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'])