MoreonHowtheInstrumentWorks

1.LightTransduction:theCMOSCamera
Computersstorealldataasbinarynumbers(zerosandones).HowdoestheCMOScamerainacellulartelephoneordigital
cameraconvertlightintonumbers?Thereareseveralsteps.
a)Lightimpingesonthecamera'sdetectorsurface.Each
absorbedphotonkicksanelectronawayfromasiliconatom
inthedetector,sothatanelectron/holepairisformed(ahole
istheabsenceofanelectronjustasaholeinthegroundis
theabsenceofrockorsoil).

b)Differentregionsonthedetectoraresensitivetored,
green,andbluelight,sotheamountoflightseenbyeach
regionhelpsestablishthecolorofeachportionoftheimage.
Inthedrawing,asinglepixelcorrespondstotheareacovered
byonesquareofeachcolor(red,green,blue,unfiltered).
Somecamerashavecolorsensingstackedvertically,
avoidingthedeadzoneforonecolorwhereanotherisbeing
sensed.Typicalpixelsrangefrom1.5mto25minwidth.

c)Themorelightthereis,thegreaterthenumberof
electron/holepairs.

d)Thereleasedelectronsandholesarestoredinseparate
partsofeachobservationregionorpixel.Theresultisthat
thecharge,Q,ineachpixelisproportionaltolightintensity.
Q=idt=CV

Anydevicethatstoreschargeiscalledacapacitor(with
capacitance,C,inFarads).Thevoltage,V,(electrical
potentialenergy)onacapacitorisproportionaltothestored
charge.Formoreuptothispoint,seeSilconImaging's
website.

Q=idt=CV

e)Ananalogtodigitalconverter(ADC)generatesanumber
proportionaltotheamountofcharge."HowdoestheADC
work?"Amoduleonthistopic,eventuallytobesubmittedto
ASDLib,isunderdevelopment(November,2009).Inthe
meantime,here'salinktofollowifyou'recurious.
f)Thedigitizedvaluesforeachpixelarereadintothe
Red(1)
computer'smemory.Atfirst,thevaluesarestoredasthree
Green(1)
arrays,oneeachforthered,green,andbluevalues.This
"stack"ofcolorsisthencopiedintoasinglearraywiththe
Blue(1)
threevaluesstuckadjacenttoeachotherRGB(1),RGB(2),...

,RGB(lastpixel).Thisarrayofpixelsisabitmapor.BMP
Red+Green+Blue
file.Thesefilesrequire3bytesofstorageforeachpixel,so
Total(1)
bigimagestakealotofmemory.
g)Tosavespace(andspeeduptransmissionofdataoverthe
internet),thefileisconvertedtoacompressedformat,
typicallyaJPGfile.Someinformationislostduring
compression,makingthisformatillsuitedtohighprecision
work.Somecamerasallowaccesstopixelbypixeldatain
additiontotheBMPformat,exampleformatsincludeTIFF
andRAW.

Red(2)
Red(3)
Green(2)
Green(3)
Blue(2)
Blue(3)

Red+Green+Blue
Red+Green+Blue
Total(2)
Total(3)

2.Software:ConvertingJPGFilestoIntensityPlots
TheJPGformatisreasonablywelldescribedinWikipedia.ThesoftwareloadsANYJPGfileithasnoknowledgewhatis
intheimage.
Aftertheuseridentifiestherangeofpixelsthatistobeconsideredaspectrum,thesoftwarereadsouttheRed,Green,and
Bluebytes.Ifonlyasinglerowofpixelsisselected,onesimplyreadsoutR,G,andB,thenaddsthe3valuestogetasum,
construedastotalintensity(sincethevaluesofthebytesareintegers0to255,thehighesttotalintensitypossibleis3*255=
765).Ifmultiplerowsareselected,allpixelsatthesameoffsetfromtheblueendofthespectrumareaddedtogether.Thus,
ifonehasaspectrumheightof9pixels,eachcolorrunsfrom0to255ineachpixel,so0to9*255=0to2295,andtotal
intensitycanbeashighas3*2295=6895.
Thesoftwareprovidesoptionstoplottheintensityfromtheindividualcolorsensorsorforallsummedtogether.The
abscissamaybeeitherpixelnumber(nowavelengthattributedtoaparticularoffsetfromtheblueendofthespectrum)or
wavelength(calibrationasgivenbyselectingreferencepointsintheimageandpresuminglineardispersionbetweenthetwo
referencepoints).

3.Software:ConvertingIntensitytoTransmittanceandAbsorbance
ThesoftwarehasNOcapabilityforstraylightorbackgroundsubtraction!Itsimplycomputes,ateachwavelength,T=I/I0,
andA=log10T.Ifthedispersion(rangeofwavelengthsperpixel)isdifferentforsampleandreferenceimages,the
softwareperformslinearinterpolationtofindanapproximateintensitybetweenmeasurements.Inallcases"intensity"(theI
orI0)isjustthenumbercomputedfortotalintensityinstep2above.

4.Software:WhyMovingDatatoaSpreadsheetMayBeUseful
Whatifyouwanttosubtractbackground?Whatifyoudon'twanttosayItotal=Ired+Igreen+Iblue?Whatifyouhavesome
othermanipulationyouwanttotry?Thesoftwareoutputsa.CSV(commaseparatedvariable)filethatcanbereadbymost
spreadsheetprograms.Toavoidmakingmassive,uninterpretablefiles,itputsoutonlythedataselectedfromwithintheJPG
(alineofpixelsorpixelsaveragedoversomeheight),listingbothpixelnumberandimputedwavelength.

EnLiSTChemistryWorkshop,UniversityofIllinois,2009