from jaratoolbox.test.nick.database import cellDB
'''Recording from thalamus with dii on the electrodes. There are some channels that look
like they are fused.
On TT5, channels 0 and 1 look fused
on TT6, channels 0 and 2 look fused
'''
thal = cellDB.Experiment()
site1 = thal.add_site(depth=3454, tetrodes=[6])
site1.add_session('12-54-32', None, 'noiseburst') # Onset responses only
site1.add_session('12-57-25', None, 'laserpulse') #1.5mW
site1.add_session('13-00-05', 'a', 'AM') #interesting tuning, possible tuning
site1.add_session('13-26-17', 'b', 'tuningCurve') #60db only
site2 = thal.add_site(depth=3603, tetrodes=[6])
site2.add_session('13-35-39', 'c', 'AM')
site2.add_session('13-56-00', 'd', 'tuningCurve') #60dB obly
site3 = thal.add_site(depth=3902, tetrodes=[4, 5, 6])
site3.add_session('14-12-11', None,
'noisebursts') #Good sound responses - 4 is funky
site3.add_session('14-14-59', None, 'laserpulse')
site3.add_session('14-17-26', None, 'lasertrain') #Some direct activation
site3.add_session('14-20-50', 'e', 'AM')
site3.add_session('14-41-15', None, 'laserpulse2')
site3.add_session('14-43-25', None, 'lasertrain2')
site3.add_session('14-47-05', 'f', 'tuningCurve') #Full TC
from jaratoolbox.test.lan.Ephys import sitefuncs_vlan as sitefuncs
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
exp0910 = cellDB.Experiment(animalName='d1pi004',
date='2015-09-10',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
site1 = exp0910.add_site(depth=3040, tetrodes=range(
1, 9)) #not laser-responsive, TT7 weakly sound-responsive
site1.add_session('16-04-48', None, sessionTypes['nb']) #amp=0.1
site1.add_session('16-13-01', None, sessionTypes['lp']) #1mW,10ms
site1.add_session('16-17-28', None, sessionTypes['lp']) #1mW, 30ms
site1.add_session('16-19-33', None, sessionTypes['lt']) #1mW
site1.add_session(
'16-23-12', 'a', sessionTypes['2afc'], paradigm='2afc'
) #need to specific paradigm to overwrite the default since it's a different paradigm
site1.add_session('18-00-49', None, sessionTypes['lp']) #1mW,50ms
site1.add_session('18-03-18', None, sessionTypes['nb']) #amp=0.15
#sitefuncs.nick_lan_daily_report_short(site1, 'site1', mainRasterInds=[0,1,2,3])
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
exp = cellDB.Experiment(animalName='adap012',
date='2016-02-07',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
site1 = exp.add_site(depth=2420, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('15-01-59', None, sessionTypes['nb']) #amp=0.1
site1.add_session('15-03-52', 'a', sessionTypes['tc']) #2-40Hz chords, 50dB
site1.add_session('15-10-08', 'b', sessionTypes['tc'])
site1.add_session('15-18-13', 'c', sessionTypes['tc'])
site1.add_session('15-23-48', 'a', sessionTypes['2afc'], paradigm='2afc')
#sitefuncs.nick_lan_daily_report(site1, 'site1', mainRasterInds=[0,2,3], mainTCind=1, mainSTRind=1)
#sitefuncs.lan_2afc_ephys_plots(site1, 'site1', main2afcind=3, tetrodes=[1,2,3,5,8])
#sitefuncs.lan_2afc_ephys_plots_each_type(site1, 'site1', main2afcind=4, tetrodes=[1,2,3,4,5,6,7,8],trialLimit=[])
#sitefuncs.lan_2afc_ephys_plots_each_block_each_type(site1, 'site1', main2afcind=5, tetrodes=[3,5],trialLimit=[],choiceSide='both')
sitefuncs.lan_2afc_ephys_plots_each_block_each_type(
site1,
from jaratoolbox.test.nick.database import cellDB
reload(cellDB)
from jaratoolbox.test.lan.Ephys import sitefuncs_vlan as sitefuncs
reload(sitefuncs)
sessionTypes = {'nb':'noiseBurst',
'lp':'laserPulse',
'lt':'laserTrain',
'tc':'tuningCurve',
'bf':'bestFreq',
'3p':'3mWpulse',
'1p':'1mWpulse',
'2afc':'2afc'}
exp = cellDB.Experiment(animalName='d1pi003', date ='2016-01-29', experimenter='lan', defaultParadigm='laser_tuning_curve')
site1 = exp.add_site(depth=2640, tetrodes=[1,2,3,4,5,6,7,8]) #TT5 is ref
site1.add_session('11-19-10', None, sessionTypes['nb']) #amp=0.15
site1.add_session('11-21-31', None, sessionTypes['lp']) #power=1mW
site1.add_session('11-23-15', None, sessionTypes['lt']) #power=1mW
site1.add_session('11-25-19', 'a', sessionTypes['tc']) #2-40Hz chords, 50dB
site1.add_session('11-32-32', 'a', sessionTypes['2afc'], paradigm='2afc')
site1.add_session('13-03-48', None, sessionTypes['lp']) #power=1mW
#sitefuncs.nick_lan_daily_report(site1, 'site1', mainRasterInds=[0,1,2,5], mainTCind=3, mainSTRind=3)
#sitefuncs.lan_2afc_ephys_plots(site1, 'site1', main2afcind=3, tetrodes=[1,2,3,5,8])
sitefuncs.lan_2afc_ephys_plots_each_type(site1, 'site1', main2afcind=4, tetrodes=[1,2,3,4,5,6,7,8],trialLimit=[])
#sitefuncs.lan_2afc_ephys_plots_each_block_each_type(site1, 'site1', main2afcind=5, tetrodes=[3,5],trialLimit=[],choiceSide='both')
#sitefuncs.lan_2afc_ephys_plots_each_block_each_type(site1, 'site1', main2afcind=4, tetrodes=[1,3,4,5,6,7],trialLimit=[],choiceSide='left')
#sitefuncs.lan_2afc_ephys_plots_each_block_each_type(site1, 'site1', main2afcind=4, tetrodes=[1,3,4,5,6,7],trialLimit=[],choiceSide='right')
reload(cellDB)
#The session types to use for this kind of experiment
#Can use a dict like this or simply write the sesison types directly
#I used this to avoid typing errors and to save time
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tc_heatmap',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse'
}
today = cellDB.Experiment('pinp003', '2015-06-24', 'nick',
'laser_tuning_curve')
# dbFn='/home/nick/data/database/nick_thalamus_cells.json'
dbFn = '/home/nick/data/database/pinp003_thalamus_cells.json'
db = cellDB.CellDB()
gc = []
site1 = today.add_site(depth=3543, tetrodes=[6])
site1.add_session('15-22-29', None, sessionTypes['nb'])
site1.add_session('15-25-08', None, sessionTypes['lp'])
site1.add_session('15-27-37', None, sessionTypes['lt'])
site1.add_session('15-31-48', 'a', sessionTypes['tc'])
site1.add_session('15-45-22', 'b', sessionTypes['bf'])
5: [222, 197, 243, 184],
6: [194, 399, 331, 239]
}
laser_calib = {1: 1.95, 1.5: 2.2, 2: 2.45, 2.5: 2.75, 3: 3.0, 3.5: 3.2}
'''
Noisetest - 2015-08-12_10-23-47 = laser pulse 1mW (no ref LFP/Spikes, spike thresh=0mV)
10-26-03: Laser 2mW
10-28-13: Laser 3mW
'''
'''
THALAMUS RECORDING
1054hrs - mouse on rig with electrodes at 1002um - waiting for 10 mins
'''
from jaratoolbox.test.nick.database import cellDB
rd = cellDB.Experiment('pinp005', '2015-08-12', 'nick', 'laser_tuning_curve')
'''
Lots of spikes on T3 around 2700um
1113hrs - letting the electrodes rest at 3000um for 5 mins.
'''
site1 = rd.add_site(depth=3833, tetrodes=[3, 4])
site1.add_session('11-34-42', None, 'NoiseBurst')
site1.add_session('11-37-03', None,
'LaserPulse') #2.5mW - strong onset response
site1.add_session('11-42-57', None,
'LaserPulseLowerPower') #1.5mW - Still onset response
site1.add_session('11-45-32', None,
'LaserPulseHigherPower') #3.5mW - Still onset response
site1.add_session('11-48-13', None, 'LaserTrain') #2.5m
site1.add_session('11-52-04', 'a', 'TuningCurve') #20-70dB
1555 - 1009um, many spikes on TT4
1556 - 1150um, more large spikes
1557 - 1445um, more large spikes
1558 - 1618um, spikes on TT4 are gone
1601 - 2000um, waiting for things to settle before moving on.
1645 - 3000um, no sound or laser responses. Waiting for a few mins before moving on.
'''
from jaratoolbox.test.nick.database import cellDB
rd = cellDB.Experiment('pinp007', '2015-11-18', 'nick', 'more_sounds_tuning')
site1 = rd.add_site(depth=3100, tetrodes=[3, 4, 5, 6])
site1.add_session(
'16-56-20', None,
'NoiseBurst') #Amplitude at 0.02, onset and offset responses on TT4
site1.add_session(
'16-59-10', None, 'LaserPulse'
) #Paradigm=laser_tuning_curve, 1mW - Responds but is then inhibited, TT4
site1.add_session('17-02-10', None,
'LaserTrain') #Paradigm=laser_tuning_curve, 1mW -
site1.add_session('17-07-37', 'a', 'AM') # Cool offset responses
site2 = rd.add_site(depth=3300, tetrodes=[3, 4, 5, 6])
site2.add_session('17-52-33', None, 'NoiseBurst') #Amplitude at 0.02,
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
badSessionList = [] #prints bad sessions at end
exp = cellDB.Experiment(animalName='test053',
date='2015-05-11',
experimenter='billy',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=1.00, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('17-06-28', 'a', sessionTypes['tc'])
site1.add_session('17-16-31', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
except:
badSessionList.append(exp.date)
exp = cellDB.Experiment(animalName='test053',
date='2015-05-12',
experimenter='billy',
from jaratoolbox.test.lan.Ephys import sitefuncs_vlan as sitefuncs
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
exp = cellDB.Experiment(animalName='adap015',
date='2016-02-04',
experimenter='billy',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.250, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('15-30-47', 'a', sessionTypes['tc'])
site1.add_session('15-41-31', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
exp = cellDB.Experiment(animalName='adap015',
date='2016-02-07',
experimenter='billy',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.375, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('15-16-27', 'a', sessionTypes['tc'])
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
exp = cellDB.Experiment(animalName='adap012',
date='2016-03-23',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
site1 = exp.add_site(depth=2940, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('12-47-28', None, sessionTypes['nb']) #amp=0.1
site1.add_session('12-49-37', 'a', sessionTypes['tc']) #2-40Hz chords, 50dB
site1.add_session('12-57-54', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=[0],
mainTCind=1)
#sitefuncs.lan_2afc_ephys_plots_each_type(site1, 'site1', main2afcind=2, tetrodes=[1,2,3,4,5,6,7,8],trialLimit=[])
#sitefuncs.lan_2afc_ephys_plots_each_block_each_type(site1, 'site1', main2afcind=2, tetrodes=[1,2,3,4,5,6,7,8],trialLimit=[],choiceSide='left')
#sitefuncs.lan_2afc_ephys_plots_each_block_each_type(site1, 'site1', main2afcind=2, tetrodes=[1,2,3,4,5,6,7,8],trialLimit=[],choiceSide='right')
1349 - 1171um - quiet
1353 - 1680um - lots of spikes on TT4, 5, 6
1354 - 1820um - probably through CA1
1406 - 2989 - had many spikes, just got quiet again - waiting for 5 mins
1418 - 3117um - good laser responses on TT4 but no sound responses yet
'''
from jaratoolbox.test.nick.database import cellDB
rd = cellDB.Experiment('pinp007', '2015-11-25', 'nick', 'am_tuning')
site1 = rd.add_site(depth=3750, goodTetrodes=[3, 4, 5, 6])
site1.add_session('14-44-56', None, 'NoiseBurst') #
site1.add_session('14-48-12', None, 'LaserPulse') #
site1.add_session('14-51-18', None, 'LaserTrain') #
site1.add_session('15-07-13', 'a', 'AM') #
'''
2mw - 15-40-02
1mw - 15-43-38
0.5mw - 15-46-52
less -
05mW, 0.1sec soa -
16-08-30 0.05sec soa, all the responses blend together
site1.add_session('15-18-46', 'a', sessionTypes['tc'])
site1.add_session('15-45-00', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
exp = cellDB.Experiment(animalName='adap017', date ='2016-04-04', experimenter='billy', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.50, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('16-46-52', 'a', sessionTypes['tc'])
site1.add_session('16-57-16', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
exp = cellDB.Experiment(animalName='adap017', date ='2016-04-06', experimenter='billy', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.625, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('17-25-26', 'a', sessionTypes['tc'])
site1.add_session('17-36-02', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
'''
exp = cellDB.Experiment(animalName='adap017',
date='2016-04-08',
experimenter='billy',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.75, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('18-32-00', 'a', sessionTypes['tc'])
site1.add_session('18-49-50', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
}
'''
exp = cellDB.Experiment(animalName='test059', date ='2015-06-17', experimenter='billy', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.00, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('21-15-19', 'a', sessionTypes['tc'])
site1.add_session('21-36-38', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
exp = cellDB.Experiment(animalName='test059', date ='2015-06-18', experimenter='billy', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.00, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('14-19-46', 'a', sessionTypes['tc'])
site1.add_session('14-41-21', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
'''
exp = cellDB.Experiment(animalName='test059',
date='2015-06-19',
experimenter='billy',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.00, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('13-49-41', 'a', sessionTypes['tc'])
site1.add_session('14-05-19', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
'''
exp = cellDB.Experiment(animalName='test059', date ='2015-06-22', experimenter='billy', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.125, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('15-01-08', 'a', sessionTypes['tc'])
site1.add_session('15-21-02', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
site1.add_session('16-32-35', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
exp = cellDB.Experiment(animalName='adap015', date ='2016-02-10', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.625, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('16-12-03', 'a', sessionTypes['tc'])
site1.add_session('16-21-25', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
except:
badSessionList.append(exp.date)
'''
#CLUSTERING CRASH: CANNOT ALLOCATE MEMORY
exp = cellDB.Experiment(animalName='adap015',
date='2016-02-12',
experimenter='',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.75, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('09-41-26', 'a', sessionTypes['tc'])
site1.add_session('09-50-06', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
'''
exp = cellDB.Experiment(animalName='adap015', date ='2016-02-16', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.875, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('14-07-20', 'a', sessionTypes['tc'])
site1.add_session('14-16-04', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
badSessionList = [] #prints bad sessions at end
exp = cellDB.Experiment(animalName='test055',
date='2015-02-20',
experimenter='',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=4.5, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('11-32-33', 'a', sessionTypes['tc'])
site1.add_session('11-42-48', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
exp = cellDB.Experiment(animalName='test055',
date='2015-02-21',
experimenter='',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=4.5, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('18-29-58', 'a', sessionTypes['tc'])
exp = cellDB.Experiment(animalName='test089', date ='2015-08-19', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.25, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('12-44-48', 'a', sessionTypes['tc'])
site1.add_session('12-53-30', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
exp = cellDB.Experiment(animalName='test089', date ='2015-08-20', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.25, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('12-39-56', 'a', sessionTypes['tc'])
site1.add_session('12-51-26', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
'''
#################SAYS THERE IS SOME MISALIGNMENT IN THIS TRIAL (411 IS OUT OF BOUNDS FOR AXIS 1 WITH SIZE 411)
exp = cellDB.Experiment(animalName='test089',
date='2015-08-21',
experimenter='',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.25, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('16-42-06', 'a', sessionTypes['tc'])
site1.add_session('16-54-19', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
'''
exp = cellDB.Experiment(animalName='test089', date ='2015-08-27', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.25, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('11-47-43', 'a', sessionTypes['tc'])
site1.add_session('11-56-32', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
reload(cellDB)
from jaratoolbox.test.nick.database import sitefuncs
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse'
}
exp0814 = cellDB.Experiment(animalName='d1pi002',
date='2015-08-14',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
#First penetration
'''
site1 = exp0814.add_site(depth = 2000, tetrodes = [6]) #cortical laser response?
site1.add_session('13-40-57', None, sessionTypes['lp']) #comment ='power=2mW'
site1.add_session('13-49-20', None, sessionTypes['lt']) #comment ='power=2mW'
site1.add_session('13-52-45', None, sessionTypes['nb']) #no response
sitefuncs.nick_lan_daily_report(site1, 'site1', mainRasterInds=[0, 1, 2], mainTCind= None)
'''
site2 = exp0814.add_site(
depth=3500,
tetrodes=[3, 6]) #TT6 long-lasting laser inhibition; TT3 sound-inhibited?
try:
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
except:
badSessionList.append(exp.date)
exp = cellDB.Experiment(animalName='adap013', date ='2016-03-19', experimenter='billy', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.125, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('16-21-54', 'a', sessionTypes['tc'])
site1.add_session('16-30-36', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
except:
badSessionList.append(exp.date)
'''
exp = cellDB.Experiment(animalName='adap013',
date='2016-03-22',
experimenter='billy',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.375, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('13-17-21', 'a', sessionTypes['tc'])
site1.add_session('13-32-19', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
except:
badSessionList.append(exp.date)
exp = cellDB.Experiment(animalName='adap013',
date='2016-03-24',
experimenter='billy',
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tcHeatmap',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse'
}
# ----------------------
##Adding an experiment, a site, and some sessions
# ----------------------
day1 = cellDB.Experiment(animalName='pinp003',
date='2015-06-24',
experimenter='nick',
defaultParadigm='laser_tuning_curve')
d1site1 = day1.add_site(depth=3543, tetrodes=[6])
d1site1.add_session('15-22-29', None, sessionTypes['nb'])
d1site1.add_session('15-27-37', None, sessionTypes['lt'])
d1site1.add_session('15-31-48', 'a', sessionTypes['tc'])
d1site1.add_session('15-45-22', 'b', sessionTypes['bf'])
###Test of sitefunc for plotting the main report Lan and I use
#sitefuncs.nick_lan_daily_report(d1site1, 'site1', mainRasterInds=[0, 1, 3], mainTCind= 2)
#Choosing good clusters for this site
d1site1.add_clusters({6: [5, 8, 11]})
# ----------------------
from jaratoolbox.test.nick.database import cellDB
rec = cellDB.Experiment('pinp013', '2016-05-25', '', 'am_tuning_curve')
site1 = rec.add_site(depth=3011, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('14-32-32', None, 'Noiseburst')
site1.add_session('14-37-43', None, 'NoiseburstRefT8')
site1.add_session('14-41-52', 'a', 'TuningCurve')
site1.add_session('14-56-38', 'b', 'AM')
site2 = rec.add_site(depth=3011, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site2.add_session('15-18-46', None, 'Noiseburst')
site2.add_session('15-22-29', 'c', 'TuningCurve')
site2.add_session('15-35-27', 'd', 'AM')
site3 = rec.add_site(depth=3300, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site3.add_session('15-56-32', None, 'Noiseburst') #Sweet offset responses
site3.add_session('16-02-29', None,
'Noiseburst_again') #after resting more time .
site3.add_session('16-04-59', 'e', 'TuningCurve')
site3.add_session('16-21-45', 'f', 'AM')
from jaratoolbox.test.nick.database import sitefuncs
sitefuncs.nick_lan_daily_report(site1,
'site1_PCA_Report',
mainRasterInds=[0, 1],
mainTCind=2)
sitefuncs.nick_lan_daily_report(site2,
'site2_PCA_Report',
mainRasterInds=[0],
mainTCind=1)
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'str': 'sortedTuningRaster',
'ls': 'lasersounds'
}
exp0918 = cellDB.Experiment(animalName='arch003',
date='2015-09-18',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
'''
site1 = exp0918.add_site(depth = 2200, tetrodes = [3,4])
site1.add_session('12-41-22', None, sessionTypes['nb']) #amp=0.1
site1.add_session('12-43-56', None, sessionTypes['lp']) #2mW,50ms
site1.add_session('12-46-49', None, sessionTypes['lp']) #2mW,100ms
site1.add_session('12-48-29', None, sessionTypes['nb']) #amp=0.2
sitefuncs.nick_lan_daily_report(site1, 'site1', mainRasterInds=[0,1,2,3], mainTCind=None, mainSTRind=None)
site2 = exp0918.add_site(depth = 2300, tetrodes = [3,4])
site2.add_session('12-52-15', None, sessionTypes['nb'])
site2.add_session('12-54-29', None, sessionTypes['lp']) #2mW
site2.add_session('12-57-34', 'a', sessionTypes['ls'], paradigm='lasersounds') #2mW, laser front&back overhang=0.05s, ITI=1.5s
exp = cellDB.Experiment(animalName='adap020', date ='2016-04-19', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.50, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('11-00-55', 'a', sessionTypes['tc'])
site1.add_session('11-10-14', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
exp = cellDB.Experiment(animalName='adap020', date ='2016-04-20', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.625, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('13-33-22', 'a', sessionTypes['tc'])
site1.add_session('13-51-59', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
'''
#CLUSTERING CRASH: MEMORYERROR
exp = cellDB.Experiment(animalName='adap020',
date='2016-04-21',
experimenter='',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.625, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('13-02-10', 'a', sessionTypes['tc'])
site1.add_session('13-19-14', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
'''
exp = cellDB.Experiment(animalName='adap020', date ='2016-04-22', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=2.75, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('17-19-38', 'a', sessionTypes['tc'])
site1.add_session('17-28-59', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
from jaratest.lan.Ephys import sitefuncs_vlan as sitefuncs
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
exp = cellDB.Experiment(animalName='adap005',
date='2015-12-21',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
site1 = exp.add_site(depth=2520, tetrodes=[7, 8])
site1.add_session('16-34-14', None, sessionTypes['nb']) #amp=0.15
site1.add_session('16-36-48', 'a', sessionTypes['tc']) #2-40Hz chords, 50dB
site1.add_session('16-46-41', 'b', sessionTypes['tc']) #6.6&12.1kHz,50dB
site1.add_session('16-50-58', 'a', sessionTypes['2afc'], paradigm='2afc')
sitefuncs.nick_lan_daily_report(site1,
'site1',
mainRasterInds=[0],
mainTCind=1,
mainSTRind=1)
#sitefuncs.lan_2afc_ephys_plots(site1, 'site1', main2afcind=3, tetrodes=[1,2,3,4,5,6,7,8])
sitefuncs.lan_2afc_ephys_plots_each_type(site1,
'site1',
676um - spikes on TT5, sound like they respond ot the light.
806um - large spikes TT5 respond to flashlight
1482um - giant spikes TT5, hippocampus probably
2000um, letting the brain rest for 5 mins
'''
from jaratoolbox.test.nick.database import cellDB
rd = cellDB.Experiment('pinp008', '2016-01-08', 'nick', 'am_tuning_curve')
site1 = rd.add_site(depth=3100, goodTetrodes=[5])
site1.add_session('20-19-40', 'nb1', 'NoiseBurst') #
site1.add_session('20-22-29', 'lp1', 'LaserPulse') #1mW No laser response
#Also tried 1.5mW, no laser response. Moving on
site2 = rd.add_site(depth=3402, goodTetrodes=[5, 6])
site2.add_session(
'20-51-44', 'nb2', 'NoiseBurst'
) # Not much of a response on TT5, good response on 6 - response on 5 my be masked by noise
site2.add_session('20-54-35', 'lp2', 'LaserPulse') #1.5mW - good response
site2.add_session('20-57-23', 'lt2', 'LaserTrain') #1.5mW - good response
site2.add_session('21-00-29', 'am2', 'AM') #
#Some changes during the recording possible, but still really nice responses
site2.add_session('21-28-12', 'tc2', 'tuningCurve') #Tuning around 6
from jaratest.lan.Ephys import sitefuncs_vlan as sitefuncs
reload(sitefuncs)
sessionTypes = {
'nb': 'noiseBurst',
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'str': 'sortedTuningRaster'
}
exp1004 = cellDB.Experiment(animalName='d1pi007',
date='2015-10-04',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
site1 = exp1004.add_site(depth=2650, tetrodes=[3])
site1.add_session('15-52-02', None, sessionTypes['nb']) #amp=0.3
site1.add_session('15-54-32', None, sessionTypes['nb']) #amp=0.15
site1.add_session('15-56-36', None, sessionTypes['lp'])
site1.add_session('15-57-56', None, sessionTypes['lt'])
site1.add_session('15-59-39', 'a', sessionTypes['tc'])
site1.add_session('16-14-01', 'b', sessionTypes['str'])
sitefuncs.nick_lan_daily_report(site1,
'site1',
mainRasterInds=[0, 1, 2, 3],
mainTCind=4,
mainSTRind=5)
'lp': 'laserPulse',
'lt': 'laserTrain',
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse'
}
# dbFn='/home/nick/data/database/nick_thalamus_cells.json'
dbFn = '/home/nick/data/database/pinp003_thalamus_cells.json'
db = cellDB.CellDB()
db.load_from_json(dbFn)
gc = []
rd = cellDB.Experiment('pinp003', '2015-07-06', 'nick', 'laser_tuning_curve')
site1 = rd.add_site(depth=3509, tetrodes=[3, 6])
site1.add_session('11-15-56', None, sessionTypes['nb'])
site1.add_session('11-18-36', None, sessionTypes['lp'])
site1.add_session('11-21-26', None, sessionTypes['lt'])
site1.add_session('11-25-58', 'a', sessionTypes['tc'])
site1.add_session('11-39-46', None, sessionTypes['bf'])
site1.add_session('11-42-37', None, sessionTypes['3p'])
site1.add_session('11-45-22', None, sessionTypes['1p'])
gc.append(sitefuncs.find_good_clusters(site1, 'site1', soundInd=0, laserInd=1))
site2 = rd.add_site(depth=3550, tetrodes=[3, 6])
site2.add_session('11-51-47', None, sessionTypes['nb'])
site2.add_session('11-54-51', None, sessionTypes['lp'])
941um - spikes on TT4 that are responsive to the flashlight
tons of spiking activity around 1100-1200um
lots of spikes around 1600um
'''
from jaratoolbox.test.nick.database import cellDB
rd = cellDB.Experiment('pinp009',
'2016-01-27',
experimenter='nick',
defaultParadigm='am_tuning_curve')
site1 = rd.add_site(depth=2935, tetrodes=[6])
site1.add_session('13-22-56', 'nb1', 'noiseburst') # Excellent sound response
site1.add_session('13-26-20', 'lp1',
'laserpulse') # No laser response, moving on..
site1.add_session('13-38-38', 'a', 'tuningCurve') # 16 freqs at 60db
site1.add_session('13-44-58', 'b', 'AM') # Not very synchronized
site1.add_session('14-05-28', 'lp2', 'laserpulse2') #No laser response
'''
Hunting for laser response.
at 3550um the responses change drastically, large fast spikes with no more sound response
I am removing the electrodes and letting the mouse rest.
'tc': 'tuningCurve',
'bf': 'bestFreq',
'3p': '3mWpulse',
'1p': '1mWpulse',
'2afc': '2afc'
}
expList = []
soundResponsiveCellCount = 0
laserResponsiveCellCount = 0
soundnlaserResponsiveCellCount = 0
soundResponsiveTuned = 0
###################Add all experiments that had good cells; recluster data using updated features, plot report for all clusters of the site, then pick out good clusters##############################
exp0701 = cellDB.Experiment(animalName='d1pi001',
date='2015-07-01',
experimenter='lan',
defaultParadigm='laser_tuning_curve')
expList.append(exp0701)
site3 = exp0701.add_site(depth=2710, tetrodes=[6])
site3.add_session('19-09-42', None, sessionTypes['nb'])
site3.add_session('19-13-36', None, sessionTypes['lp'])
site3.add_session('19-16-32', None, sessionTypes['lt'])
site3.add_session('19-23-35', None, sessionTypes['1p'])
site3.add_session('19-30-41', 'c', sessionTypes['tc'])
cluster2 = site3.add_cluster(
cluster=2, tetrode=6
) #soundResponsive=True, laserPulseResponse=False, followsLaserTrain=False, comments='fair cell, no obvious tuning')
cluster3 = site3.add_cluster(
cluster=3, tetrode=6
) #soundResponsive=True, laserPulseResponse=False, followsLaserTrain=False, comments = 'tuned')
3.5:2.8}
'''
Running regular tuning curve with the electrodes not in saline.
file = noisetest/2015-08-10_10-13-55
behav = 'a'
at 1339 um we have a sound responsive site with (several?) large neurons. I am waiting a few mins for stability and then I will start recording
'''
from jaratoolbox.test.nick.database import cellDB as db
from jaratoolbox.test.nick.database import sitefuncs
rd = db.Experiment('pinp005', '2015-08-10', 'nick', 'laser_tuning_curve')
site1 = rd.add_site(depth = 1399, tetrodes = [3, 6])
site1.add_session('11-33-40', None, 'NoiseBurst') #Ref channel 19
site1.add_session('11-37-15', None, 'LaserPulse') #Good laser responses T3 and T6
site1.add_session('11-39-34', None, 'LaserTrain') #Ref channel 19
site1.add_session('11-43-28', 'a', 'TuningCurve') #30-60dB 16freqs
site1.add_session('11-56-52', 'b', 'auxTuningCurve') #adding trials at 20dB and 70dB
site1.add_session('12-03-03', 'c', 'bestfreq') #7000-8000, 60db, 100 trials
#sitefuncs.nick_lan_daily_report(site1, 'site1', mainRasterInds = [0, 1, 2, 5], mainTCind=3)
site2 = rd.add_site(depth = 1491, tetrodes = [3, 5, 6]) #Ref channel 14
badSessionList = [] #prints bad sessions at end
'''
exp = cellDB.Experiment(animalName='test017', date ='2015-02-21', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=3.5, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('20-01-33', 'a', sessionTypes['tc'])
site1.add_session('20-08-51', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1, 'site1', mainRasterInds=None, mainTCind=0)
except:
badSessionList.append(exp.date)
'''
#SOMETHING WENT WRONG WHILE CLUSTERING
exp = cellDB.Experiment(animalName='test017',
date='2015-02-23',
experimenter='',
defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=4.00, tetrodes=[1, 2, 3, 4, 5, 6, 7, 8])
site1.add_session('15-16-40', 'a', sessionTypes['tc'])
site1.add_session('15-31-40', 'a', sessionTypes['2afc'], paradigm='2afc')
try:
sitefuncs.nick_lan_daily_report_v2(site1,
'site1',
mainRasterInds=None,
mainTCind=0)
except:
badSessionList.append(exp.date)
'''
exp = cellDB.Experiment(animalName='test017', date ='2015-02-25', experimenter='', defaultParadigm='tuning_curve')
site1 = exp.add_site(depth=4.5, tetrodes=[1,2,3,4,5,6,7,8])
site1.add_session('13-54-31', 'a', sessionTypes['tc'])
