[04/2020] add juxta settings

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
 

labrotation/macros.cfg

@@ -30,6 +30,8 @@ switch macrosAlexandra.cfg
 $Carlos
 switch macrosCarlos.cfg
 
+$Ramona
+switch macrosRamona.cfg
 #$JAR
 #JAR
 

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

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_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=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=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=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=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=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=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=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=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=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=10.0%; repeats=1; plotpsd=true
 
 $Back
 switch macros.cfg

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

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
+          Weight      : 12g
-          Identifier  : "2017lepto04"
+          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
+      minspace     : 500ms
-      firstspace   : 200ms
+      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
+      deltaf  : -425Hz
-      contrast: 20%
+      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
 

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

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)
+        am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t) * 0.5
-        dc = np.sin(2*np.pi*self._dcf*t)
+        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)
+        dc = np.sin(2*np.pi*m*t*t) * 0.5
-        am = np.sin(2*np.pi*(m*t + self._eod_freq)*t)
+        am = np.sin(2*np.pi*(m*t + self._eod_freq)*t) * 0.5
-        self._zap_stimulus = np.hstack((dc, am, dc+am))
+        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()
 

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;

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"; 

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
 

torus/relacsplugins.cfg

@@ -1,24 +1,24 @@
 *Metadata
   Recording:
-      Recording quality: [ Good, ~, good, poor, Poor, Fair, Good ]
+      Recording quality: [ Fair, ~, good, poor, Poor, Fair, Good ]
-      Comment          : ~
+      Comment          : strange cell
-      Experimenter     : [ Jan Grewe, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ]
+      Experimenter     : [ Lisa Vial, Lisa Vial, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ]
-      WaterTemperature : 24.5°C
+      WaterTemperature : 23.4°C
-      WaterConductivity: 330uS/cm
+      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
+          Depth                         : 1212.3um
-          Lateral position              : -1.4mm
+          Lateral position              : -0.6mm
-          Transverse section            : 7
+          Transverse section            : 18
       Subject:
           Species     : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ]
           Gender (Sex): [ unknown, unknown, Male, Female ]
-          Size        : 17cm
+          Size        : 16.2cm
-          Weight      : 13.6g
+          Weight      : 10g
-          Identifier  : "2018lepto24"
+          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
+      reset    : true
-      resetval : 0.1
+      resetval : 0.24
-      am       : false
+      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 ]
+      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 ]
-      sigstdev : 0.25
+      name     : zap
-      duration : 20000ms
+      sigstdev : 1
+      duration : 30000ms
       pause    : 1000ms
       amplsel  : [ contrast, absolute ]
-      contrast : 20%
+      contrast : 10%
       amplitude: 1mV/cm
-      am       : true
+      am       : false
-      repeats  : 5
+      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
 

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 }');  
+  [ $DS -lt 1000 ] && echo "<h1>! Warning !</h1> <h2>Less than <b>${DS}MB</b> 
+  of free disk space left!
+  </h2> 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
+

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

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
+

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
+