From a2a6d8312b33c49fb51a033f32e6f1f0b89d47cd Mon Sep 17 00:00:00 2001 From: efish Date: Thu, 30 Apr 2020 14:54:13 +0200 Subject: [PATCH] [04/2020] add juxta settings --- gp/relacs.cfg | 4 +- labrotation/macros.cfg | 2 + labrotation/macrosAlexandra.cfg | 6 +- labrotation/macrosCarlos.cfg | 14 +- labrotation/relacs.cfg | 8 +- labrotation/relacsplugins.cfg | 52 +- moving_objects/relacsplugins.cfg | 21 +- torus/code/multisensory_stimuli.py | 16 +- torus/macros.cfg | 5 + torus/macrotorus.cfg | 8 +- torus/relacs.cfg | 8 +- torus/relacsplugins.cfg | 61 ++- torus_juxta/macros.cfg | 44 ++ torus_juxta/macrotorus.cfg | 35 ++ torus_juxta/relacs.cfg | 228 +++++++++ torus_juxta/relacsplugins.cfg | 771 +++++++++++++++++++++++++++++ 16 files changed, 1185 insertions(+), 98 deletions(-) create mode 100644 torus_juxta/macros.cfg create mode 100644 torus_juxta/macrotorus.cfg create mode 100644 torus_juxta/relacs.cfg create mode 100644 torus_juxta/relacsplugins.cfg diff --git a/gp/relacs.cfg b/gp/relacs.cfg index a135b24..8c44fff 100644 --- a/gp/relacs.cfg +++ b/gp/relacs.cfg @@ -45,7 +45,7 @@ inputtracecapacity : 600s inputunipolar : false inputtraceid : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] - inputtracescale : [ 100, 1, 20, 5 ] + inputtracescale : [ 100, 1, 10, 5 ] inputtraceunit : [ mV, mV, mV, mV ] inputtracedevice : [ ai-1, ai-1, ai-1, ai-1 ] inputtracechannel : [ 6, 0, 2, 4 ] @@ -62,7 +62,7 @@ outputtracemodality: [ voltage, voltage, voltage, current ] *Macros - file : [ macrosam.cfg, macros.cfg ] + file : [ macrosam.cfg, macros.cfg, macrosCarlos.cfg ] mainfile : macros.cfg fallbackonreload: true diff --git a/labrotation/macros.cfg b/labrotation/macros.cfg index 3efdb52..0e13134 100644 --- a/labrotation/macros.cfg +++ b/labrotation/macros.cfg @@ -30,6 +30,8 @@ switch macrosAlexandra.cfg $Carlos switch macrosCarlos.cfg +$Ramona +switch macrosRamona.cfg #$JAR #JAR diff --git a/labrotation/macrosAlexandra.cfg b/labrotation/macrosAlexandra.cfg index 3f7c3ab..a43485f 100644 --- a/labrotation/macrosAlexandra.cfg +++ b/labrotation/macrosAlexandra.cfg @@ -10,7 +10,10 @@ $FICurve AM FICurve: am=true; $Chirps -Chirps: chirpsize=100Hz; deltaf=(-500..500..75, random); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false; minspace=500ms; firstspace=500ms +Chirps: chirpsize=100Hz; deltaf=(-500..750..75, random); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false; minspace=500ms; firstspace=500ms + +$ChirpsFine +Chirps: chirpsize=100Hz; deltaf=(-25, -10, -5, 5, 10, 50, -100, -150, -250, -75, random); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false; minspace=500ms; firstspace=500ms #Chirps: chirpsize=100Hz; deltaf=(10, 100, -200, -60); contrast=10%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false #Chirps: chirpsize=100Hz; deltaf=(10, 100, -200, -60); contrast=5%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false #Chirps: chirpsize=60Hz; deltaf=(10, 100, -200, -60); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false @@ -34,6 +37,5 @@ Chirps: chirpsize=100Hz; deltaf=(-500..500..75, random); contrast=20%; chirpwidt #$Chirps test #Chirps: chirpsize=100Hz; deltaf=(-200..200..25, random); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false - $Back switch macros.cfg diff --git a/labrotation/macrosCarlos.cfg b/labrotation/macrosCarlos.cfg index 2470e57..3f06712 100644 --- a/labrotation/macrosCarlos.cfg +++ b/labrotation/macrosCarlos.cfg @@ -5,16 +5,16 @@ BaselineActivity: repeats=3000; saveeodtrace=true; $FICurve AM FICurve: am=true; -$noise Stimuli +$Noise Stimuli #FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=1.0%; repeats=1; plotpsd=true #FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=5.0%; repeats=1; plotpsd=true #FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=40.0%; repeats=1; plotpsd=true -FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=20.0%; repeats=1; plotpsd=true -FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=20.0%; repeats=1; plotpsd=true -FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=20.0%; repeats=1; plotpsd=true -FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=20.0%; repeats=1; plotpsd=true -FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_250to300hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=20.0%; repeats=1; plotpsd=true -FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_150to200hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=20.0%; repeats=1; plotpsd=true +FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat ; duration=30000ms; sigstdev=0.25; am=true; contrast=10.0%; repeats=1; plotpsd=true +FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=10.0%; repeats=1; plotpsd=true +FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_50hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=10.0%; repeats=1; plotpsd=true +FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=10.0%; repeats=1; plotpsd=true +FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_250to300hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=10.0%; repeats=1; plotpsd=true +FileStimulus: file=/home/efish/stimuli/whitenoise/dennis/InputArr_150to200hz_30s.dat; duration=30000ms; sigstdev=0.25; am=true; contrast=10.0%; repeats=1; plotpsd=true $Back switch macros.cfg diff --git a/labrotation/relacs.cfg b/labrotation/relacs.cfg index 9d5f8fa..2cf4157 100644 --- a/labrotation/relacs.cfg +++ b/labrotation/relacs.cfg @@ -45,12 +45,12 @@ inputtracecapacity : 600s inputunipolar : false inputtraceid : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] - inputtracescale : [ 100, 1, 20, 5 ] + inputtracescale : [ 100, 0.2, 10, 5 ] inputtraceunit : [ mV, mV, mV, mV ] inputtracedevice : [ ai-1, ai-1, ai-1, ai-1 ] inputtracechannel : [ 6, 0, 2, 4 ] inputtracereference: [ ground, ground, ground, ground ] - inputtracemaxvalue : [ 100, 5, 3, 1 ] + inputtracemaxvalue : [ 100, 2, 3, 1 ] inputtracecenter : [ true, true, true, true ] output data: outputtraceid : [ GlobalEField, GlobalEFieldAM, V, I ] @@ -62,7 +62,7 @@ outputtracemodality: [ voltage, voltage, voltage, current ] *Macros - file : [ macrosCarlos.cfg, macrosAlexandra.cfg, macros.cfg, macrosam.cfg ] + file : [ macrosAlexandra.cfg, macrosRamona.cfg, macrosCarlos.cfg, macros.cfg, macrosCalib.cfg, macrosam.cfg ] mainfile : macros.cfg fallbackonreload: true @@ -160,7 +160,7 @@ 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" ] + device : [ "-1 default", "2 HDA Intel PCH: HDMI 0 (hw:0,3) (8 channels)", "3 HDA Intel PCH: HDMI 1 (hw:0,7) (8 channels)", "5 hdmi (8 channels)", "6 pulse (32 channels)", "7 default (32 channels) - default" ] enable : true mute : false gain : 1 diff --git a/labrotation/relacsplugins.cfg b/labrotation/relacsplugins.cfg index 9bd54bd..8327405 100644 --- a/labrotation/relacsplugins.cfg +++ b/labrotation/relacsplugins.cfg @@ -1,24 +1,24 @@ *Metadata Recording: - Recording quality: [ good, poor, fair, Good, ~, good, Poor, Fair ] + Recording quality: [ Good, poor, fair, Good, ~, good, Poor, Fair ] Comment : ~ - Experimenter : [ Ramona Schaefer, Christina Weiss, Christina Langenberger, Ramona Schaefer, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] + Experimenter : [ Ramona Schaefer, Alexandra and Carlos, Christina Weiss, Christina Langenberger, Ramona Schaefer, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] WaterTemperature : 23.7°C - WaterConductivity: 488uS/cm + WaterConductivity: 300uS/cm Cell: CellType (Cell type) : [ P-unit, Pyramidal, 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., TSd, Torus, n.A., ELL ] BrainSubRegion : [ ~, ~, LS, CLS, CMS, MS ] - Depth : -166um + Depth : 0um Lateral position : 0mm Transverse section : 0 Subject: Species : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ] Gender (Sex): [ unknown, unknown, Male, Female ] Size : 17cm - Weight : 12.9g - Identifier : "2017lepto04" + Weight : 12g + Identifier : "2018lepto74" -Preparation-: Type : [ in vivo, in vivo, slice ] Anaesthesia : true @@ -28,7 +28,7 @@ LocalAnaesthetic (Drug) : Lidocaine Immobilization : true ImmobilizationDrug (Drug) : Tubocurarin 5mg/L - ImmobilizationDose : 75ul + ImmobilizationDose : 50ul *Control: Session ephys: true @@ -51,7 +51,7 @@ vctau : 1ms *Control: SpectrumAnalyzer - intrace : [ LocalEOD-1, V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] + intrace : [ EOD, V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] origin : [ before end of data, before signal, after signal ] offset : 0ms duration : 1000ms @@ -194,7 +194,7 @@ *Event Detector: Spikes-1 Detector: - minthresh: 3.0mV + minthresh: 2.0mV decay : 1sec ratio : 12% testwidth: false @@ -205,21 +205,21 @@ trendtime : 2.0sec *Event Detector: EOD - threshold : 0.64mV + threshold : 0.77mV interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *Event Detector: Chirps minthresh: 10Hz *Event Detector: LocalEOD-1 - threshold : 0.22mV + threshold : 0.6mV interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *Event Detector: LocalBeat-1 - minthresh: 0.050mV + minthresh: 0.131mV *Event Detector: GlobalEFieldStimulus - threshold : 0.046195mV + threshold : 0.11759mV interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *RePro: Pause @@ -420,7 +420,7 @@ General: reset : false resetval : 0.1 - am : false + am : true beatfreq : 20Hz frequency: 600Hz duration : 600ms @@ -429,7 +429,7 @@ amplsel : [ contrast, amplitude ] targetcontrast : 20% mincontrast : 10% - maxcontrast : 40% + maxcontrast : 35% targetamplitude: 1mV/cm minamplitude : 0.5mV/cm maxamplitude : 2mV/cm @@ -569,8 +569,8 @@ nchirps : 10 beatpos : 10 beatstart : 0.25 - minspace : 200ms - firstspace : 200ms + minspace : 500ms + firstspace : 500ms chirpsize : 100Hz chirpwidth : 14ms chirpampl : 2% @@ -578,13 +578,13 @@ chirpkurtosis: 1 file : [ /home/efish/Desktop/doublePeakChirp.dat, ~, /home/efish/Desktop/doublePeakChirp.dat ] Beat parameter: - deltaf : 200Hz - contrast: 20% + deltaf : -425Hz + contrast: 5% am : false sinewave: true playback: false pause : 1000ms - repeats : 6 + repeats : 16 Analysis: sigma : 2ms adjust: false @@ -618,16 +618,16 @@ *RePro: FileStimulus Stimulus: - file : [ /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, ~, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat ] + file : [ /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, ~, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat ] name : ~ sigstdev : 0.25 - duration : 20000ms + duration : 30000ms pause : 1000ms amplsel : [ contrast, absolute ] - contrast : 20% + contrast : 10% amplitude: 1mV/cm am : true - repeats : 5 + repeats : 1 Additional noise: noisetype : [ none, Gaussian-White, Ornstein-Uhlenbeck ] uppercutoff : 600Hz @@ -749,7 +749,7 @@ frequencyname : ~ frequencyunit : Hz frequencyformat: %7.0f - gain : 1.7375 + gain : 0.13747 offset : 0 *Attenuator-1 @@ -765,6 +765,6 @@ frequencyname : ~ frequencyunit : Hz frequencyformat: %7.0f - gain : 0.074344 + gain : 0.092205 offset : 0 diff --git a/moving_objects/relacsplugins.cfg b/moving_objects/relacsplugins.cfg index d6e334f..6e06d29 100644 --- a/moving_objects/relacsplugins.cfg +++ b/moving_objects/relacsplugins.cfg @@ -227,7 +227,7 @@ interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *Event Detector: LocalBeat-1 - minthresh: 0.100mV + minthresh: 0.040mV ratio : 35% *Event Detector: GlobalEFieldStimulus @@ -663,10 +663,9 @@ adjust : false *RePro: FileStimulus - General: - name: ~ Stimulus: file : /home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat + name : ~ sigstdev : 0.3 duration : 0ms pause : 1000ms @@ -695,10 +694,10 @@ startpos : [ -60mm, 0mm, -8mm ] traveldist : 120mm travelspeed : 10mm/s - movementaxis: [ x, x, y, z ] + movementaxis: [ x, y, z ] repeats : 4 pause : 0.1s - object : [ small, small, medium comb, ~, pvc comb 4cm, pvc comb 1cm, perspex bar, metal sphere, large comb ] + object : [ small, pvc comb 4cm, pvc comb 1cm, perspex bar, metal sphere, small ] Parameter space: distmin : 0mm distmax : 0mm @@ -707,11 +706,11 @@ speedmax : 240mm/s speedstep: 40mm/s Robot setup: - xmapping: [ y, y, z, x ] + xmapping: [ y, z, x ] xinvert : true - ymapping: [ z, z, x, y ] + ymapping: [ z, x, y ] yinvert : false - zmapping: [ x, x, y, z ] + zmapping: [ x, y, z ] zinvert : false safepos : [ 450, 0, 0 ] outpos : [ 450, 300, 100 ] @@ -754,11 +753,11 @@ destination : [ 0mm, 0mm, 0mm ] followmidline: true Robot setup: - xmapping: [ y, y, z, x ] + xmapping: [ y, z, x ] xinvert : true - ymapping: [ z, z, x, y ] + ymapping: [ z, x, y ] yinvert : true - zmapping: [ x, x, y, z ] + zmapping: [ x, y, z ] zinvert : false *RePro: SAM diff --git a/torus/code/multisensory_stimuli.py b/torus/code/multisensory_stimuli.py index 4a48746..e8274ed 100755 --- a/torus/code/multisensory_stimuli.py +++ b/torus/code/multisensory_stimuli.py @@ -33,12 +33,12 @@ class MultichannelStimulus(object): def create_contrast_stim(self): t = np.arange(0, self._contrast_sweep_duration, self._dt) sweep_up = np.linspace(0., 1.0, len(t)) - am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t) - dc = np.sin(2*np.pi*self._dcf*t) + am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t) * 0.5 + dc = np.sin(2*np.pi*self._dcf*t) * 0.5 am_sweep = am * sweep_up dc_sweep = dc * sweep_up - self._contrast_stimulus = np.hstack((am_sweep, dc_sweep, am + dc_sweep, dc + am_sweep)) + self._contrast_stimulus = np.hstack((am_sweep, dc_sweep, (am + dc_sweep), (dc + am_sweep))) header = {" ": "Contrast sweeps for ampullary and tuberous pathways", "sd": 1.0, "deltat": "%.5f s" % self._dt, @@ -55,7 +55,7 @@ class MultichannelStimulus(object): am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t) dc = np.sin(2*np.pi*self._df*t + phase_sweep) - self._phase_stimulus = am + dc + self._phase_stimulus = (am + dc)/2. header = {" ": "Phase sweep stimulating ampullary and tuberous pathways", "sd": 1.0, "deltat": "%.5f s" % self._dt, @@ -68,9 +68,9 @@ class MultichannelStimulus(object): t = np.arange(0, self._zap_duration, self._dt) m = self._maxfreq/self._zap_duration - dc = np.sin(2*np.pi*m*t*t) - am = np.sin(2*np.pi*(m*t + self._eod_freq)*t) - self._zap_stimulus = np.hstack((dc, am, dc+am)) + dc = np.sin(2*np.pi*m*t*t) * 0.5 + am = np.sin(2*np.pi*(m*t + self._eod_freq)*t) * 0.5 + self._zap_stimulus = np.hstack((dc, am, (dc + am))) header = {" ": "Zap stimulus for ampullary and tuberous pathways", "sd": 1.0, "deltat": "%.5f s" % self._dt, @@ -112,7 +112,7 @@ if __name__ == "__main__": help=args.dt_help) parser.add_argument('-mf', '--maxfreq', type=float, default=100., help=args.maxfreq_help) - parser.add_argument('outfile prefix', help="name of the output file may include the path") + parser.add_argument('outfile', help="prefix name of the output file may include the path") args = parser.parse_args() diff --git a/torus/macros.cfg b/torus/macros.cfg index 2cc4d42..89a5bbb 100644 --- a/torus/macros.cfg +++ b/torus/macros.cfg @@ -15,6 +15,11 @@ SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=true; fr SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=false; freqsel=absolute; sinewave=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% $Calib direct CalibEField: am=0; diff --git a/torus/macrotorus.cfg b/torus/macrotorus.cfg index 668bb82..bc7954b 100644 --- a/torus/macrotorus.cfg +++ b/torus/macrotorus.cfg @@ -9,13 +9,15 @@ $FICurve DC: trials=5 FICurve: nints=10; am=false; blockrepeats=$trials $SAMs AM -SAM: deltaf=(5,10,20)Hz; am=true; freqsel="relative to EOD"; duration=1s; repeats=5; contrast=10; name="SAM AM"; +SAM: deltaf=(5,10,20,40,60,80,100)Hz; am=true; freqsel="relative to EOD"; duration=1s; repeats=5; contrast=10; name="SAM AM"; $SAMs DC -SAM: deltaf=(5,10,20)Hz; am=false; freqsel=absolute; duration=1s; repeats=5; contrast=10; name="SAM DC"; +SAM: deltaf=(5,10,20,40,60,80,100)Hz; am=false; freqsel=absolute; duration=1s; repeats=5; contrast=10; name="SAM DC"; $Multisensory -FileStimulus: file=/home/efish/stimuli/torus/multisams.dat; sigstdev=0.3; am=false; contrast=$contrast; repeats=10; noisetype="none"; name="multisensory"; +FileStimulus: file=/home/efish/stimuli/torus/zap.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="zap"; +FileStimulus: file=/home/efish/stimuli/torus/contrast_sweep.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="contrast_sweep"; +FileStimulus: file=/home/efish/stimuli/torus/phase_sweep.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="phase_sweep"; $Noise FileStimulus: file=/home/efish/stimuli/whitenoise/gwn250Hz50s0.3.dat; duration=10000ms; sigstdev=0.3; am=true; contrast=10; repeats=10; noisetype="none"; name="noise AM"; diff --git a/torus/relacs.cfg b/torus/relacs.cfg index 02d9e10..1e3365d 100644 --- a/torus/relacs.cfg +++ b/torus/relacs.cfg @@ -45,12 +45,12 @@ inputtracecapacity : 600s inputunipolar : false inputtraceid : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] - inputtracescale : [ 100, 1, 20, 5 ] + inputtracescale : [ 100, 1, 10, 5 ] inputtraceunit : [ mV, mV, mV, mV ] inputtracedevice : [ ai-1, ai-1, ai-1, ai-1 ] inputtracechannel : [ 6, 0, 2, 4 ] inputtracereference: [ ground, ground, ground, ground ] - inputtracemaxvalue : [ 100, 5, 3, 1 ] + inputtracemaxvalue : [ 200, 5, 2, 1 ] inputtracecenter : [ true, true, true, true ] output data: outputtraceid : [ GlobalEField, GlobalEFieldAM, V, I ] @@ -62,7 +62,7 @@ outputtracemodality: [ voltage, voltage, voltage, current ] *Macros - file : [ macros.cfg, macrotorus.cfg, macrosdc.cfg, macrosam.cfg, macro_ELL_MS.cfg, macros_fakefish.cfg, macro_ELL_AM.cfg, /home/efish/data/ephys/pyramidals/macros.cfg ] + file : [ macrotorus.cfg, macros.cfg, macrosdc.cfg, macrosam.cfg, macro_ELL_MS.cfg, macros_fakefish.cfg, macro_ELL_AM.cfg, /home/efish/data/ephys/pyramidals/macros.cfg ] mainfile : macros.cfg fallbackonreload: true @@ -176,7 +176,7 @@ bridgepin : 10 cclamppin : 9 vclamppin : 8 - dclamppin : 13 + dclamppin : -1 syncpin : 7 buzzerpulse : 500 diff --git a/torus/relacsplugins.cfg b/torus/relacsplugins.cfg index c353958..de3fa17 100644 --- a/torus/relacsplugins.cfg +++ b/torus/relacsplugins.cfg @@ -1,24 +1,24 @@ *Metadata Recording: - Recording quality: [ Good, ~, good, poor, Poor, Fair, Good ] - Comment : ~ - Experimenter : [ Jan Grewe, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] - WaterTemperature : 24.5°C - WaterConductivity: 330uS/cm + Recording quality: [ Fair, ~, good, poor, Poor, Fair, Good ] + Comment : strange cell + Experimenter : [ Lisa Vial, Lisa Vial, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] + WaterTemperature : 23.4°C + WaterConductivity: 289uS/cm Cell: CellType (Cell type) : [ unkown, Pyramidal, E-cell, E-cell deep, unknow, E-Cell, unkown, E-cell superficial, I-Cell, P-unit, Ampullary, T-unit ] Structure (Recording location): [ Brain, Nerve, Brain ] BrainRegion : [ TSd, TSd, Torus, n.A., ELL ] BrainSubRegion : [ ~, ~, LS, CLS, CMS, MS ] - Depth : 535.7um - Lateral position : -1.4mm - Transverse section : 7 + Depth : 1212.3um + Lateral position : -0.6mm + Transverse section : 18 Subject: Species : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ] Gender (Sex): [ unknown, unknown, Male, Female ] - Size : 17cm - Weight : 13.6g - Identifier : "2018lepto24" + Size : 16.2cm + Weight : 10g + Identifier : "2018lepto89" -Preparation-: Type : [ in vivo, in vivo, slice ] Anaesthesia : true @@ -51,7 +51,7 @@ vctau : 1ms *Control: SpectrumAnalyzer - intrace : [ LocalEOD-1, V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] + intrace : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ] origin : [ before end of data, before signal, after signal ] offset : 0ms duration : 1000ms @@ -194,9 +194,9 @@ *Event Detector: Spikes-1 Detector: - minthresh: 8.4mV + minthresh: 20.0mV decay : 1sec - ratio : 12% + ratio : 5% testwidth: false maxwidth : 2.0ms Indicators: @@ -205,7 +205,7 @@ trendtime : 2.0sec *Event Detector: EOD - threshold : 0.26mV + threshold : 0.051mV interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *Event Detector: Chirps @@ -216,10 +216,10 @@ interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *Event Detector: LocalBeat-1 - minthresh: 0.022mV + minthresh: 0.028mV *Event Detector: GlobalEFieldStimulus - threshold : 0.044256mV + threshold : 0.10465mV interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] *RePro: Pause @@ -418,9 +418,9 @@ *RePro: CalibEField General: - reset : false - resetval : 0.1 - am : false + reset : true + resetval : 0.24 + am : true beatfreq : 20Hz frequency: 600Hz duration : 600ms @@ -428,7 +428,7 @@ Range: amplsel : [ contrast, amplitude ] targetcontrast : 20% - mincontrast : 10% + mincontrast : 5% maxcontrast : 40% targetamplitude: 1mV/cm minamplitude : 0.5mV/cm @@ -617,18 +617,17 @@ adjust : false *RePro: FileStimulus - General: - name: ~ Stimulus: - file : [ /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, ~, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat ] - sigstdev : 0.25 - duration : 20000ms + file : [ /home/efish/stimuli/torus/zap.dat, ~, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat, /home/efish/stimuli/torus/zap.dat, /home/efish/stimuli/torus/phase_sweep.dat ] + name : zap + sigstdev : 1 + duration : 30000ms pause : 1000ms amplsel : [ contrast, absolute ] - contrast : 20% + contrast : 10% amplitude: 1mV/cm - am : true - repeats : 5 + am : false + repeats : 2 Additional noise: noisetype : [ none, Gaussian-White, Ornstein-Uhlenbeck ] uppercutoff : 600Hz @@ -750,7 +749,7 @@ frequencyname : ~ frequencyunit : Hz frequencyformat: %7.0f - gain : 0.91411 + gain : 0.71863 offset : 0 *Attenuator-1 @@ -766,6 +765,6 @@ frequencyname : ~ frequencyunit : Hz frequencyformat: %7.0f - gain : 0.059032 + gain : 0.12211 offset : 0 diff --git a/torus_juxta/macros.cfg b/torus_juxta/macros.cfg new file mode 100644 index 0000000..c455610 --- /dev/null +++ b/torus_juxta/macros.cfg @@ -0,0 +1,44 @@ +$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!") + + +############################################################################# +$Search fallback keep +BaselineActivity: repeats=0; isimax=20ms; isistep=0.2ms; auto=always; +SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=true; freqsel=relative to EOD; sinewave=true; +SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=false; freqsel=absolute; sinewave=true; +############################################################################# +$Search Pulses +Iontophoresis: durationpos=200ms; amplitudepos=1.1nA; pausepos=800ms; durationneg=0s; amplitudeneg=0nA; pauseneg=0s; fortuneperiod=30s; + +$Noise AM: contrast=10% +Pause: duration=200ms +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=10%; repeats=5 +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=5%; repeats=5 +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=20% + +$Calib direct +CalibEField: am=0; + +$Calib AM +CalibEField: am=1; + +$Check SAM +SAM: am=false; freqsel=relative to EOD; repeats=0; contrast=20%; deltaf=22Hz; + +############################################################################# + +$Idle +Pause: duration=0; + +############################################################################# + +$Torus +switch macrotorus.cfg + diff --git a/torus_juxta/macrotorus.cfg b/torus_juxta/macrotorus.cfg new file mode 100644 index 0000000..f9b4dd2 --- /dev/null +++ b/torus_juxta/macrotorus.cfg @@ -0,0 +1,35 @@ +############################################################################# +$Search Pulses +Iontophoresis: durationpos=200ms; amplitudepos=1.1nA; pausepos=800ms; durationneg=0s; amplitudeneg=0nA; pauseneg=0s; fortuneperiod=30s; + +$Staining +Iontophoresis: durationpos=200ms; amplitudepos=1.1nA; pausepos=800ms; durationneg=0s; amplitudeneg=0nA; pauseneg=0s; fortuneperiod=30s; + +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$FICurve AM: trials=5 +FICurve: nints=10; am=true; blockrepeats=$trials + +$FICurve DC: trials=5 +FICurve: nints=10; am=false; blockrepeats=$trials + +$SAMs AM +SAM: deltaf=(5,10,20)Hz; am=true; freqsel="relative to EOD"; duration=1s; repeats=5; contrast=10; name="SAM AM"; + +$SAMs DC +SAM: deltaf=(5,10,20)Hz; am=false; freqsel=absolute; duration=1s; repeats=5; contrast=10; name="SAM DC"; + +$Multisensory +FileStimulus: file=/home/efish/stimuli/torus/zap.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="zap"; +FileStimulus: file=/home/efish/stimuli/torus/contrast_sweep.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="contrast_sweep"; +FileStimulus: file=/home/efish/stimuli/torus/phase_sweep.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="phase_sweep"; + +$Noise +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn250Hz50s0.3.dat; duration=10000ms; sigstdev=0.3; am=true; contrast=10; repeats=10; noisetype="none"; name="noise AM"; + +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn250Hz50s0.3.dat; duration=10000ms; sigstdev=0.3; am=false; contrast=10; repeats=10; noisetype="none"; name="noise DC"; + + +$Back +switch macros.cfg diff --git a/torus_juxta/relacs.cfg b/torus_juxta/relacs.cfg new file mode 100644 index 0000000..3f6156a --- /dev/null +++ b/torus_juxta/relacs.cfg @@ -0,0 +1,228 @@ +*Settings + Plugins: + pluginpathes : [ base*, base*, misc*, ephys*, efield*, efish*, patchclamp, comedi*, attcs3310* ] + pluginhelppathes: ~ + controlplugin : [ Session, AmplifierControl, SpectrumAnalyzer ] + modelplugin : PUnitModel + Pathes: + pathformat : %04Y-%02m-%02d-%a2a-invivo-1 + defaultpath: dry/ + repropath : [ stimuli/repros/, reprodata, stimuli/repros/ ] + infofile : info.dat + Save: + saverelacsfiles : true + saveodmlfiles : false + savenixfiles : true + savenixcompressed: 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: + 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 : 40kHz + inputtracecapacity : 600s + inputunipolar : false + inputtraceid : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus, FilteredVoltage ] + inputtracescale : [ 100, 1, 10, 5, 100 ] + inputtraceunit : [ mV, mV, mV, mV, mV ] + inputtracedevice : [ ai-1, ai-1, ai-1, ai-1, ai-1 ] + inputtracechannel : [ 6, 0, 2, 4, 5 ] + inputtracereference: [ ground, ground, ground, ground, ground ] + inputtracemaxvalue : [ 200, 5, 2, 1, 200 ] + inputtracecenter : [ true, true, true, true, true ] + output data: + outputtraceid : [ GlobalEField, GlobalEFieldAM, V, Current ] + outputtracedevice : [ ao-1, ao-1, ao-1, ao-1 ] + outputtracechannel : [ 1, 0, 2, 3 ] + outputtracescale : [ 1, 1, 1, 1 ] + outputtraceunit : [ V, V, V, nA ] + outputtracemaxrate : [ 100kHz, 100kHz, 100kHz, 100kHz ] + outputtracemodality: [ voltage, voltage, voltage, current ] + +*Macros + file : [ macros.cfg, macrotorus.cfg, macrosdc.cfg, macrosam.cfg, macro_ELL_MS.cfg, macros_fakefish.cfg, macro_ELL_AM.cfg, /home/efish/data/ephys/pyramidals/macros.cfg ] + mainfile : macros.cfg + fallbackonreload: true + +*FilterDetectors + Filter1: + name : Spikes-1 + filter : DynamicSUSpikeDetector + inputtrace : FilteredVoltage + save : true + savesize : true + savewidth : true + savemeanrate : true + savemeansize : true + savemeanwidth : true + savemeanquality: true + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter2: + name : EOD + filter : EODDetector + inputtrace : EOD + save : false + savesize : false + savewidth : false + savemeanrate : true + savemeansize : true + savemeanwidth : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter3: + name : Chirps + filter : ChirpDetector + inputtrace : EOD + save : true + savesize : true + savewidth : true + savemeanrate : true + savemeansize : false + savemeanwidth : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : true + Filter4: + name : LocalEOD-1 + filter : EODDetector + inputtrace : LocalEOD-1 + save : false + savesize : false + savewidth : false + savemeanrate : true + savemeansize : true + savemeanwidth : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter5: + name : LocalBeat-1 + filter : BeatDetector + inputtrace : LocalEOD-1 + save : true + savesize : true + savewidth : false + savemeanrate : true + savemeansize : true + savemeanwidth : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + othertrace : Chirps + Filter6: + name : GlobalEFieldStimulus + filter : EODDetector + inputtrace : GlobalEFieldStimulus + save : false + savesize : false + savewidth : false + savemeanrate : true + savemeansize : true + savemeanwidth : 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: [ "48", "8", "16", "22.05", "44.1", "48", "96" ]kHz + +*Devices + Device1: + plugin : AmplMode + device : dio-1 + ident : ampl-1 + buzzerpin : 14 + resistancepin: 15 + bridgepin : 10 + cclamppin : 9 + vclamppin : 8 + dclamppin : -1 + syncpin : 7 + buzzerpulse : 500 + +*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 + +*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 + diff --git a/torus_juxta/relacsplugins.cfg b/torus_juxta/relacsplugins.cfg new file mode 100644 index 0000000..32cb973 --- /dev/null +++ b/torus_juxta/relacsplugins.cfg @@ -0,0 +1,771 @@ +*Metadata + Recording: + Recording quality: [ Good, ~, good, poor, Poor, Fair, Good ] + Comment : "boring cell, only a few spikes, so no labelling attempt" + Experimenter : [ Lisa Vial, Guiseppe Balsamo, Lisa Vial, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] + WaterTemperature : 23.8°C + WaterConductivity: 254uS/cm + Cell: + CellType (Cell type) : [ unkown, Pyramidal, E-cell, E-cell deep, unknow, E-Cell, unkown, E-cell superficial, I-Cell, P-unit, Ampullary, T-unit ] + Structure (Recording location): [ Brain, Nerve, Brain ] + BrainRegion : [ TSd, TSd, Torus, n.A., ELL ] + BrainSubRegion : [ ~, ~, LS, CLS, CMS, MS ] + Depth : 1488um + Lateral position : -0.3mm + Transverse section : 13 + Subject: + Species : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ] + Gender (Sex): [ unknown, unknown, Male, Female ] + Size : 10.8cm + Weight : 7g + Identifier : "2019lepto28" + -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 : 50ul + +*Control: Session + ephys: true + +*Control: AmplifierControl + initmode : [ Bridge, Current-clamp, Dynamic-clamp, Voltage-clamp, Manual selection ] + resistancecurrent: 1nA + adjust : false + maxresistance : 100MOhm + buzzpulse : 500ms + showswitchmessage: true + showbridge : true + showcc : false + showdc : false + showvc : false + showmanual : false + syncpulse : 10us + syncmode : 0samples + vcgain : 100 + vctau : 1ms + +*Control: SpectrumAnalyzer + intrace : [ EOD, V-1, EOD, LocalEOD-1, GlobalEFieldStimulus, FilteredVoltage ] + 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 + peak : true + pmin : -50dB + +*Model: PUnitModel + General: + EOD: + eodtype : [ Sine, None, Sine, Apteronotus, Eigenmannia ] + eodfreq : 800Hz + eodfreqsd : 10Hz + eodfreqtau : 10000s + eodlocalamplitude : 1mV/cm + eodglobalamplitude: 1mV/cm + localstimulusgain : 1.00 + globalstimulusgain: 0.00 + stimulusgain : 1.00 + Spikes: + voltagescale: 0.5 + General: + Spike generator: + spikemodel: [ Wang-Buzsaki, Stimulus, Passive membrane, Morris-Lecar, Hodgkin-Huxley, Connor, Wang-Buzsaki ] + noised : 0 + deltat : 0.05ms + integrator: [ Euler, Midpoint, Runge-Kutta 4 ] + Voltage clamp: + vcgain: 10 + vctau : 0.1ms + Currents: + Voltage-gated current 1 - activation only: + gmc : 0 + emc : -90mV + mvmc : -40mV + mwmc : 10mV + taumc: 10ms + 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 : 40muA/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 : 1 + offset: 0muA/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 : 1 + offset: 0muA/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 : 1 + offset: 0muA/cm^2 + +*RePro: Pause + duration : 1sec + 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-GlobalEFieldStimulus: true + trace-FilteredVoltage : 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-GlobalEFieldStimulus: true + +*RePro: SetAttenuatorGain + outrace : V-1 + gain : 1 + interactive: true + +*RePro: SetDigitalOutput + device : dio-1 + line : 0 + value : 0 + interactive: false + +*RePro: SetInputGain + intrace : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus, FilteredVoltage ] + gainindex : 0 + interactive: true + +*RePro: SetOutput + outtrace : [ GlobalEField, GlobalEFieldAM, V, Current ] + value : 0V + intensity : 1 + interactive: true + +*RePro: Spectrogram + intrace : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus, FilteredVoltage ] + 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, V, Current ] + 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, GlobalEFieldStimulus, FilteredVoltage ] + 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: BridgeTest + amplitude : 1000nA + duration : 10ms + pause : 100ms + average : 10 + skipspikes : true + dynamicrange: false + rate : 0.01 + plottrace : true + +*RePro: CalibrateSyncPulse + imin : -1000nA + imax : 1000nA + istep : 1000nA + skipwin : 1000ms + duration: 1000ms + +*RePro: CapacityCompensation + amplitude : 1000nA + duration : 200ms + frequency : 100Hz + showcycles : 10 + pause : 100ms + average : 10 + skipspikes : true + dynamicrange: false + rate : 0.01 + +*RePro: Iontophoresis + durationpos : 0.2s + amplitudepos : 1.1nA + pausepos : 0.8s + durationneg : 0s + amplitudeneg : 0nA + pauseneg : 0s + fortunes : true + fortuneperiod: 30s + +*RePro: SetLeak + interactive : true + preset : [ previous, zero, custom ]values + g : 0nS + E : 0mV + reversaltorest: true + involtage : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus, FilteredVoltage ] + 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, GlobalEFieldStimulus, FilteredVoltage ] + duration : 100ms + +*RePro: Beats + Stimulation: + name : ~ + 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 : 0.4 + am : false + beatfreq : 20Hz + frequency: 600Hz + duration : 600ms + pause : 10ms + Range: + amplsel : [ contrast, amplitude ] + targetcontrast : 20% + mincontrast : 5% + maxcontrast : 40% + targetamplitude: 1mV/cm + minamplitude : 0.5mV/cm + maxamplitude : 2mV/cm + numintensities : 10 + +*RePro: CalibrateRobot + robot: robot-1 + +*RePro: DualBeat + Stimulus: + rewarded : [ A, B ] + eodf : 0.0Hz + duration : 10seconds + deltafA : 25.0Hz + harmonicA : false + amplitudeA: 1.000V + deltafB : -50.0Hz + harmonicB : false + amplitudeB: 1.000V + Experiment: + noFish : false + randomizeAmpl : true + amplitudeRange : 20% + randomSminus : false + sminusRange : 200Hz + training : true + randomElectrode : true + rewardedElectrode: [ "1", "2" ] + trainingTrials : 10 + testTrials : 5 + testBeat : -25.0Hz + testAmplitude : 1.000V + stimOff : true + rewardInTest : true + harmonic : true + Setup: + scaling1: 1.000 + scaling2: 1.000 + EOD estimation: + intrace : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus, FilteredVoltage ] + usepsd : true + mineodfreq : 100Hz + maxeodfreq : 2000Hz + eodfreqprec: 1Hz + averagetime: 2s + +*RePro: EFieldGeometry + Enviroment data: + temperature : 26°C + conductivity: 330µS + water_level : 20cm + Measurement data: + robot : robot-1 + 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 : 60Hz + chirpwidth : 14ms + chirpampl : 2% + chirpsel : [ generated, from file ] + chirpkurtosis: 1 + file : [ /home/efish/Desktop/doublePeakChirp.dat, ~, /home/efish/Desktop/doublePeakChirp.dat ] + Beat parameter: + deltaf : 10Hz + contrast: 20% + am : true + sinewave: true + playback: false + pause : 1000ms + repeats : 16 + Analysis: + sigma : 2ms + adjust: false + +*RePro: FICurve + Test-Intensities: + duration : 400ms + maxintfac : 130% + minintfac : 70% + nints : 10 + 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 : 3 + 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/torus/zap.dat, ~, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat, /home/efish/stimuli/torus/zap.dat, /home/efish/stimuli/torus/phase_sweep.dat ] + name : zap + sigstdev : 1 + duration : 30000ms + pause : 1000ms + amplsel : [ contrast, absolute ] + contrast : 20% + amplitude: 1mV/cm + am : false + repeats : 2 + Additional noise: + noisetype : [ none, Gaussian-White, Ornstein-Uhlenbeck ] + uppercutoff : 600Hz + lowercutoff : 0Hz + noisetau : 10ms + noisecontrast: 0% + noiseampl : 80mV/cm + Analysis: + binwidth: 5ms + before : 0ms + after : 0ms + plotpsd : true + psdsize : [ "256", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + adjust : false + +*RePro: MovingObjects + Movement: + startpos : [ 0, 0, 0 ] + traveldist : 0mm + travelspeed : 40mm/s + movementaxis: [ x, y, z ] + repeats : 1 + pause : 1.5s + object : [ pvc comb 4cm, pvc comb 1cm, perspex bar, metal sphere ] + Parameter space: + distmin : 0mm + distmax : 0mm + diststep : 1mm + speedmin : 0mm/s + speedmax : 0mm/s + speedstep: 0mm/s + Robot setup: + xmapping: [ y, z, x ] + xinvert : true + ymapping: [ z, x, y ] + yinvert : false + zmapping: [ x, y, z ] + zinvert : false + safepos : [ 0, 0, 0 ] + outpos : [ 0, 0, 0 ] + +*RePro: ReceptiveField + 2D search: + name : ~ + xmin : 0mm + xmax : 0mm + xspeed : 10mm/s + ymin : 0mm + ymax : 0mm + yspeed : 10mm/s + zpos : 5mm + followmidline: true + npasses : 1 + pause : 1000ms + Stimulation: + deltaf : 50Hz + amplitude: 1mV + Analysis: + nfft : 1024 + nshift : 128 + kernelwidth: 0.001ms + Robot setup: + robotdev : robot-2 + xmapping : [ y, z, x ] + xinvert : true + ymapping : [ z, x, y ] + yinvert : false + zmapping : [ x, y, z ] + zinvert : false + safex : 350mm + safey : 0mm + safez : 0mm + taxispeed: 40mm/s + +*RePro: RobotToFishPosition + Position: + destination : 0mm + followmidline: true + Robot setup: + xmapping: [ y, z, x ] + xinvert : true + ymapping: [ z, x, y ] + yinvert : false + zmapping: [ x, y, z ] + zinvert : false + +*RePro: SAM + General: + name: ~ + Stimulus: + duration : 400ms + pause : 100ms + freqsel : [ relative to EOD, absolute ] + deltaf : 20Hz + contrast : 20% + repeats : 0 + 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 + +*Event Detector: Spikes-1 + Detector: + minthresh: 60.9mV + decay : 1sec + ratio : 25% + testwidth: false + maxwidth : 2.0ms + Indicators: + resolution : 0.10mV + trendthresh: 10% + trendtime : 2.0sec + +*Event Detector: EOD + threshold : 3.2mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: Chirps + minthresh: 10Hz + +*Event Detector: LocalEOD-1 + threshold : 1.7mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: LocalBeat-1 + minthresh: 0.050mV + +*Event Detector: GlobalEFieldStimulus + threshold : 0.09009mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*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 : 0.38663 + 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 : 0.095324 + offset : 0 +