User guide

iScan System User Guide 71
Auto-Alignment Issues
Auto-Alignment Issues
Unabletosuccessfullycompleteauto‐alignment
Abletoauto‐align,butunabletoscansectionssuccessfully
Cause Resolution
BeadChipsnotproperly
seatediniScanReader
tray.
EjectthetrayandremovetheBeadChips.Reloadthe
BeadChipsandensureproperseatingflatonthecarrier
tray.EnsurethattheBeadChipissecurelyandproperly
snappedontothetray.Itsnotchesshouldmatchthe
postsbuiltintothecarriertray,and
thelongedgeofthe
carrierclosesttotheiScanReadershouldpushdown 
thesensorbutton.Ensurethatthebackofthearraysare
freeofcoating,andcleanthemiftheyaredirty.
Carriertraynotproperly
seatediniScanReader
tray.
Ejectthetray.Removethecarrierfrom
thetray.Replace
thecarrierintheiSca nReadertrayandensureproper
seating.
Sectionsmaybebrokenor
dirty.
EjecttheBeadChipsandvisuallyinspectsectionsto
ensurethatnonearebrokenordirty.Followlab
protocolsforcleaningsections,andreportbroken
sectionstotheresponsiblescientist.Tryscanningthe

BeadChipagain.
Lasersmaynolongerbe
withinfactory
specifications.
TheiScanReadermayneedtoberecalibrated.Please
contactIlluminaTechnicalSupporttorebalancelasers.
Optical‐mechanicalfailure. CallIlluminaTechnicalSupporttoinvestigatethis
further.
Cannotfindfiducials. Cleanfiducialswithanethanolwipeandrescan.
SometimestheXC4protectivecoatingon 
the
BeadChipsinhibitsthelasersfromfindingfiducials.
Cameratimesout. Performapowercycle.
Systementersaninfinite
auto‐tiltloop.
Performapowercycle.
Instrumentcannotfocus. Inabilitytofocusmayresultfromusingadifferent
adaptertray.Replaceoriginaladaptertray.
Cause Resolution
ProblemsduringBeadChip
preparationmayresultin
somesectionsappearing
too
dimtoperform
registrationandbead
intensityextraction.
Contacttheresponsiblescientisttodiscussthehistoryof
theassaypreparationfortheBeadChipsandthe
scientist’sexpectation.Evaluatetheimageoutputof
nearbyimagesusingimages storedintheworkspacefor
thisBeadChip.Ifthisdoesnotresolvetheissue,contact

IlluminaTechnicalSupportforwaystocompensate.
BeadChipshavebeen
exposedtoadverse
environmentalconditions.
Evaluatetheeffectoftheenvironmentonsignalquality
pertainingtotheBeadChipsections.