From fc135147d825ca2bdf95cd8ec5d11b3604d61b19 Mon Sep 17 00:00:00 2001 From: efish Date: Wed, 10 Jul 2019 12:09:46 +0200 Subject: [PATCH] [receptive fields] add configurations --- .gitignore | 10 +- rfs/macrorfs.cfg | 35 ++ rfs/macros.cfg | 51 +++ rfs/macrosam.cfg | 38 +++ rfs/macrosdc.cfg | 69 ++++ rfs/mirob2.t.zip | Bin 0 -> 3889 bytes rfs/relacs.cfg | 236 +++++++++++++ rfs/relacsplugins.cfg | 752 ++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 1186 insertions(+), 5 deletions(-) create mode 100644 rfs/macrorfs.cfg create mode 100644 rfs/macros.cfg create mode 100644 rfs/macrosam.cfg create mode 100644 rfs/macrosdc.cfg create mode 100644 rfs/mirob2.t.zip create mode 100644 rfs/relacs.cfg create mode 100644 rfs/relacsplugins.cfg diff --git a/.gitignore b/.gitignore index fa6d2d8..2e36968 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ 20* -*.cfg~ -*.log -relacsdebug* -bugs -coredumps \ No newline at end of file +*/*.cfg~ +*/*.log +*/relacsdebug* +*/bugs +*/coredumps \ No newline at end of file diff --git a/rfs/macrorfs.cfg b/rfs/macrorfs.cfg new file mode 100644 index 0000000..2318234 --- /dev/null +++ b/rfs/macrorfs.cfg @@ -0,0 +1,35 @@ +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$Calibrate Robot +CalibrateRobot: + +$Receptive Field low +ReceptiveField: amplitude=10mV, repeats=4 + +$Receptive Field mid +ReceptiveField: amplitude=20mV, repeats=4 + +$Receptive Field high +ReceptiveField: amplitude=40mV, repeats=4 + +$Robot to fish position +RobotToFishPosition: + +$FICurve AM +FICurve: am=true; + +$Noise AM: contrast=10% +Pause: duration=200ms +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=10%; repeats=5 +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=5%; repeats=5 +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=20% + +$Back +switch macros.cfg + + +#$SAMs AM +#SAM: deltaf=(100..300..10,alternateout,r=3)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=2; +#SAM: deltaf=(20..90..10,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=4; +#SAM: deltaf=(2..18..2,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=2s; repeats=4; diff --git a/rfs/macros.cfg b/rfs/macros.cfg new file mode 100644 index 0000000..fec4638 --- /dev/null +++ b/rfs/macros.cfg @@ -0,0 +1,51 @@ +$START startup nobutton keep +shell rm -f $RELACSDEFAULTPATH/* + +$DISKSPACE stopsession nobutton keep +message Diskspace: $(DS=$(df -B 1M . | tail -n 1 | awk '{ print $4 }'); + [ $DS -lt 1000 ] && echo "

! Warning !

Less than ${DS}MB + of free disk space left! +

Please make backups and clean up to make room for the next recording!") + + +############################################################################# +$Search fallback keep +BaselineActivity: repeats=0; isimax=20ms; isistep=0.2ms; auto=always; +SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=true; freqsel=relative to EOD; sinewave=true; +SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=false; freqsel=absolute; sinewave=true; + + +############################################################################# +$Start startsession keep overwrite +Pause: duration=0.2s; +detector: autoconfigure 0.2 +macro Baseline +detector Spikes-1: save + +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + + +############################################################################# +$AM +switch macrosam.cfg + +$Receptive fields +switch macrorfs.cfg + + +############################################################################# +$Calib direct +CalibEField: am=0; + +$Calib AM +CalibEField: am=1; + +$Check SAM +SAM: am=false; freqsel=relative to EOD; repeats=0; contrast=20%; deltaf=20Hz; + + +############################################################################# + +$Idle +Pause: duration=0; diff --git a/rfs/macrosam.cfg b/rfs/macrosam.cfg new file mode 100644 index 0000000..9ad83ef --- /dev/null +++ b/rfs/macrosam.cfg @@ -0,0 +1,38 @@ +############################################################################# +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$SAMs AM +SAM: deltaf=(100..300..10,alternateout,r=3)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: deltaf=(20..90..10,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: deltaf=(2..18..2,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=2s; repeats=4; + +$Chirps EOD +#Chirps: chirpsize=100Hz; deltaf=(-250,-240,-230,-220,-210,-200,-190,-180,-170,-160,-150,-140,-130,-120,-110,-100,-90,-80,-70,-60,-50,-40,-30,-20,-10,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false +Chirps: chirpsize=60Hz; deltaf=(-250,-200,-150,-100,-80,-60,-40,-20,-10,10,20,40,60,80,100,150,200,250); contrast=10%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false + +$Nervetest +Chirps: chirpsize=100Hz; deltaf=(20); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false + +$FICurve AM +FICurve: am=true; + +$Noise AM: contrast=10% +Pause: duration=200ms +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=10% +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=5% +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=20% + +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn200Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn100Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn50Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn25Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast + + +############################################################################# +$DC +switch macrosdc.cfg + +$Back +switch macros.cfg diff --git a/rfs/macrosdc.cfg b/rfs/macrosdc.cfg new file mode 100644 index 0000000..09ec73a --- /dev/null +++ b/rfs/macrosdc.cfg @@ -0,0 +1,69 @@ +############################################################################# +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$SAMs 60Hz +SAM: contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; deltaf=60Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=5; + +$SAMs 250Hz +SAM: contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; deltaf=250Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=5; + +$SAMs 40% +SAM: contrast=40%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=40%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=40%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 20% +SAM: contrast=20%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=20%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=20%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 10% +SAM: contrast=10%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=10%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=10%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 5% +SAM: contrast=5%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=5%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=5%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 1% +SAM: contrast=1%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=1%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=1%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 0.1% +SAM: contrast=0.1%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=0.1%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=0.1%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$Chirps A +Chirps: chirpsize=120Hz; deltaf=60Hz; contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=250Hz; contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false + +$Chirps f +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=10%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=5%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=1%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.5%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.1%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.05%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.01%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false + +#$FICurve DC +#FICurve: am=false; + +#$Noise DC +#FileStimulus: file=/home/efish/stimuli/whitenoise/gwn150Hz10s0.3.dat; sigstdev=0.3; am=false; contrast=10% +#FileStimulus: 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+++ b/rfs/relacs.cfg @@ -0,0 +1,236 @@ +*Settings + Plugins: + pluginpathes : [ base*, calibration*, misc*, ephys*, efield*, efish*, comedi*, attcs3310* ] + pluginhelppathes: ~ + controlplugin : [ Session, Robot, AmplifierControl, SpectrumAnalyzer ] + modelplugin : PUnitModel + Pathes: + pathformat : %04Y-%02m-%02d-%a2a + defaultpath: dry/ + repropath : [ stimuli/repros/, reprodata, stimuli/repros/ ] + infofile : info.dat + Save: + saverelacsfiles : true + saveodmlfiles : false + savenixfiles : true + saverelacscore : true + saverelacsplugins: true + saverelacslog : true + saveattenuators : true + Date/time formats: + elapsedformat : "%02H:%02M" + sessiontimeformat: %Hh%02Mmin%02Ssec + reprotimeformat : %Mmin%02Ssec + Plotting: + printcommand: ~ + Data acquisition: + readinterval : 10ms + processinterval: 50ms + aitimeout : 10seconds + +*Metadata + -Setup-: + Identifier (Name): invivo1 + Maintainer : Jan Grewe + Creator : Jan Grewe and Jan Benda + Location (Room) : "5A17" + Lab : Neuroethology Lab + Institute : Institute for Neurobiology + University : University Tuebingen + Address : Auf der Morgenstelle 28 + +*RELACS + input data: + inputsamplerate : 20kHz + inputtracecapacity : 600s + inputunipolar : false + inputtraceid : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + inputtracescale : [ 100, 1, 10, 10, 100 ] + inputtraceunit : [ mV, mV, mV, mV, mV ] + inputtracedevice : [ ai-1, ai-1, ai-1, ai-1, ai-1 ] + inputtracechannel : [ 8, 0, 2, 4, 6 ] + inputtracereference: [ ground, ground, ground, ground, ground ] + inputtracemaxvalue : [ 200, 5, 3, 10, 10 ] + inputtracecenter : [ true, false, false, false, false ] + output data: + outputtraceid : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + outputtracedevice : [ ao-1, ao-1, ao-1, ao-1 ] + outputtracechannel : [ 1, 0, 2, 3 ] + outputtracescale : [ 1, 1, 1, 1 ] + outputtraceunit : [ V, V, V, V ] + outputtracemaxrate : [ 1kHz, 1kHz, 1kHz, 1kHz ] + outputtracemodality: [ electric, electric, electric, current ] + +*Macros + file : [ macrorfs.cfg, macros.cfg, macrosam.cfg, macrosdc.cfg ] + mainfile : macros.cfg + fallbackonreload: true + +*FilterDetectors + Filter1: + name : Spikes-1 + filter : DynamicSUSpikeDetector + inputtrace : V-1 + save : true + savemeanquality: true + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter2: + name : EOD + filter : EODDetector + inputtrace : EOD + save : true + savemeanquality: false + plot : true + trigger : true + buffersize : 300000 + storesize : true + storewidth : false + Filter3: + name : Chirps + filter : ChirpDetector + inputtrace : EOD + save : true + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : true + Filter4: + name : LocalEOD-1 + filter : EODDetector + inputtrace : LocalEOD-1 + save : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter5: + name : LocalBeat-1 + filter : BeatDetector + inputtrace : LocalEOD-1 + save : true + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + othertrace : Chirps + Filter6: + name : LocalEOD-2 + filter : EODDetector + inputtrace : LocalEOD-2 + save : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter7: + name : GlobalEFieldStimulus + filter : EODDetector + inputtrace : GlobalEFieldStimulus + save : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + +*AudioMonitor + device : [ "-1 default", "0 HDA Intel PCH: CX20642 Analog (hw:0,0) (2 channels)", "2 HDA Intel PCH: HDMI 0 (hw:0,3) (8 channels)", "3 HDA Intel PCH: HDMI 1 (hw:0,7) (8 channels)", "4 sysdefault (128 channels)", "5 front (2 channels)", "6 surround40 (2 channels)", "7 surround51 (2 channels)", "8 surround71 (2 channels)", "9 hdmi (8 channels)", "10 pulse (32 channels)", "11 dmix (2 channels)", "12 default (32 channels) - default" ] + enable : true + mute : false + gain : 1 + audiorate: [ "44.1", "8", "16", "22.05", "44.1", "48", "96" ]kHz + +*Devices + Device1: + plugin : AmplMode + device : dio-1 + ident : ampl-1 + buzzerpin : 14 + resistancepin: 15 + bridgepin : -1 + cclamppin : -1 + vclamppin : -1 + dclamppin : -1 + buzzerpulse : 500 + Device2: + plugin: [ Mirob, Mirob ] + device: dev + ident : robot-1 + Device3: + plugin: [ XYZRobot, XYZRobot ] + device: robot-1 + ident : robot-2 + +*Analog Input Devices + Device1: + plugin: ComediAnalogInput + device: /dev/comedi0 + ident : ai-1 + +*Analog Output Devices + Device1: + plugin: ComediAnalogOutput + device: /dev/comedi0 + ident : ao-1 + +*Digital I/O Devices + Device1: + plugin: ComediDigitalIO + device: /dev/comedi0 + ident : dio-1 + +*Attenuator Devices + Device1: + plugin: [ CS3310DIO, AttSim ] + device: dio-1 + ident : attdev-1 + Device2: + plugin : [ CS3310DIO, AttSim ] + device : dio-1 + ident : attdev-2 + cspin : 9 + mutepin : 10 + zcenpin : 11 + dataoutpin: 8 + datainpin : 12 + strobepin : 13 + +*Attenuator Interfaces + Device1: + plugin : LinearAttenuate + device : attdev-1 + line : 0 + aodevice : ao-1 + aochannel : 0 + ident : Attenuator-0 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + Device2: + plugin : LinearAttenuate + device : attdev-1 + line : 1 + aodevice : ao-1 + aochannel : 1 + ident : Attenuator-1 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + Device3: + plugin : LinearAttenuate + device : attdev-2 + line : 0 + aodevice : ao-1 + aochannel : 2 + ident : Attenuator-2 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + diff --git a/rfs/relacsplugins.cfg b/rfs/relacsplugins.cfg new file mode 100644 index 0000000..63f3b67 --- /dev/null +++ b/rfs/relacsplugins.cfg @@ -0,0 +1,752 @@ +*Metadata + Recording: + Recording quality: [ Fair, ~, good, poor, Poor, Fair, Good ] + Comment : "RF acoustically at 27, noise AM with LOCAL EOD, use 2nd baseline repro for baseline activity!" + Experimenter : [ Tim Hladnik, Tim Hladnik, MZ/TH, Martin Zeller, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] + WaterTemperature : 23.8°C + WaterConductivity: 330uS/cm + Cell: + CellType (Cell type) : [ P-unit, E-cell, E-cell deep, unknow, E-Cell, unkown, E-cell superficial, I-Cell, P-unit, Ampullary, T-unit ] + Structure (Recording location): [ Nerve, Nerve, Brain ] + BrainRegion : [ n.A., Torus, n.A., ELL ] + BrainSubRegion : [ ~, ~, LS, CLS, CMS, MS ] + Depth : 0um + Lateral position : 0mm + Transverse section : 0 + Subject: + Species : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ] + Gender (Sex): [ unknown, unknown, Male, Female ] + Size : 13cm + Weight : 5.1g + Identifier : "2018lepto28" + -Preparation-: + Type : [ in vivo, in vivo, slice ] + Anaesthesia : true + Anaesthetic (Drug) : MS 222 + AnaestheticDose (Concentration): 100mg/l + LocalAnaesthesia : true + LocalAnaesthetic (Drug) : Lidocaine + Immobilization : true + ImmobilizationDrug (Drug) : Tubocurarin 5mg/L + ImmobilizationDose : 70ul + +*Control: Session + ephys: true + +*Control: Robot + General: + robot: robot-2 + Stored positions: + FishHeadPosition : "(362.162,407.166,223.354)" + FishTailPosition : "(362.162,277.865,250.954)" + MovementAreaStart : "(0,0,0)" + MovementAreaEnd : "(0,0,0)" + ForbiddenAreaStart: "(0.499,93.490,0.196)" + ForbiddenAreaEnd : "(340.000,447.802,253.921)" + CustomPosition : "(400.0,0.1,0.1)" + Tool clamp: + toolreleasedelay: 1s + toolfixdelay : 2.5s + autoclamp : true + +*Control: AmplifierControl + initmode : [ Bridge, Current-clamp, Dynamic-clamp, Voltage-clamp, Manual selection ] + resistancecurrent: 1nA + adjust : false + maxresistance : 100MOhm + buzzpulse : 500ms + showbridge : true + showcc : false + showdc : false + showvc : false + showmanual : false + syncpulse : 10us + syncmode : 0samples + +*Control: SpectrumAnalyzer + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + origin : [ before end of data, before signal, after signal ] + offset : 0ms + duration : 1000ms + resolution: 10Hz + overlap : true + window : [ Hanning, Bartlett, Blackman, Blackman-Harris, Hamming, Hanning, Parzen, Square, Welch ] + fmax : 500Hz + decibel : true + pmin : -50dB + +*Model: PUnitModel + General: + EOD: + eodtype : [ Apteronotus, None, Sine, Apteronotus, Eigenmannia ] + eodfreq : 800Hz + eodfreqsd : 10Hz + eodfreqtau : 10000s + eodlocalamplitude : 1mV/cm + eodglobalamplitude: 1mV/cm + localstimulusgain : 5.00 + globalstimulusgain: 0.00 + stimulusgain : 1.00 + Spikes: + voltagescale: 0.5 + Spike generator: + spikemodel: [ Wang-Buzsaki, Stimulus, Passive membrane, Morris-Lecar, Hodgkin-Huxley, Connor, Wang-Buzsaki ] + noised : 0.1 + deltat : 0.05ms + integrator: [ Euler, Midpoint, Runge-Kutta 4 ] + Voltage-gated current 1 - activation only: + gmc : 2 + emc : -90mV + mvmc : -35mV + mwmc : 10mV + taumc: 30ms + Voltage-gated current 2 - activation and inactivation: + gmhc : 0 + emhc : -90mV + mvmhc : -40mV + mwmhc : 10mV + taummhc: 10ms + pmmhc : 1 + hvmhc : -40mV + hwmhc : 10mV + tauhmhc: 10ms + pmhhc : 1 + +*Model: Stimulus + Input: + gain : 1 + offset: 0muA/cm^2 + +*Model: Passive membrane + Parameter: + R: 50MOhm + C: 25pF + Input: + gain : 1 + offset: 0muA/cm^2 + +*Model: Morris-Lecar + General: + params: [ Custom, Type I, Type II ] + Calcium current: + gca : 4nS + eca : 120mV + mvca: -1.2mV + mkca: 18mV + Potassium current: + gk : 8nS + ek : -84mV + mvk : 12mV + mkk : 17.4mV + mphik: 0.067kHz + Leak current: + gl: 2nS + el: -60mV + c : 20pF + Input: + timescale: 10 + gain : 1 + offset : 0muA/cm^2 + +*Model: Hodgkin-Huxley + Sodium current: + gna: 120mS/cm^2 + ena: 50mV + Potassium current: + gk: 36mS/cm^2 + ek: -77mV + Leak current: + gl : 0.3mS/cm^2 + el : -54.4mV + c : 1muF/cm^2 + phi: 1 + Input: + gain : 50 + offset: 10muA/cm^2 + +*Model: Connor + Sodium current: + gna: 120mS/cm^2 + ena: 50mV + Potassium current: + gk: 20mS/cm^2 + ek: -77mV + A current: + gka: 47mS/cm^2 + eka: -80mV + Leak current: + gl : 0.3mS/cm^2 + el : -22mV + c : 1muF/cm^2 + phi: 1 + Input: + gain : 50 + offset: 30muA/cm^2 + +*Model: Wang-Buzsaki + Sodium current: + gna: 35mS/cm^2 + ena: 55mV + Potassium current: + gk: 9mS/cm^2 + ek: -90mV + Leak current: + gl : 0.1mS/cm^2 + el : -65mV + c : 1muF/cm^2 + phi: 5 + Input: + gain : 50 + offset: 6muA/cm^2 + +*Event Detector: Spikes-1 + Detector: + minthresh: 23.0mV + ratio : 15% + testwidth: false + fitwidth : 3.00ms + +*Event Detector: EOD + threshold : 0.44mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: Chirps + minthresh: 10Hz + +*Event Detector: LocalEOD-1 + threshold : 1mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: LocalBeat-1 + minthresh: 0.050mV + ratio : 35% + +*Event Detector: LocalEOD-2 + threshold : 1mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: GlobalEFieldStimulus + threshold : 0.052837mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*RePro: Pause + duration : 0sec + savedata : false + plotwidth: 0sec + +*RePro: Record + duration : 1sec + plotwidth: 0sec + dioout : false + diodevice: dio-1 + dioline : 0 + +*RePro: SaveTraces + General: + duration : 1sec + savedata : false + split : false + dioout : false + diodevice: dio-1 + dioline : 0 + Analog input traces: + trace-V-1 : true + trace-EOD : true + trace-LocalEOD-1 : true + trace-LocalEOD-2 : true + trace-GlobalEFieldStimulus: true + Events: + events-Spikes-1 : true + events-EOD : true + events-Chirps : true + events-LocalEOD-1 : true + events-LocalBeat-1-1 : true + events-LocalBeat-1-2 : true + events-LocalEOD-2 : true + events-GlobalEFieldStimulus: true + +*RePro: SetAttenuatorGain + outrace : V-1 + gain : 1 + interactive: true + +*RePro: SetInputGain + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + gainindex : 3 + interactive: true + +*RePro: SetOutput + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + value : 0V + intensity : 1 + interactive: false + +*RePro: Spectrogram + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + width : 100ms + step : 0ms + tmax : 10s + duration: 0s + size : [ "1024", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + overlap : true + window : [ Hanning, Bartlett, Blackman, Blackman-Harris, Hamming, Hanning, Parzen, Square, Welch ] + powermax: true + fmax : 2000Hz + pmax : 0dB + pmin : -50dB + +*RePro: TransferFunction + Stimulus: + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + offsetbase: [ custom, current ]value + offset : 0V + amplitude : 1V + clip : 4 + intensity : 1 + fmin : 0Hz + fmax : 1000Hz + duration : 1s + pause : 1s + repeats : 100 + Analysis: + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + size : [ "1024", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + overlap : true + window : [ Hanning, Bartlett, Blackman, Blackman-Harris, Hamming, Hanning, Parzen, Square, Welch ] + plotstdevs : true + plotcoherence: true + plotdecibel : false + +*RePro: Wait + absdate: false + date : ~ + days : 0days + time : "00:00:00.000" + +*RePro: AttenuatorCheck + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration : 1s + type : [ attenuation, noise ] + frequency: 50Hz + amplitude: 1Vmax + minlevel : 0dB + maxlevel : 100dB + dlevel : 1dB + adjust : true + +*RePro: InputRangeCheck + outtrace: [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration: 1000ms + pause : 1000ms + amplnum : 10 + +*RePro: RestartDelay + duration: 100ms + repeats : 100 + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + +*RePro: StimulusDelay + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + samplerate: 10kHz + duration : 10ms + pause : 50ms + repeats : 100 + setdelay : [ none, minimum, mean ] + +*RePro: BridgeTest + amplitude : 1V + duration : 10ms + pause : 100ms + average : 10 + skipspikes : true + dynamicrange: false + rate : 0.01 + plottrace : true + +*RePro: CalibrateSyncPulse + imin : -1 + imax : 1 + istep : 0.001 + skipwin : 1000ms + duration: 1000ms + +*RePro: CapacityCompensation + amplitude : 1V + duration : 200ms + frequency : 100Hz + showcycles : 10 + pause : 100ms + average : 10 + skipspikes : true + dynamicrange: false + rate : 0.01 + +*RePro: Iontophoresis + durationpos : 1s + amplitudepos : 1V + pausepos : 1s + durationneg : 1s + amplitudeneg : 1V + pauseneg : 1s + fortunes : true + fortuneperiod: 10s + +*RePro: SetLeak + interactive : true + preset : [ previous, zero, custom ]values + g : 0nS + E : 0mV + reversaltorest: true + involtage : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration : 100ms + +*RePro: SetVGate + interactive : true + preset : [ previous, zero, custom ]values + g : 0nS + E : 0mV + vmid : 0mV + width : 0mV + tau : 10ms + reversaltorest: true + involtage : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration : 100ms + +*RePro: Beats + Stimulation: + duration : 10seconds + pause : 20seconds + ramp : 0.5seconds + deltafrange : "10"Hz + deltafshuffle: [ Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + fixeddf : false + amplitude : 1mV/cm + amtype : [ none, sine, rectangular ] + amfreq : "1"Hz + amamplitude : "100"% + repeats : 10 + fakefish : 0Hz + Chirps: + generatechirps : false + chirpsize : 100Hz + chirpwidth : 100ms + chirpampl : 0% + chirpkurtosis : 1 + chirpfrequencies: ~Hz + chirptimesfile : ~ + chirptimeshuffle: [ Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + Analysis: + before : 1seconds + after : 1seconds + averagetime : 1seconds + usepsd : true + mineodfreq : 100Hz + maxeodfreq : 2000Hz + eodfreqprec : 1Hz + neod : 2 + showstimulus: false + split : false + savetraces : false + +*RePro: CalibEField + General: + reset : true + resetval : 0.1 + am : false + beatfreq : 10Hz + frequency: 670Hz + duration : 600ms + pause : 10ms + Range: + amplsel : [ contrast, amplitude ] + targetcontrast : 25% + mincontrast : 25% + maxcontrast : 65% + targetamplitude: 1mV/cm + minamplitude : 0.5mV/cm + maxamplitude : 2mV/cm + numintensities : 10 + +*RePro: CalibrateRobot + robot: robot-2 + +*RePro: EFieldGeometry + Enviroment data: + temperature : 26°C + conductivity: 330µS + water_level : 20cm + Measurement data: + robot : robot-2 + type : ~ + distance : 0mm + head_length : 20mm + tail_length : 20mm + width_posY : 50mm + width_negY : 50mm + height : 50mm + depth : 50mm + step_length_x: 5mm + step_length_y: 5mm + step_length_z: 5mm + +*RePro: JAR + Stimulation: + duration : 10seconds + pause : 10seconds + ramp : 0.5seconds + deltafstep : 2Hz + deltafmax : 12Hz + deltafmin : -12Hz + deltafrange : ~ + deltafshuffle: [ Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + repeats : 200 + Amplitudes: + amplsel : [ contrast, absolute ] + contrastmax : 20% + contrastmin : 10% + contraststep: 20% + amplmin : 1mV/cm + amplmax : 2mV/cm + amplstep : 1mV/cm + S&timulus: + genstim : true + sinewave: true + file : ~ + sigstdev: 1 + warpfile: false + fakefish: 0Hz + A&nalysis: + before : 1seconds + after : 8seconds + savetraces : true + jaraverage : 500ms + chirpaverage: 20ms + eodsavetime : 1000ms + +*RePro: LinearField + duration: 1s + +*RePro: ManualJAR + deltaf : 0.0Hz + lineardeltaf : false + deltaf2 : 0.0Hz + amplitude : 1.0mV + duration : 10seconds + ramp : 0.5seconds + fakefish : 0Hz + showlineardeltaf: false + before : 1seconds + after : 1seconds + averagetime : 1seconds + split : false + savetraces : false + +*RePro: BaselineActivity + Timing: + duration: 300ms + repeats : 0 + Analysis: + isimax : 20ms + isistep : 0.2ms + ratedt : 0.05ms + ratetmax: 2ms + Files: + eodduration : 2000ms + saveeodtrace: false + saveeodtimes: false + Control: + auto : [ never, once, always ] + adjust: false + +*RePro: Chirps + Chirp parameter: + nchirps : 10 + beatpos : 10 + beatstart : 0.25 + minspace : 200ms + firstspace : 200ms + chirpsize : 100Hz + chirpwidth : 14ms + chirpampl : 2% + chirpsel : [ generated, from file ] + chirpkurtosis: 1 + file : ~ + Beat parameter: + deltaf : 10Hz + contrast: 20% + am : false + sinewave: true + playback: false + pause : 1000ms + repeats : 6 + Analysis: + sigma : 2ms + adjust: true + +*RePro: FICurve + Test-Intensities: + duration : 400ms + maxintfac : 180% + minintfac : 20% + nints : 16 + repeats : 1 + blockrepeats : 10 + singlerepeats: 1 + intshuffle : [ AlternateOutUp, Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + intincrement : -2 + Pre-Intensities: + preduration : 0ms + maxpreintfac : 140% + minpreintfac : 60% + npreints : 2 + preintshuffle: [ AlternateInDown, Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + Control: + am : true + pause : 1000ms + delay : 200ms + onsettime : 50ms + rangeintincrement: 4 + minrate : 40Hz + minratefrac : 15% + adjust : false + +*RePro: FileStimulus + Stimulus: + file : /home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat + sigstdev : 0.3 + duration : 0ms + pause : 1000ms + amplsel : [ contrast, absolute ] + contrast : 20% + amplitude: 1mV/cm + am : true + repeats : 10 + Additional noise: + noisetype : [ none, Gaussian-White, Ornstein-Uhlenbeck ] + uppercutoff : 300Hz + lowercutoff : 0Hz + noisetau : 100ms + noisecontrast: 5% + noiseampl : 80mV/cm + Analysis: + binwidth: 5ms + before : 0ms + after : 0ms + plotpsd : false + psdsize : [ "256", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + adjust : false + +*RePro: ReceptiveField + Quick Search: + xmin : 27mm + xmax : 128mm + xstep : 5mm + ymin : 0mm + ymax : 0mm + ystep : 1mm + ystart : 0mm + zmin : -20mm + zmax : -20mm + zstep : 1mm + followmidline: true + Stimulation: + deltaf : 20Hz + amplitude: 10mV + duration : 1000ms + pause : 250ms + repeats : 4 + binwidth : 20ms + Robot setup: + xmapping: [ y, z, x ] + xinvert : true + ymapping: [ z, x, y ] + yinvert : true + zmapping: [ x, y, z ] + zinvert : false + safex : 410mm + safey : 315mm + safez : 205mm + +*RePro: RobotToFishPosition + Position: + destination : "(27,0,-20)" + followmidline: true + Robot setup: + xmapping: [ y, z, x ] + xinvert : true + ymapping: [ z, x, y ] + yinvert : true + zmapping: [ x, y, z ] + zinvert : false + +*RePro: SAM + Stimulus: + duration : 1000ms + pause : 1000ms + freqsel : [ relative to EOD, absolute ] + deltaf : 20Hz + contrast : 20% + repeats : 6 + am : true + sinewave : true + ampl : "0.0" + phase : "0.0"pi + contrastsel: [ fundamental, peak amplitude ] + Analysis: + skip : 0.5Periods + ratebins: 10 + before : 0ms + after : 0ms + adjust : false + +*Attenuator-0 + plugin : LinearAttenuate + ident : Attenuator-0 + device : attdev-1 + line : 0 + aodevice : ao-1 + aochannel : 0 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + frequencyname : ~ + frequencyunit : Hz + frequencyformat: %7.0f + gain : 0.43737 + offset : 0 + +*Attenuator-1 + plugin : LinearAttenuate + ident : Attenuator-1 + device : attdev-1 + line : 1 + aodevice : ao-1 + aochannel : 1 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + frequencyname : ~ + frequencyunit : Hz + frequencyformat: %7.0f + gain : 0.045983 + offset : 0 + +*Attenuator-2 + plugin : LinearAttenuate + ident : Attenuator-2 + device : attdev-2 + line : 0 + aodevice : ao-1 + aochannel : 2 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + frequencyname : ~ + frequencyunit : Hz + frequencyformat: %7.0f + gain : 1 + offset : 0 +