User guide

iScan System User Guide 43
Starting a Scan
Starting a Scan
AfterselectingtheBeadChipstoscanandconfirmingtheirsettings,clickScanontheICS
Setupscreen.Befo rescanning,theiScanControlSoftware:
` Checksavailablediskspace
TheiScanControlSoftwarewarnsyouifthereislessthan75GBoffreediskspacefor
theimageandintensityfilesandwillnotperformthescanifthereislessthan12
GB
offreediskspaceonthedrive.
` Loadsthe*.dmapfilesforeachBeadChipinthecarrier
TheiScanControlSoftwarewarnsyouifany*.dmapfilesaremissing.
` CalibratestheiScanReader
CalibrationincludesanautofocusprocessatthreecornersoftheBeadChiptoensure
thattheimagesareclear,andanautocenterprocesstoensurethattheBeadChipis
properlypositionedrelative totheoptics.Thecalibrationprocessmaytakeseveral
minutestocomplete.
Iftherearedefectiveordirtysectionsatanyofthethreealignmentcorners,the
softwareattemptstousealternatesectionsuntilsatisfactorycalibrationisachieved.If
noalternatesectionsareavailable,calibrationfailsandanerrormessageisdisplayed.
` TiltsandalignstheBeadChipsinthecarrier
TheiScanReaderAut ofocusfeaturerecordstheZ‐position(height)ofthreecornersof
theBeadChiptodetermineitscurrenttiltandadjuststheBeadChipuntilitisflat.
Then,theiScanReaderi dentifiestheX‐Yposition(laterallocation)ofthefiducials
(focuspoints)ontheBeadChipedgesandadjuststhestagetoaligntheBeadChips
undertheoptics.
OncetheTiltandAlignfunctionsarecomplete,thescanprocessbegins.
Aseachsectionisscanned,theimageandintensitydataaresavedontheiScanSystem
computerorinanetworklocationintheoutputpathspecifiedontheICSSetupscreen.
Thescanningprocesscontinuesuntilallsections
arescannedoruntilyoupauseorstop
thescan,unlessaseriouserrorhaltsthescanprocess.