Getting started with Spike Recorder on PC/Mac/Linux
YoucanconnectyourSpikerBoxtoyourcomputerusingeitherthebluelaptopcable,orthegreensmartphone
cable.
How do I connect SpikerBox to computer using USB cable?
Youcanconnectyour:
● NeuronSpikerBoxPro
● MuscleSpikerBoxPro
● PlantSpikerBox
● HeartandBrainSpikerBox
toyourlaptoporcomputerwiththeprovidedmicroUSBCable:
WhenyouconnectUSBcabletoyourcomputerandturnthepowerswitchONonSpikerBoxanewUSBbutton
willappearonthetopoftheSpikeRecorder’swindow.WhenyouclickonthebuttonSpikeRecorderwill
connecttoSpikerBoxandstartacquiringdatafromit.Byclickingonthesamebuttonagainyouwilldisconnect
fromSpikerBoxandreturntorecordingofdefaultaudioinputsonyourcomputer.
How do I connect a SpikerBox to my computer using green smartphone cable?
Itdependsonyourlaptop.MostPClaptopshaveaseparateheadphoneandlineinjack.Youwanttopluginto
thelinein(microphone)jack.
IfyouhaveaMacLaptopwithtwoaudioports(likesomeMacBookPro'sandolderiBooksandMacBooks),
youwanttoplugthegreensmartphonecableintothelineinport(hasaweirdsymbol).
IfyouhaveaMacBook,MacBookPro,oranycomputerwithonly1headphoneport,thenpluginthegreen
smartphonecableintotheheadphoneport.Theselaptopsonlyhaveoneaudiojackanditisacombinedmono
micinputandheadphonejack.
WhileallSpikerBoxescanbeconnectedusingthismethod,thefollowingSpikerBoxesonlysupporttheGreen
SmartphoneCable:
● MuscleSpikerBox
● NeuronSpikerBox
Andareconnectedlikeinthephotobelow.Notethatthe“Smartphone”endisgoingintothelaptop.Thisis
importantasthiscableisnotreversible.
Configure Inputs
Tosetthingsup,youcanuseconfigscreen(gearinupperleftcorner)toselectthechannelsdisplayedaswell
aschangethecolorofthewaveformoradd/removechannelfromrealtimeview.
Allthesignalinputsthroughwhichyoucanacquireandrecordthesignalwillbelistedoutintheconfigscreen.
Theitemsdisplayedisbasedonyourcomputer’saudioconfigurationandtypeofthedeviceconnectedtoyour
computer.
Byusingcolordropdownchooser,youcanchangethecolorofthechannel’swaveformorturnoffthechannel
byselectingblackcolor.
Onthesamescreenyoucanmutesoundonyourcomputer’sspeakerduringrecordingbyclickingthe
selectionboxonthetopoftheconfigscreen.
Also,inconfigurationyoucanenablerealtimedigitalfilteringofthesignalthatyouarerecording.Inorderto
enablebandpassfilteryoucanchangecutofffrequenciesusingsliderorbyenteringexactfrequencyforlow
andhighcutofffrequencyinboxesaboveslider.Afteryouchangecutofffrequenciesnewfilter’ssettingswillbe
automaticallyappliedtosignalandfrequenciesoutsideselectedband(markedgreenonslider)willbe
attenuated.
BesidebandpassfilteryoucanenableNotchfilterbytickingthecheckboxatthebottomoffiltersection.Notch
filtersaremadetostronglyattenuatejustonefrequency.Thisisveryusefulforeliminatingmainsnoise
commonlypresentinelectrophysiologicalsignals(50Hzor60Hzdependingoncountry).
Arduinobaseddevices
● MuscleSpikerShield,
● MuscleSpikerShieldPro,
● Heart&BrainSpikerShield
haveadditionaldropdownchooserthatenablesyoutosetthenumberofchannelsthedevicewillrecord.When
youconnecttothosedevices,initially,youwillacquireonlyonechannelatthesamplingrateof10kilosamples
persecond(10000samplespersecond).
Ifyouchangethenumberofchannelsusingthisdropdownlist,SpikeRecorderwillinstantlystartrecording
multiplechannelsfromdeviceanditwillaccommodatethesamplingrateofeachchannelsothatit
cumulativelydoesnotbreachthesamplinglimitof10kilosamplespersecond.Therefore,ifyouselecttouse
justonechannel,thesamplingrateofthatchannelwillbe10kilosamplespersecond.But,ifyouselecttwo
channels,thesamplingrateofbothchannelswillbesetto5kilosamplesperseconds(threechannelswill
havethesamplingrateof3.3ksamples/s,4channels2.5ksamples/sandsoon).
Real‐time view
Bydefault,SpikeRecorderwillbeintherealtimeviewuponstartupandwilldisplaythewaveformofthesignal
recordedthroughyourSpikerBoxorSpikerShield.
Byscrollingupanddown,youcanchangethetimescaleofyoursignalpresentedattherighthandbottom
sideofthewindow.WeaddedgreatmemorydepthtoSpikeRecordersothatyoucanobserveanyaspectof
thesignalyouwantfromeventsasshortas0.1mstolongtrendsofuptodozensofseconds.
Sometimes,especiallywhenrecordingamultichannelsignal,itwillbeusefultochangetheverticalpositionof
thesignalaxis.Forthispurpose,youcanusethehandleonthelefthandsideoftheaxis.Withasingleclick
onthehandleyoucangrabandmoveyouraxisvertically.
Youwillfindzoombuttonsnexttotheaxishandle.With“+”and“”buttonsyoucanchangetheverticalscaleof
thesignaland,bydoingthis,zoominthedetailsofthewaveform.
Aswehavementionedearlier,SpikeRecorderhasgreatmemorydepth.Therefore,ifyouthinkyouhave
missedaninterestingevent,youcanpressthe“Pause”buttonatanytimeatthebottomofthescreenand
scrollthesignalwaveformbackintime.Afteryouhavefoundtheeventofinterest,youcanplaybacksignal
againbyclickingontheplaybutton.
Toreturnbacktorealtimesignalacquiringusethe“Forward”buttonnexttothe“Play”/”Pause”button.
Recording
Whenyouhavesetupyourexperimentandyouarereadytorecord,simplyclickonthe“Record”button(a
roundbuttonwithareddotinthecenter)andSpikeRecorderwillautomaticallystartsavingsignalstoanaudio
file.
Duringtherecording,youcanmarkeventsinyourexperimentbypressingkeysfrom0to9onyourkeyboard.
Theeventmarkersandtheirprecisetimingswillbeautomaticallysavedtoaseparatetextfileinthesame
directorywhereyoursignalrecordingshadbeensaved.SpikeRecorderwillnameeventsfilewiththesame
nameasthesignalrecordingfile,exceptforthefactthattheeventsfilewillhaveanadditional“events”suffix.
Byusingthatname,codingSpikeRecorderwillbeabletoautomaticallyloadandpresenteventmarkersonthe
waveformthenexttimeyouplaybackyourexperiment’srecording.
Whenyouclickforthesecondtimeonthe“Recording”button,SpikeRecorderwillstoptherecordingsignal
andpresentyouwithapopupwiththefullpathoftherecordedfileonyourcomputer.
Thresholding
Ifyouwanttoaverageneuronspikesortakeasnapshotofasinglespike,youcanusethresholdview.By
clickingonthe“Threshold”button,SpikeRecorderwillenterthethresholdmodethatwillcatchthesnapshotof
thesignaleverytimethewaveformcrossesthethresholdlevel.
Therewillbeanadditionalslideronthetopofthescreeninthethresholdmode.Withthisslideryoucanadjust
thenumberofconsecutivespikesthatwillbeusedforthecalculationoftheaveragespike.Forexample,ifyou
selecttoaverage25consecutivespikes,SpikeRecorderwillalwaysusethe25mostrecentlycapturedspikes
forthecalculationoftheaveragespike.Inextremecases,whenyousetslidertothevalueofone,Spike
Recorderwillpresentonlyarawsignalofthemostrecentspike.
Byusingthehandleontherighthandsideofthescreen,youcanadjustathresholdlevelthatsuitsyourneeds
inanexperiment.
Spike Analysis
Onceyouhaverecordedandsavedanexperiment,youcanopenitforanalysis.Toopentheexperiment
recording,clickonthe“Browse”buttonontherighthandtopsideofthewindow.Afterthefilebrowserhas
appeared,youcanlocatetheaudiofilewiththerecordedsignalandopenit(audiofileswillhave.wavfiletype
extension).SpikeRecorderwillautomaticallyloadtheotherfilescreatedduringtherecordingortheanalysisof
thesignal(timestampsofeventsandsortedspiketrains).
Whenyouopenasavedexperiment,SpikeRecorderwillshowoneadditionalbuttonthatyoucanusetoenter
SpikeAnalysisview.
TheSpikeAnalysisviewwillinitiallydetectallthepotentialneuronspikesinthesignalandmarkthemwitha
whitedot.Detectionalgorithmisverysensitiveanditwilltypicallydetectalotofspikecandidatesthatcan
representaspikeoftheneuronweareinterestedinorthespikesofadistantneuronorevennoiseglitches.
Therefore,inordertofilterthespikeset,youwillneedtoadjustavalidpeakamplitudeintervalusingtwo
handlesontherighthandsideofthewindow.
Duringthefiltering,youcanusethescrollbaratthebottomtocheckifthefilteringintervaliscompliantwiththe
restofthesignal.
Formultichannelfilesyoucanuselistontherighthandsideofthewindowtoswapbetweenthechannels.
Also,youcanuse“+”and“”signinthesamelisttoaddnewspiketrainsandremoveexistingones.
Whenyouaresatisfiedwiththefilteringresults,youcanclickonthesavebuttonatthebottomrightcornerof
thescreentosaveallcreatedspiketrains.
Inordertoopenstatisticalanalysisgraphsforcreatedspiketrainsclickonthearrowinbottomleftcornerofthe
window.
Statistical analysis graphs
OnceyoucreatespiketrainsforyourrecordingSpikeRecorderwillautomaticallycalculatefouranalysisof
yourspiketrains:
● Averagewaveformgraph
● Autocorrelogram
● Crosscorrelogram
● InterSpikeIntervalgraph
YoucanaccessgraphsinSpikeAnalysiswindowbyclickingonthearrowbuttoninthebottomrightcornerof
thescreen.
Eachanalysiswillbepresentedinseparatetab.Ifyoucreatedmultiplespiketrainsyouwillfindmultiplegraphs
ineachanalysis.Everygraphcorrespondstoonespiketrainanditscolormatchestocolorofthespiketrain.
Average waveform
Averagewaveformgraphdisplayswaveformofaveragespikecalculatedbyaveragingallspikesinspiketrain
centeredaroundpositivepeak.Horizontallinearaxisrepresentstimeinmillisecondscenteredaroundpositive
peakandverticalaxisdisplaysamplitudeofaveragespikewaveforminmillivolts(mV)units.Besideaverage
waveform(brightlineinthemiddleofeverygraph)graphalsodisplaysstandarddeviationofwaveformasa
coloredareaaroundaveragewaveform.
Inter Spike Interval graph
Thisgraphisderivedfromsinglespiketrain.Horizontalaxisrepresenttimedifferencebetweentwoadjacent
spikesinsinglespiketrain.Forthisgraphweusedlogarithmictimescaletobeabletoshowsmallinterspike
intervalsandgreaterinterspikeintervalsonthesamegraph.So,forexample,2onhorizontalaxisrepresents
secondswhichisequalto0.01secondsor10ms.01
2
ForYaxisapplicationcalculatesinterspikeintervalsforalladjacentspikesandsorttheminbins.Namely,
heightofonebinrepresentsnumberofoccasionsweencounteredgiveninterspikeintervalinsignal.
Autocorrelogram
AutocorrelogramgraphisverysimilartoISIgraphandisalsocalculatedonsinglespiketrain.Thehorizontal
linearaxisrepresenttimedifferencebetweenanytwodifferentspikes(notethatISIiscalculatedonlyfor
consecutivespikes).Unitonthetimescaleissecond.Verticalaxisrepresentsabsolutenumberofspikepairs
wemeasuredinspiketrain.Thereforeheightofonehistogram’sbinrepresentsnumberofoccasionswe
encounteredgiventimedifferencebetweentwospikesinsignal.
Cross‐correlogram
Crosscorrelationisusedtodiscoverhiddenrelationbetweentwoneurons.Thereforeitiscalculatedusing
informationfromtwospiketrains.Whenyouselectcrosscorrelationtabfirstthingyoushoulddoistoselect
spiketraininthelistattherighthandsideofthescreen.AfteryouselectspiketrainSpikeRecorderwill
calculatecrosscorrelationbetweenselectedspiketrainandallotherspiketrains.
Similarlytopreviousgraphshorizontalaxisrepresentstimedifferencebetweentwospikesgiveninseconds.
Onverticalaxisheightofonehistogram’sbinrepresentsnumberofoccasionsweencounteredgiventime
differencebetweentwospikesfromdifferentspikestrains.
Notethatifcrosscorrelationiscalculatedbetweentwosamespiketrainsresultinggraphisequalto
autocorrelationgraph.
Signal measurement
Duringtheplaybackoftherecordersignal,youcanpauseitatanytimeandinspectaninterestingpartofthe
signalinmoredetails.Youcanholdtherightclickbutton(presstwofingersontrackpadonMacOSX)anddrag
themousecursortoselecttheintervalofthesignal.SpikeRecorderwillshowyouthetimelengthofthe
intervalinmillisecondsandcalculateRMS(Rootmeansquare)oftheselectedportionofthesignal.
IfyouhaveaddedspiketrainstoyourrecordingSpikeRecorderwilldisplaynumberofspikesandfrequencyof
spikesinselectedintervalforalladdedspiketrains.
Updating firmware on SpikerBox Pro
Note:UpdateoffirmwarefortheSpikerBoxProworksonlyontheWindowsoperatingsystems
InordertoupdatefunctionalityofyourSpikerBoxProyoucanchoosetoupdatefirmwareondevicethrough
Configscreen.
EachtimeyoustartSpikeRecordertheapplicationwilldownloadinformationaboutavailableupdatesfor
SpikerBoxProfromBackyardBrainswebsite.Ifyourdevicehasavailablenewupdatesforfirmwareyouwillbe
presentedwithadditionaldropdownchooserinConfigmenu.Usingthedropdownyoucanchoosenewversion
offirmwarethatyouwanttouploadtoSpikerBoxPro.
InordertoupdatefirmwareyoumustfirstturnOFFpowerswitchonSpikerBoxProandthenclickonbuttonon
righthandsideoffirmwaredropdownchooser(seeimagebelow).
WhenupdateoffirmwarestartsSpikeRecorderwilldisplayascreenthatshowsprogressoffirmwareupdate.
PleasedonotunplugtheSpikerBoxProfromUSBduringfirmwareupdate.WhenSpikeRecorderuploadnew
firmwaretodeviceSpikerBoxProwilldisconnectfromSpikeRecorderandsoftwarewilldisplayscreenwith
message”FirmwareupdateSuccessfully”.
AftersuccessfulupdateoffirmwareyoucanimmediatelyconnectagaintoSpikerBoxProandcontinueusing
devicewithupdatedfunctionalities.
Atanytimeyoucanchooseoldfirmwarefromdropdownchooseranddowngradetopreviousfunctionalityof
SpikerBoxPro.
IfyouloseinternetconnectionoraccidentallyunplugUSBcableduringupdateoffirmwareSpikeRecorderwill
displayerrormessageonthescreen.Ifyouseeerrormessageyoucantrytouploadfirmwareagainfollowing
procedurebelow:
● unplugSpikerBoxfromcomputer,
● turnOFFSpikerBox
● makesurethatyouhaveinternetconnectiononcomputer
● restartSpikeRecorder
● pluginSpikerBoxProagaintoUSB
● connecttoSpikerBoxfromSpikeRecorder
● choosefirmwareinConfigscreen
● startfirmwareuploadagain
Updating firmware on Arduino based products
Products:
● MuscleSpikerShield,
● MuscleSpikerShieldPro,
● Heart&BrainSpikerShield,
● PlantSpikerBox
areallbasedonArduinoplatformandyoucanupdatefirmwareforthedeviceusingArduinoIDEsoftware.
Youcanfindlatestcodeforeachdeviceonit’sproductpageonBackyardBrainswebsite.
YoucanfindadetailedexplanationonhowtoinstalltheArduinoIDEsoftwareanduploadsketchtothe
Arduinoboardonthearduino.ccwebsite.
Note:ItisimportanttounderstandthatSpikeRecorderandArduinoSoftwareareusingthesameserialport
andUSBcabletocommunicatewithArduinoboard.Becauseofthis,youcannotconnecttoArduinoboard
fromSpikeRecorderandArduinoIDEsoftwareatthesametime.Therefore,thesafestthingtodoisto
simplycloseSpikeRecorderwhenyouareupdatingcodeonthedeviceandtocloseArduinoIDEsoftware
whenyoustartusingSpikeRecorder.