PicoQuant MultiHarp 150 - External Markers

PicoQuantGmbH MultiHarpSoftwareV.3.1.0.0
AmeasurementcanbestoppedatanytimebyclickingtheStopbutton.Thedatarecordeduptothispointwill
bestoredinthefile.Whenthemeasurementhascompleted,theStopbuttonwillbegrayedout(disabled).Use
theExitbuttontoreturntothenormalinteractivemode.Again,thiswilltakesometimeforhardwarereconfigura-
tion.
Asoutlinedabove,TTTRdatacollectionathighratesisademandingreal-timestreamingprocess.Thehard-
wareandsoftwaremustensurenottoloseanydata.InordertoimplementthisefficientlytheMultiHarpsoftware
employsmultiplethreads(concurrentCPUprocesses).AfirstthreadcontinuouslyreadstheMultiHarp‘shard-
wareFIFOandputstheretrieveddatainasoftwarequeue.Asecondthreadconcurrentlyreadsthissoftware
queueandwritesthedatatodisk.Ifreal-timecorrelationisbeingperformedthenthisisdoneinfurtherseparate
threads.Userinterfaceandinteractionarehandledinyetanotherthread.Multi-coreCPUsareparticularlyuseful
hereastheycanrunthethreadsinparallelratherthanswitchingbetweenthem.Therearetwotypicalerrorsce-
nariosthatyoumayencounterinthisprocess.Thefirstisasituationwherethefirstthreaddoesnotemptythe
hardwareFIFOquicklyenoughandtheFIFOrunsfull.ThesoftwarethenreportstheerrorFIFO_OVERRUN.In
ordertoavoidthisyoumayhavetoreducetheinputdatarate.Anothererrorsituationmayresultwhenthesec-
ondthreadcannotwritetodiskquicklyenoughandthesoftwarequeuerunsfull.Thesoftwarethenreportsthe
errorSTORAGE_QUEUE_OVERRUN.Inordertoavoidthisyoumaywanttocheckthewritespeedofyour
harddiskandseehowitcanbeimproved.
5.3.5. External Markers
OftenitisdesirabletosynchronizeTCSPCmeasurementswithotherinformationorprocessesofcomplexmea-
surementtasks.Inordertoperforme.g.,FluorescenceLifetimeImaging,thespatialoriginofthephotonsmust
berecordedaswellastheirtiming.Forthispurposeoneneedsamechanismtoassignexternalsynchronization
informationtotheTCSPCdata.InthespecialcaseofFluorescenceLifetimeImaging,conventionalsystemsuse
on–boardmemoryandswitchtonewblocksofmemoryuponarrivalofe.g.,apixelclockpulse.Accommodating
thelargeamountofdatageneratedbythe3–dimensionalmatrixofpixelco–ordinatesandlifetimehistogram
binsisaseriouschallenge.Evenwithmodernmemorychips,thisapproachislimitedinimagesizeand/or
number.Inaddition,itisexpensive,andimplieslossofinformationabouttheindividualphotonarrivaltimes.To
solvetheprobleminamuchmoreelegantmanner,theTTTRdatastreamgeneratedbytheMultiHarpcancon-
tainmarkersforsynchronizationinformationderivedfromanimagingdevice,e.g.,ascancontroller.Forthis
purposethecontrolportoftheMultiHarpprovidesfourTTLinputsforsynchronizationsignalsM1..M4(seesec-
tion8.3.2fortheconnectorspecification).
Thefigurebelowillustrateshowtheexternalmarkersignalsarerecordedinthedatastream.
Bulletsdenoteaphoton,bluepulsesdenoteamarkersignal.Theexternalmarkersaretreatedalmostasifthey
wereregularphotoneventrecords.Aspecialchannelcodeallowstodistinguishtruephotonrecordsfrom
markerrecords.SoftwarereadingtheTTTRfilecantherebyfilteroutthemarkerse.g.,forlineandframeclock
inimagingapplications.Thismakespossibletoreconstructthe2DimagefromthestreamofTTTRrecords,
sincetherelevantXYpositionofascannercanbedeterminedduringthedataanalysis.Thedatageneratedthis
wayisnearlyfreeofredundancyandcanthereforebetransferredinreal–time.Theimagesizeisunlimitedboth
inXYandincountdepth.Sincetherearefoursuchsynchronizationsignals,allimagingapplicationscanbeim-
plementedandevenotherexperimentcontrolsignalscanberecorded.Thismarkerschemeisaveryspecial
featureofPicoQuant'sTCSPCelectronics.ItmaybeworthnotingthatinventingthistechnologyenabledPico-
QuanttodevelopthecuttingedgeMicroTime200FluorescenceLifetimeMicroscope.
TheTTLcompatibleinputsacceptthesynchronizationsignalsthatwillberecordedasmarkers.Theactive
edgesofthesesignalscanbechoseninthegeneralsettingsdialog(availablethroughtheToolbar).Bothhigh
andlowstatemustbeatleast50nslong.Theperiodmaytherefore(inprinciple)beasshortas100nsbutdata
busthroughputconstraintswillapply.EachmarkercreatesanadditionalTTTRrecord,sothatonemustensure
nottoswampthedatastreamwithtoomanymarkerrecords.Incaseofdatabuscongestionmarkerstake
precedenceoverphotonrecords,sothatexcessivemarkertrafficcansuppressphotonrecords.Infastimaging
applicationsitisthereforerecommendednottouseapixelclockbutalineclockonly.Sinceeachphotonhasa
timetag,itisusuallynotnecessarytouseanadditionalpixelclock.Instead,virtualpixelscanbedefinedby
Page39