.7.3

1.7.4

1.7.5

1.7.6

1.7.7

1.7.8

1.8

1.9

TableofContentsINTRODUCTION

FEATURESANDSPECIFICATIONS

Specifications

SOFTWAREINSTALLATION

HARDWAREINSTALLATION

GETTINGSTARTED

StartingtheApplication

EnablingGPS

Recordingyourfirstmeasurement

APPLICATIONFUNCTIONALITY

MEASUREMENTTAB

Brightness,Contrast&Gamma

Location

PARandSunflecks

PARLAICalculation

Sky&LeafFilter

GapFractionThreshold

AzimuthDivisions

ZenithDivisions

BROWSERECORDSTAB

ADVANCEDSETTINGSTAB

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1.9.1

1.9.2

1.9.3

1.9.4

1.10

1.11

1.11.1

1.11.2

1.12

1.13

OutputFolder

CameraLensAlignment

PARSensorCalibration

CompassCalibration

THEORY

TECHNICALSUPPORT

FrequentlyAskedQuestions

TroubleshootingandTips

HARDWAREWARRANTY

PRODUCTTESTCHECKSHEET

3

CI-110PlantCanopyImager

CIDBio-Science,Inc.1554NE3rdAvenueCamas,WAUSA98607

[email protected]@cid-inc.com

+1(360)833-8835

Manualavailableonlineathttps://cid-felix.gitbooks.io/ci-110-operation-manual/content/

Revised01/03/17

INTRODUCTION

4

mailto:[email protected]


https://cid-felix.gitbooks.io/ci-110-operation-manual/content/

CI-110PlantCanopyImagerTheCI-110'sdigitalplatformenablesyoutosimultaneouslycapturewide-angleplantcanopyimagesandestimateLeafAreaIndex(LAI)andPhotosyntheticallyActiveRadiation(PAR)levelsfromasinglecanopyscan.LAIisusedtocharacterizeplantandforestcanopies.Thisvaluerangesfrom0-10,with0representingnocanopyorbaregroundand10representingadenseconiferforestcanopy.

FEATURESANDSPECIFICATIONS

5

SpecificationsImager

Specifications

Lens Self-levelinghemisphericallens

ImageResolution 768x494Interface USBMeasuringTime 0.5-1secFish-EyeLensAngle 150OperatingTemperature 5-50°C

ProbeSize 20x20mmArmLength 440mmProbeandArmWeight 500g

Thereare24PARsensorsontheCI-110,locatedalongthetopofthearmspaced10mmapart.ThePARsensorsarefilteredGaAsP(galliumarsenidephosphide)photodiodes.Thespecificationsareinthefollowingtable.

Specifications

6

ParSensorSpecificationsRange 0-2500μmol/m2sAccuracy 5μmol/m2sResponse 400-700nm

Specifications

7

SoftwareInstallationTheCI-110softwarearrivespre-installedonatabletcomputer.TheCI-110softwarecanbeinstalledonanothercomputer,eitherforfielduseortoanalyzeimageslater,andthefollowingstepsshouldberepeatedoneachcomputerusedwiththeCI-110PlantCanopyImager.

Tocheckforupdatesonsoftware,navigatetothesoftwaresupportlinkbelow,orwithinthePlantCanopyAnalysisSoftwareunderAdvancedSettings>CheckforUpdates(internetconnectionrequired).

TheinstructionsforinstallingCI-110PlantCanopyAnalysisSoftwareversion6.0arethesameforWindows7,8and10.ThecurrentversionofCI-110softwarecanbedownloadedfromthewebat:https://www.cid-inc.com/support/CI-110/software/

Navigatetothewebpageandselectthedownloadforthe“currentversion”ofsoftwareorsoftwareversioncompatibletoyourunitserialnumber.Runthe.exefiletoinstallthesoftware.FollowthepromptstodownloadandinstallthesoftwareonyourPC.


8

https://www.cid-inc.com/support/CI-110/software/


9


10

HardwareInstallationTheCI-110issuppliedwiththehardwareanddriverinstalledonatabletcomputer.ThefollowingstepsshouldberepeatedoneachcomputerusedwiththeCI-110PlantCanopyImager.Thedriveriscompatiblewith32and64bitoperatingsystems.

ThedriverisinstalledthroughtheCI-110PlantCanopyAnalysissoftware.Toinstallthedriverafterdownloadingthesoftware:

1. ConnecttheCI-110tothePC’sUSBport.2. OpentheCI-110software.3. SelecttheAdvancedSettingsTab.4. SelectInstallDriver.5. ClickNextintheDeviceDriverInstallationWizard.6. ClickFinishtocompletethedriverinstallation.


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12


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GettingStartedTheseinstructionswillwalkyouthroughbasicoperationoftheCI-110software.Thesectionsthatfollowwillgointomoredetailonfunctionalityandfeatures.

GETTINGSTARTED

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StartingtheApplication1. ClickontheCI-110softwareicon toopenthe

software.Or,clicktheWindowsStartbuttonandgotoProgramsandfindtheCID-BioSciencefolder.SelectCI-110PlantCanopyImager.

2. Thedialogboxbelowwillappear.

StartingtheApplication

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EnablingGPSTheCI-110softwarewillautomaticallyrecordyourcurrentGPSpositionwithmeasurementswhentheGPSdevicebuiltintothehandleoftheCI-110isconnected.Formoreinformation,seetheLocationsectionofthismanual.

1. Clickthedrop-downlistandselectLocation.2. TheGPSon-boardtheCI-110softwarewill

automaticallysearchthesystemforaGPSdeviceandautomaticallyconnecttoitifsatellitesareavailable.

TheCI-110softwarewillattempttore-connecttheGPSeverytimetheapplicationstartsafterthefirstconnectionisestablished.Itmaytake10-15minutestoestablishaconnectionwiththerightnumberofsatellitesthefirsttimetheCI-110isusedinanewlocation.DuringthetimetheCI-110isallowedtosearchforsatellites,itshouldbeoutsideornearawindowforthefastestresults**.

EnablingGPS

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Recordingyourfirstmeasurement1. AttachtheCI-110cameratothearmusingthetwotop

buttonsforproperalignment.2. AttachtheCI-110hardwareviaUSBtothecomputer.3. OpenthePlantCanopyAnalysisSystemsoftware.

TheStart,DataandSavebuttonswillbeenabledoncethedeviceisdetected.

4. ClicktheStartbutton.ThiswillcausetheroundimageareaontherighttobeupdatedwithalivevideostreamfromtheCI-110device.

5. PlacetheCI-110underthecanopyareatomeasure.Besurethecameraisfacingnorthforaccuratereadings(asindicatedbythecompassneedlewhichturnsgreenwhenaimingnorth).

6. ClickthePausebuttontopreviewyourmeasurement.AdjusttheBrightness,Contrast&Gamma,etc.asneededtoincreasethecontrastbetweenskyandfoliage.

7. ClickDataandEdittoviewyourmeasurementdetails


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andmakechanges.

8. ClicktheSavebutton.Holdthecamerasteadyforthe1-2seconddelaywhiletheimageissaving.Theapplicationwillsaveyourmeasurement.ToreviewyourmeasurementclickontheBrowseRecordstab.Aftersavingtheappwillautomaticallygobackintolivevideomode.Alternatively,thetriggerbuttononthearmoftheCI-110canbeusedtosaveanimage.ThetriggerbuttononthewandofCI-110willautomaticallysaveanimage.IfthisispushedbeforestartingthelivepreviewoftheimagebyselectingtheStartbutton,theimagewillsaveimmediatelyuponenablingthelivepreview.


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ApplicationFunctionalityThefollowingaresummariesofeachapplicationtabandtheirpurpose.Thesectionsthatfollowdetailapplicationfunctionalityareuserinteraction.

Measurement

Recordmeasurementsandviewtheirdetails.Thedataonthisscreenisstoredwitheachmeasurementrecord,alongwithsettingsandotherinformation(seeApplicationOutput).Theoptionsavailableinthedrop-downlistwilldifferiftheCI-110hardwareisenabledorifanimageisbeingedited.TheoptionsforExposure,ColorControlandPARandSunflecksareonlyseenwhenanimageisbeingacquired.Theseoptionsarehiddenduringpostmeasurementanalysis.

BrowseRecords

Search,export,delete,editandreviewsavedrecords.

AdvancedSettings

Configurestheapplicationandallowsaccesstocalibratethedevice.


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MeasurementTabThistabisusedtorecordmeasurementsandviewtheirdetails.Thedataonthisscreenisstoredwitheachmeasurementrecord,alongwithsettingsandotherinformation(seeApplicationOutput).

Start/Pausebutton

ClickingtheStartbuttonenablesalivevideofeedfromtheCI-110deviceordisplaysadialogtoselectanimagefile(whentheCI-110isnotphysicallyattached).Clickingthe

MEASUREMENTTAB

27

PausebuttonstopsthevideofeedandchangesthebuttontextbacktoStart.

Data/Editbutton

ClickingtheDatabuttonmeasuresthecurrentimageanddisplaysstatistics.ClickingtheEditbuttondisplaystheoptionstomanipulatethemeasurementimage.

Savebutton

Thisbuttonsavesthecurrentimageandmeasurements.ThefolderandformatusedtostoremeasurementscanbeconfiguredintheAdvancedSettingstab.ReviewtheApplicationOutputsectionofthisdocumentfordetailsonthedatasaved.

Original/MeasuredImageTogglebutton

Intheupperrightcornerofthescreenisatinypreviewofthemeasuredimageororiginalcameraimage.Clickingonthissmallcircletogglestheimagedisplayedbetweenthesetwo.

GPSLock

MEASUREMENTTAB

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ThisindicatesifthereisaGPSsatellitelockonyourcurrentposition.RecordssavedwithoutaGPSLockmaystorethewrongGPSlocation,ornoGPSlocation.Thetextwilltogglefromared“No”togreen“Yes”whenaGPSlockhasbeenacquired.TheCI-110shouldbeoutsideornearawindowtogetthefastestGPSlock.

Exposure

Thisfeatureisusedtooptimizetheimageexposureforaccurateprocessing.Theexposureshouldbeadjustedsothatadifferencebetweenleafmaterialandskycanbeseen.Itisrecommendedtoalwaysadjustthecameraexposurefirst,beforesavinganyimages.

Therearetwomodesforthecameraexposure,automaticandmanual.Ifoutdoors,theautomaticexposurefeatureshouldprovideanaccurateimageforprocessing.Ifindoorsorunderlow-lightconditions,themanualexposureoptionallowstheusertoadjusttheexposureandseetheaffectdirectlyintheimage.

MEASUREMENTTAB

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ColorControl

Thisfeatureisusedtooptimizetheimagecolorsforaccurateprocessing.Ifneeded,thecolorcontrolgainandsaturationlevelscanbeadjustedtohelprenderleafelementsasgreenandskyelementsasblue.

Saturationdescribestheintensityofthecolorintheimage.Thegainwilladjustthebrightpartoftheimageandissimilartothecontrastcontrol.

MEASUREMENTTAB

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MEASUREMENTTAB

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Brightness,Contrast&GammaThisfeatureisusedtooptimizetheimageforaccurateprocessing.Thesesettingscanbemanipulatedatanytime.Forexample,measurementscanberecordedoutsidethenlateroptimizedinsidewhereit’seasiertoseethecomputer’sdisplay.Itisrecommendedtoadjustthebrightnessandcontrastbeforesavingthecanopyimageinordertomakeallplantelementsgreen.Afteranimageissaved,thegammacanalsobeadjusted.


32

Contrast

Controlstheratiobetweenbrighteranddarkerpixelsinthemeasurementimage.

Brightness

Controlstheluminanceofthemeasurementimage.

Gamma

Controlsthegammacorrectionofthemeasurementimage.Thegammaadjustmentisonlyavailableafterthe“data/edit”buttonisselected.


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LocationThisscreenisusedtospecifythelocationoftheCI-110device.UserscanchoosetoenterLongitudeandLatitudemanually,orusetheGPSdeviceintheCI-110,orenteratextbasedtagtoidentifydifferentlocations.TheCI-110shouldbeoutsideornearawindowtogetthefastestGPSlockandtheGPSmaynotworkindoors.

LongitudeandLatitude

Thesevaluescanbechangedbyclickingthekeyboardiconortypingwithinthefield.

Location

34

Tags

Thisfieldcanbeusedtostoretextthatidentifiesaspecificlocation,projectorotherdetails.Forexample,“Project#57,Flag#101”mightdenotetheprojectandmeasurementplotlocation.ThetagfeatureisstillusefulevenwhenGPSisnotusable.

Location

35

PARandSunflecks

ThisscreenisusedtoviewthecurrentPAR(photosyntheticallyactiveradiation)intensityandsunflecksvalue.Thereare24PARsensorspositionedalongthetopoftheCI-110arm.ThelightintensityoverthesesensorsisaveragetogethertoprovidethePARvalue.

Sunflecksarebriefperiodsofanincreasedamountofsolarradiationreachingbelowthecanopy.Sunflecksarecausedbywindmovingleavesinthecanopyorbythesun’smovementthroughouttheday.Thefractionofthegroundcoveredbysunfleckscanbeusefultoresearcherswhen

PARandSunflecks

36

determiningtheamountofcanopycover.Thesunfleckvaluecanalsobedirectlyrelatedtocanopystructurecharacteristics.

ThesunfleckvalueisapercentageofthePARsensorsexposedtoaradiationlevelgreaterthanthesetthreshold.ThedefaultsunfleckminimumPARissetat300μmol/ms.AdjustmentstothePARandsunfleckcalibrationscanbemadethroughtheAdvancedSettingstab.

2

PARandSunflecks

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PARLAICalculationThisscreenisusedtochangethewayPARdataisrecoded.Severalfactorsarepossibletoadjustbytheuser:lightabovethecanopy,leafdistributionfactorandthesolarzenith.

The“LightAboveCanopy”shouldbesettothePARintensityabovethecanopyatthetimeofthemeasurement.ThePARsensorsoftheCI-110canbeusedtomeasurethePARdirectly,oranestimateofthePARabovethecanopycanbeused.Thelightabovethecanopyrangesfrom1to2000μmol/m s.

The“LeafDistributionFactor(chi)”isthedistributionofleafangleswithinacanopy.Itrangesfrom0.01to10.Thedefaultvalueforchiis1.0.Atthisleafdistributionfactor,thecanopyangledistributionisassumedtobespherical.Averticalcrop,likeonions,mayhaveachioflessthan1(ex:0.7),whileastronglyhorizontalcrop,suchasstrawberries,mayhaveachiof3orgreater.Manyplantshavearangeorvariationforthisfactor,suchasmaize(0.7-2.5).TheleafdistributionfactordoesnotproducesignificanterrorintheLAIequation.

2

PARLAICalculation

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The“SolarZenith”rangesfrom1to90degrees.Thesolarzenithangleismeasuredfromdirectlyoverheadtothegeometriccenterofthesun'sdisc.Itisbasedonyourcurrentpositiongloballyandthetimeofday.Thesolarzenithangleatsunriseandsunsetis90degrees.

PARLAICalculation

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Sky&LeafFilterThisfeatureallowsuserstodarkenspecificcolors(foliagearea)andlightenothers(skyarea).Intheexamplebelowfoliagecolorsthatshouldbegreenareblurredbytheskywithabluehue.AfterapplyingtheSky&LeafFilterthesecondimageshowsthoseareasaredarkenedsotheywillbecountedasfoliageinsteadofsky.

Sky&LeafFilter

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Tousethisfilterclickonacolorsquare,clickonthecolorintheimagetoworkwithandthenselectthe“ColorMatchTolerance”.Increasethistolerancetoincludepixelswithcolorssimilartotheselectedcolor.

Sky&LeafFilter

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GapFractionThresholdCanopygapfractionistheprobabilityofarayoflightpassingthroughthecanopywithoutencounteringfoliageorotherplantelements.TheCI-110PlantCanopyAnalysissoftwareincludesseveraldifferentmethodstoanalyzetheGapFraction,includingtheOtsumethod,EntropyCrossovermethodandmanualthreshold.TheEntropyCrossovermethodisautomatic,astheuserisnotrequiredtoinputanything.

ThechoiceofappropriateGapFractionmethodislefttothediscretionoftheuser.Itisrecommendedtoexperimentandusethethresholdmethodthatbestseparatescanopy


42

andsky.Mostlikely,verysimilarresultswillbeacquiredwithanymethodused.Thefollowingresearchinvolvesthecomparisonofseveralgapfractionmethods:

AnImprovedEstimateofLeafAreaIndexBasedontheHistogramAnalysisofHemisphericalPhotographs

AgriculturalandForestMeteorology,volume149,pages920-928,2009.Juarez,R.,RiberiodaRocha,H.,SilvaeFigueira,A.,Goulden,M.,Miller,S.


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https://cid-inc.com/publication/an-improved-estimate-of-leaf-area-index-based-on-the-histogram-analysis-of-hemispherical-photographs/

AzimuthDivisionsThisscreenallowsuserstocontrolhowthemeasurementisseparatedinazimuthdivisions,andselecttheareatobemeasured.Azimuthdivisionscanbethoughtofaspieslices,makingupthehemisphericalpicture.

NumberofAzimuthDivisions

Thisfieldindicateshowmeasurementdatawillbedivided.Measurementscanautomaticallybesplitintoupto10azimuthdivisions.

AzimuthDivisions

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ExcludedArea

Thesefieldsindicatewhichpartofthecameraimageshouldbemeasured.Theareamaskedinbluewillbeexcluded.Inadditiontousingtheslidercontrolsuserscanselectusingtheirfingerbyslidingafingerclockwiseovertheareatoexclude,orcounterclockwiseovertheareatoexclude.

AzimuthDivisions

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ZenithDivisionsThisscreenallowsuserstocontrolhowthemeasurementisseparatedinzenithdivisions,andselecttheareatobemeasured.Zenithdivisionsarerepresentedasringsinthehemisphericalpicture.

NumberofZenithDivisions

Thisfieldindicateshowmeasurementdatawillbedivided.Measurementscanautomaticallybesplitintoupto10zenithdivisions.

ZenithDivisions

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ExcludedArea

Thesefieldsindicatewhichpartofthecameraimageshouldbemeasured.Theareamaskedinbluewillbeexcluded.Inadditiontousingtheslidercontrolsuserscanselectusingtheirfingerbyslidingafingerclockwiseovertheareatoexclude,orcounterclockwiseovertheareatoexclude.

FormoreinformationonhowazimuthandzenithdivisionsinfluenceLAIestimation:

CanadianJournalofForestResearch,volume40,pages1588-1603,2010.Gonsamo,A.,Walter,J.,Pellikka,P.

ZenithDivisions

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BrowseRecordsTabThistabisusedtobrowsethroughmeasurementrecords.Double-clickonarecordtoselectit.Whenarecordisselected,acheckmarkwillappearnexttotheleftoftherecord.Arecordcanalsobeselectedbysimplyclickingontheleftwherethatcheckboxappears/disappears.

Oncearecordisselected,Delete,ExportbuttonswillappearnexttotheOpenbuttoninthelowerright.Allrecordscanbeselectedbyclickingthe“SelectAll”button.Filescanbeexportedasa.csv(MicrosoftExcelcompatible)or.KML(GoogleEarthcompatible).

BROWSERECORDSTAB

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SearchKeywords

ThistextboxcanbeusedtofilterresultsintheBrowseRecordstab.TypeavaluethenclicktheSearchbuttontoonlyshowrecordswiththatvalue.ClicktheResetbuttontoclearthisvalue.

ConvertingPreviousRecords

FordatafilescreatedwithapreviousCI-110softwareversion,navigatetotheBrowseRecordsTabtoconvertthefilestobecompatiblewiththissoftwareversion.

Ifrecordsarefoundfromapreviousversionofthesoftware,youwillbeasked“Wouldyouliketoautomaticallyconverttheserecordsnow?”Beforeconversion,afullbackupoftheserecordswillbemadeunderasubfolderinyourdatafolder.Ifyouremovethe.ci110filenameextension,therecordwillnolongerbevisiblefromtheBrowseRecordstab.

BROWSERECORDSTAB

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Exportingtoexcel

NavigatetotheBrowseRecordstab,selectthefilesforexportandclickontheExportbutton.Therearetwoformatsforexport:CSVandKML.ToworkwithdatainExcel,optforCSVformat(commaseparatedvalues).

SelectanameandlocationfortheCSVfileandopenthefileinExcel.

BROWSERECORDSTAB

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BROWSERECORDSTAB

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AdvancedSettingsTabThistabisusedtocontrolfeaturesinthesoftwarethatarenottypicallychangedbetweenmeasurements.DetailsaboutthehardwareandsoftwareversionarelocatedtowardsthebottomoftheAdvancedSettingsTab.

TheAdvancedSettingsTabalsobuttonstoinstalltheCI-110driver,checkforsoftwareupdatesandaccessthereleasenotes.

ADVANCEDSETTINGSTAB

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OutputFolderTheOutputFoldertextboxcontainsthepathtostoremeasurementrecords(seeApplicationOutput).UsetheBrowsebuttontochangetheoutputfolderbybrowsingtoyourselection.

OutputFilenamePrefix

TheOutputFilenamePrefixcontainstheprefixtousefornewmeasurementrecords.Forexample,aprefixof“CI-110DemoSurvey_”wouldcauseallnewmeasurementstobesavedasfileswiththatprefix.Thiscanbeusedtokeepprojectdataorganizedwithintheapplicationandelsewhere.

OutputImageFormat

TheOutputImageFormatselectionspecifiestheimageformattouseforeachsavedimage(seeApplicationOutput).

OutputFolder

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ApplicationOutput

BydefaultCI-110imagesanddatawillbestoredundertheWindowsuser’sDocumentsfolderinasubfoldercalledCI-110.Eachmeasurementissavedasa.ci110file.Withinthe.ci110file,therearethreeseparatefilesthatcanbeaccessedbyre-namingtherecordintheCI-110software.Thethreefilesare:

1. CameraImage(.png,.bmp,etc.)2. Measurement.XML3. Cache.dat

Toopenafile,double-clickonthefilenamewhichwillopentheCI-110softwareandloadthedata.

OutputFolder

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Toviewthe.xmldatainVersion6ofthesoftware:

1. Re-openthe.ci110fileinthesoftware.

2. GotoFileDetailsonthedropdownmeasurementmenulist.

3. Changetheendofthefilenameto.zip.Itwillwarnthatchangingfrom.ci110to.zipwillnotallowthesoftwaretosearchforthefilewhenyouclickbrowseintheBrowseRecordstab.

4. ClickYesonthewarning.

5. Exitthesoftwareandopenthe.zipfile.Inthe.zipfilethereisthe.xml,whichhasthenumericaldatainit,aswellasthe.pngimagefile.

6. Remembertochangetheextensionbackto.ci110tobeabletobrowse/searchforthefileintheCI-110software.

OutputFolder

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TheMeasurement.XMLfile

Thisfilecontainsmeasurementdataincluding…

ImagefileformatandlocationImagethresholdCamerasettingsTimestampCompassbearingGPSquality,numberofsatellites,GPSlockindicatorLongitude,latitudeandaltitudeLocationtagsZenithdivisions,extinctioncoefficient,transmissioncoefficientAzimuthdivisions,leafdistributionImagecontrast,brightness,gamma

OutputFolder

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ThresholdmethodSkyandleaffilterdetailsPARSunflecksLeafareaindexMeanleafangleGapfractionLeafdistributionfactor(chi)PARabovecanopySolarzenith

OutputFolder

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CameraLensAlignmentTheCI-110hardwareandtabletcomputerarepairedtogetherasacompletesystembeforeleavingthefactory.Eachsystemhasaslightlydifferentoffset.

Theimagesareautomaticallyalignedbythesoftwarefromafactorycalibrationoftheoffset.Thisoffsetistotheopticalcenterofthefisheyecameralens.

TheoffsetvaluesforeachCI-110arepre-enteredinthesoftwareandincludedontheCI-110ProductTestCheckSheetintheCI-110UserManual.

CameraLensAlignment

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PARSensorCalibrationThe24PARsensorslocatedalongthearmoftheCI-110arecalibratedatthefactory.Typically,thePARsensorsdonotrequirere-calibration.ThereisawarningbeforeenteringthePARsensorcalibrationthatthisshouldonlybeperformedbythemanufacturer.ThecalibrationvaluesfoundatthefactoryfortheCI-110canbefoundonintheCI-110ProductTestCheckSheetattheendoftheCI-110UserManual.

PARSensorCalibration

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CompassCalibrationThecompassoftheCI-110islocatedinthehandle.Thecompassshouldbecalibratedwheneveritisn’tpointingnorth,orwhenevertheCI-110istakentoalocationwithadifferentmagneticfield.Tocalibratethecompass,followtheinstructionsthatappearintheapplication.Wheninstructedtorotatethewand(arm)alongeveryaxis,becarefultoholdtheCI-110cameraheadsecurelysoitdoesnotfalloff.

CompassCalibration

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TheoryTheCI-110softwarecalculatesthesolarbeamtransmissioncoefficients,orthefractionoftheskyvisiblefrombeneaththeplantcanopyusingtheGap-FractionInversionProcedure(NormanandCampbell,1989).

THEORY

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Imagesofplantcanopyarebrokendownintozenithandazimuthdivisions.Thefractionofsky(solarbeamtransmissioncoefficient)visibleineachdivisionisanalyzedbytallyingtheskyportionoftheimagepixels.

Avaluebetween0and1isassigned;with0meaningnoskyisvisiblebelowtheplantcanopy,and1meaningthattheentireareaisskyornofoliagecoverage.Afractionnumberindicatespartialfoliagecover.Whenthedivisionshavebeenanalyzed,theaveragesolarbeamtransmissioncoefficients,hemisphericaldiffuseradiationtransmissioncoefficient(theskyviewfactor),meanfoliageinclinationangles,andplantcanopyextinctioncoefficientsarecomputed.

Thekeyequationsinvolvedinthisprocessareasfollow:

THEORY

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THEORY

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TechnicalSupportIfyouhaveaquestionabouttheCI-110,firstlookintheCI-110OperationManual.ThereisalsoonlinesupportavailablefortheCI-110athttp://cid-inc.com/support.Ifyoucannotfindtheanswer,youcancontactaTechnicalSupportRepresentativelocatedinyourcountry.CIDBio-Science,Inc.iscommittedtoprovidecustomerswithhighquality,timelytechnicalsupport.Technicalsupportrepresentativesaretoansweryourtechnicalquestionsbyphoneorbye-mailatsupport@cid-inc.com.Includetheserialnumberoftheinstrumentintheemailsupportrequest.

Contactinformation:

CIDBio-Science,Inc.1554NE3rdAveCamas,WA98607USA

Phone:800-767-0119(U.S.andCanada)360-833-8835

Fax:360-833-1914

TECHNICALSUPPORT

64

http://cid-inc.com/support


Website:http://www.cid-inc.com

E-mail:[email protected]

CustomerService

CustomerServiceRepresentativesanswerquestionsaboutspecificationsandpricing,andsellalloftheCIDBio-Science,Inc.products.CustomerssometimesfindthattheyneedCIDBio-Science,Inc.toupgrade,recalibrateorrepairtheirsystem.InorderforCIDBio-Science,Inc.tooffertheseservices,thecustomermustfirstcontactusandobtainaReturnMerchandiseAuthorization(RMA)number.Pleasecontactacustomerservicerepresentativeforspecificinstructionswhenreturningaproduct.

TECHNICALSUPPORT

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http://www.cid-inc.com


FrequentlyAskedQuestionsIfthereareanyquestionsabouttheCI-110,pleasechecktheFrequentlyAskedQuestionsbelow,aswellastheCIDBio-Sciencesupportwebpageandforumathttp://cid-inc.com/support.

1. WheredoIdownloadthemostcurrentversionofCI-110software?

ThelatestversionofsoftwareandthedrivercanbedownloadedatClickthemostrecentversionofCI-110softwaretostartthedownload.Ifpromptedthatthepublisherisnotverified,clickRunorInstalltocontinuethesetup.Next,installthedriveraccordingtotheInstructionManual.

Makesuretocompletelyerasetheoldversionofsoftwareandthedriverbeforedownloadingthenewversion.Todothis,gotoAddorRemoveProgramsinyourcomputer’sControlPanel.UninstallthePlantCanopyAnalysisSystemsoftwareandtheCI-110driver(USBTVDeviceDriver).

2. WheredoIfindaCI-110driver?


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http://cid-inc.com/support

TheCI-110driveriscompatiblewith32or64bitsystems.YoucaninstallthedriverbygoingtotheAdvancedSettingstab,clickingonInstallDriverandfollowingtheInstallationWizardprompts.Alternatively,youcandownloadtheCI-110driverat:http://www.cid-inc.com/Software/CI-110/V6Driver.zip.InstructionstoinstallthedrivercanbefoundintheHardwareInstallationsectionoftheCI-110UserManual.

3. Whywon’ttheGPSlockorfindalocation?

TheGPScantakeupto15minutestolocatesatellitesandestablishlongitude,latitudeandaltitudeparameters.Thistimeshouldbeshorteraftertheinitialconnection.TheGPStypicallyneedstobeoutdoorstoconnecttosatellites.

4. WhatistheaccuracyoftheCI-110GPS?

Position:5mCEPwithoutSAVelocity:0.1m/sec,withoutSATime:+/-50nssynchronizedtoGPStime

CEPisCircularErrorProbability.CEPisdefinedastheradiusofacirclecenteredonthetruevaluethatcontains50%oftheactualGPSmeasurements.Soareceiverwith1meterCEP


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http://www.cid-inc.com/Software/CI-110/V6Driver.zip

accuracywillbewithinonemeterofthetruemeasurement50%ofthetime.Theother50%ofthetimethemeasurementwillbeinerrorbymorethanonemeter.

5. WherearethePARsensorslocated?

ThePARsensorsarelocatedalongthetopofthewand/armthatthecameraconnectsto.

6. HowdoItellwhentheCI-110isfacingnorth?

Thetickorarrow-tipontheoutsideoftheimagewillchangefromredtogreenwhentheCI-110cameraandwandarepointednorth.Northorgreenisatthe12o’clockpositionontheimage.

7. WhatisthedifferencebetweentheCI-110andtheCI-120?

TheCI-110lensprobeandtheaccompanyingsoftwarethatcalculatesLeafAreaIndexwasdesignedtomeasureforestcanopies.TheCI-120compactlensprobewasdesignedlatertomeasureinricepaddiesandwetlandconditionswheretheCI-110lensprobecouldnotgetlow


68

enoughtotaketheimage.ThecurrentCI-110hasevenlowerclearancethanpreviously,sotheCI-120isnolongeroffered.

Theself-levelingfeatureoftheCI-110isaverysignificantadvantagewhenmeasuringtreecanopies.TheCI-110lensprobehasa170°viewingangle.

8. CanIusetheCI-110tostudythecanopyofgrapes?

Unfortunately,duetotheirirregularcanopyshape,thegapfractionmethodforcalculatingtheLightAreaIndexofcanopiesofgrapesgrownonverticaltrellisescannotbeaccuratelymeasured.Sotheinstrumentcannotberecommendedforthestudyofverticallygrowinggrapes.

9. Whattypesofcanopiesisthe110usedfor?

FortypesofcanopiesthatworkwellwiththeCI-110,pleaserefertothelistofpublishedresearch(http://www.cid-inc.com/resources).TheCI-110hasbeenusedtoeffectivelymeasuretheLAIofforests,rice,pastureland,sub-Mediterraneangrasslands,winterwheat,Quercusspecies,ShpaeralceaandShepherdiaspecies,Amaranthuspowellii,


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http://www.cid-inc.com/resources

Erythroxylumcoca,Oleaeuropaea,andCypripediumflavum,amongothers.

10. Whydopastimagesappeardarkerinsoftwareversion5.3andlatersoftwareversions?

Softwareversion5.3.1includesafixtoabugthatpreventedthesoftwarefromproperlycontrollingthecameraexposure.Imagestakenwithpreviousversionsofsoftwaremayappeardarkerwhenopenedinversion5.3.1orlater.Afterproperlyadjustingtheexposure,theimageshouldappearcorrectly.

11. WhataretheimprovementswiththenewCI-110Spring2013?

Newandimprovedcameraandfilter.NewandimprovedGPS.Updatedsoftwarewithmanybugfixes.

12. HowdoIaccesstheCI-110logfileifanerroroccurs?

ToaccesstheLogFiles:

i. StarttheCI-110softwareii. PressControlandEscapeatthesametimeor

Ctrl+Alt+Delete(thislaunchestheTask


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Manager).Or,right-clickorclickandholdonthethetaskbar(thebarthathasthesystemtry/notificationareaandthestartmenubuttonatthebottomofthescreen).SelectStartTaskManagerfromthelist.

iii. FromtheTaskManager,clickontheProcessestab.

iv. RightclickonCID.CI110.exeandselectOpenFileLocation(thislaunchesthefilebrowser)

v. YoushouldseeseveralApplicationLogandErrorLogfiles.

13. HowdoIcalibratetheSolTabtablettouchscreen?

TocalibratetheSolTabtabletdaylightvisibletouchscreen:

i. GotoStartandControlPanelii. GotoHardwareandSoundiii. UnderTabletPCSettings,chooseCalibratethe

screenforpenortouchinputiv. Clickthecalibratebuttonv. Followtheinstructionstotouchthescreenand

choosetosavethecalibrationdata.

14. WhichGapFractionMethodshouldIuse?


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FormoreinformationonGapFractionMethodspleaserefertothearticlebyJuarezetal.:

AnImprovedEstimateofLeafAreaIndexBasedontheHistogramAnalysisofHemisphericalPhotographs

AgriculturalandForestMeteorology,volume149,pages920-928,2009.Juarez,R.,RiberiodaRocha,H.,SilvaeFigueira,A.,Goulden,M.,Miller,S.

15. Whyistheimagesodark?

TheCI-110camerawasmodifiedtouseabluelens,thecontrastandotherparametershavebeenadjustedforoptimumaccuracy.Indoorlightsarenotusuallystrongenoughtoshowanythingotherthanadarkorblackimage.

16. Whichsideisuponthestickandcamera?

Thebottomofthecameramounthasacableattachedtoitandthestickhasopaquewhiteplasticonthetop.BothshouldhavelabelsindicatingTOP.

17. Thehandleonthestickgetwarm,isthisnormal?


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https://cid-inc.com/publication/an-improved-estimate-of-leaf-area-index-based-on-the-histogram-analysis-of-hemispherical-photographs/

Yes,thisisnormal.ThepowertorunthePARsensorsandcamerarunthroughthehandleofthestick.Thisgeneratestheheatinthehandle.

18. Theimageseemstobecenteredincorrectly.HowdoIcentertheimage?

GototheAdvancedSettingstabandchangetheTopandLeftoffsetstothevaluesintheProductTestCheckSheetpageofthismanual.

19. HowdoIfocustheimage?

ThelensoftheCI-110canbetwistedtobringthecanopyimageintofocus.

20. Howmuchstoragedoesthetabletcomputerhave?

TheSolTabcomputerandtheAcertabletcomputerbothhave32GBofstoragecapacity.

21. HowdoesadjustingbrightnessaffectLAI?

Theeffectofadjustingthebrightnessdependsonwhetheritisdoneduringimageacquisitionorafterwards,duringimageprocessing.Ifyouhavealreadytakentheimageandarenowprocessingit


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afterwards,thefollowingrelationshipisexpected:LAIwilldecreasewithincreasingbrightness.Thisisbecauseplantelements,suchasback-litleavesorlightgreenleaves,willbewashed-outinthephotoandwillappearasskytothesoftware.Increasedbrightness=moresky=decreasedLAI.Tocounter-actthis,re-assignFoliageandSkycolorsintheSkyandLeafFilteroptionaftersettingthedesiredbrightness.

Itisrecommendedto:

Adjustthebrightnesssotheimageappearsproperlyexposed.GototheThresholdmenuandchooseamethod.Adjusttheslideruntilalltheplantelementsappeargreen.PresstheDatabutton.Gobackandadjustthebrightness/contrastuntilalltheplantelementsaregreen.Keeptweakingthesettingsuntilyouhavegroupedalltheplantelementstogetherandseparatedtheskyorbackground.

22. HowdoIanalyzeimagesonadifferentcomputer?

DownloadandinstalltheCI-110PlantCanopyAnalysissoftwareonthecomputer.Then,transferthe.ci110filestothecomputer.Createafolderinyourpicturestobeabletousethesearchfunctionin


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BrowseRecords.Double-clickingonthe.ci110filewillopenthesoftwarewiththefileloaded.

23. Whattypeofexternalbatterywillworkwiththetabletcomputer?

ThebatterylifeoftheCI-110isdirectlyrelatedtothetabletthatoperatestheinstrument.Currently,thebatterylifeforusingtheCI-110andAcerIconiaW3tabletisaround4hours.ThisiswiththeCI-110softwareopenandrunningtheentiretimeonthetablet.Batterylifecanbelengthenedbyclosingthesoftware,dimmingorturningoffthedisplayorputtingthetablettosleepbetweenmeasurements.

Ifextrabatterylifeisneeded,therearemanyuniversalbatteries(normallymarketedforlaptops)thatcouldbeused.Essentially,thesearebrickswithawirethatplugsintothetabletwheretheACadapternormallywouldgo.UsingauniversalbatteryinconjunctionwiththeCI-110andtabletcouldextendthebatterylifebyseveralhours,orallowforadditional"battery".

USBbatterydevicesgenerallydonotworkwiththetabletandatruelaptopexternalbatteryshouldbeused.


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24. HowfarfromthecanopydoestheCI-110cameralensneedtobe?

ThedistancefromtheCI-110lenstotheleafatanangleof30°fromzenithshouldbeatleastfourtimestheleafwidth.

25. WhatshouldIdoifthesunflecksalwaysread100%,eventhoughsomeofthePARsensorsarecovered?

IntheAdvancedSettingstab,gotoParSensorCalibrationandhitYestoproceed.Whiletestingindoors,wherePARis12.5,changetheSunfleckMinimumPARto10.Sunflecksvaluewillnowrespondasexpectedwhensomesensorsarecovered.Thedefaultvalueis300.


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TroubleshootingandTipsThissectionofthedocumentoutlinessuggestionsortipstoresolveissuesusingtheCI-110software.

CanopyGaps

TheCI-110employsthegapfractioncomputationmethodandassumesrandomleafdistribution.Anon-uniformlydistributedcanopywithgapswillcauseover-estimationsofthesolarbeamtransmissionandunder-estimationsofLAI.

IncircumstancesthatdonotsatisfytheassumptionusetheZenithandAzimuthselectionstoexcludelargecanopygaps,andmakemultiplemeasurementsthenaverageyourresults.Thenumberofmeasurementsneededforaveragingdependsonthecanopystructureanditsdistribution.

CanopySize

Observethecanopysize.Iftheplotistoosmall,thefish-eyelens’field-of-viewwillextendbeyondtheedgeofthefoliagebeingmeasured,andLAIwillbeunderestimated.Thereverseistruewhenmeasurementsaretakeninaplotsurroundedbyadensercanopy.


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Thesuggestedminimumplotradiusfromthefish-eyelensisapproximately3timestheplotheight.Theexceptiontothesuggestedminimumplotradiusisindenseplantcanopies,lessdistancemayberequiredbecausethefish-eyemaynotbeabletoseetotheedgeofthecanopies.

IfyoumustmeasureasmallplotadjusttheZenithandAzimuthselectionstoexcludeeverythingbeyondyourplot.

DistancefromCanopy

ThedistancefromtheCI-110lenstotheleafatanangleof30°fromzenithshouldbeatleastfourtimestheleafwidth.

SkyConditions

Theoptimalskyconditionsformeasurementsareunderevencloudcoverageduringearlymorningorlateafternoon(whentheamountofscatteredradiationislow).UndersunnyskyconditionsthelensshouldbeshadedtominimizetopreventunderestimationofLAIandoverestimationofsolarbeamradiationanddiffuseradiation.

RowCrops


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Onemeasurementtechniqueistotakefourevenlyspacedreadingsalongadiagonaltransectthatrunsbetweentworows,andtodoseveraltransectstopreventthesamefewplantsfromdominatingtheentiresetofreadings.Itisbestnottoexcessivelyweighthe“inrow”or“betweenrow”situations.

GoogleEarthdisplaysiconsinsteadofCI-110images

GoogleEarthiscommonlyusedtoreadtheKMLfilesexportedfromtheCI-110application’sBrowseRecordstab.BydefaultGoogleEarthdoesnotallowyoutoloadKMLfilesfromyourlocaldrives.Toresolvethisissuefollowtheinstructionsbelow.

1. StartGoogleEarth2. ClicktheToolsmenuatthetopofthescreen.3. ClickOptions.4. ClicktheGeneraltab.5. CheckAllowplacemarkballoonstoaccesslocal

filesandpersonaldata.6. ClickOK.7. ReloadyourKMLfile,orexitGoogleEarthandrestart

itfromtheCI-110application.


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CIDBio-Science,Inc.HardwareWarrantyImportant:PleaseRead!

Seller’sWarrantyandLiability:Sellerwarrantsnewequipmentofitsownmanufacturingagainstdefectiveworkmanshipandmaterialsforaperiodofoneyear,ofasingleshiftoperation,fromdateofreceiptofequipment-theresultsofordinarywearandtear,neglect,misuse,accidentandexcessivedeteriorationduetocorrosionfromanycauseisnottobeconsideredadefect.AnydefectmustbecalledtotheattentionofCIDBio-Science,Inc.,Camas,Washington,USA,inwriting,within90daysafterreceiptoftheunit.

Seller’sliabilityfordefectivepartsislimitedtotherepairorreplacementofanypartoftheinstrumentwithoutcharge,ifCIDBio-Science,Inc.’sexaminationdisclosesthatparttohavebeendefectiveinmaterialorworkmanship,andinnoeventshallexceedthefurnishingofreplacementpartsF.O.B.thefactorywhereoriginallymanufactured.NoequipmentmayberepairedoralteredbyanyonenotauthorizedbyCIDBio-Science,Inc.

HARDWAREWARRANTY

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Materialandequipmentcoveredhereby,whichisnotmanufacturedbySeller,istobecoveredonlybythewarrantyofitsmanufacturer.SellershallnotbeliabletotheBuyerforloss,damage,orinjurytopersons(includingdeath),ortopropertyorthings,whatsoever,including,butwithoutlimitation,productsprocessedbytheuseoftheequipment;orfordamagesofanykindornature(including,butwithoutlimitation,lossofanticipatedprofits),occasionedbyorarisingoutofinstallation,operation,use,misuse,nonuse,repair,orreplacementofsaidmaterialandequipment,oroutoftheuseofanymethodorprocessforwhichthesamemaybeemployed.Thepurchaseristopack,ship,ordelivertheinstrumenttoCIDBio-Science,Inc.,inCamas,Washington,USA,within30daysafterCIDBio-Science,Inc.hasreceivedwrittennoticeofthedefectatthecustomer’sexpense.NootherarrangementsmaybemadeunlessotherwiseapprovedinwritingbyCIDBio-Science,Inc.

TheuseofthisequipmentconstitutesBuyer’sacceptanceofthetermssetforthinthiswarranty.Therearenounderstandings,representations,orwarrantiesofanykind,express,implied,statutory,orotherwise(including,butwithoutlimitation,theimpliedwarrantiesofmerchantabilityandfitnessforaparticularpurpose),notexpresslysetforthherein.

HARDWAREWARRANTY

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HARDWAREWARRANTY

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CI-110ProductTestCheckSheetTestDate:SerialNumber:

ParSensorCalibration

PARZeroCalibration:

PARSpanCalibration:

SunflecksZeroCalibration:

SunflecksSpanCalibration:

Compass,Lens,andCameraSettings

TopOffset:

LeftOffset:

Comments:

PRODUCTTESTCHECKSHEET

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