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