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Update 'README.md'

Sebastian Bitzenhofer 1 year ago
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README.md

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 # GammaDevelopment
 
-Ephys data development P5-40
+Ephys data development P5-40
+
+Elecrophysiological data used for manuscript
+'Gamma activity accelerates during prefrontal development'
+Sebastian H. Bitzenhofer, Jastyn A. Pöpplau, Ileana L. Hanganu-Opatz
+
+
+
+------------- INFORMATION ABOUT FILES -------------
+
+
+--------------------------------------------------------
+--------------------------------------------------------
+--- ExperimentsOverview.xlsx
+
+Summary of animals, recording configurations, optogenetic stimulations, and analysis
+
+
+--------------------------------------------------------
+--------------------------------------------------------
+--- StimulationPropertiesBaselinePeriods
+
+folder structure containing .mat files for each recording (subfolders named by animalID from ExperimentsOverview.xlsx)
+
+- BaselinePeriods.mat
+cell
+contains information about period where spontaneous activity without stimulation was recorded (about 15 min)
+Information is strucutred as follows (columns) (times and samples refer to start of recording as 0 ms / sample 1)
+{1} BaslineStart (in ms)
+{2} BaselineEnd (in ms)
+{3} BaselinDuration (in minutes)
+{4} BaselinStart (in samples)
+{5} BaselinEnd (in samples)
+{6} BaselinDuration (in samples)
+{7} SamplingRate (in samples per s)
+
+- StimulationProperties.mat
+cell
+contains information about optogenetic stimulations
+Further information (Laser power, wavelength, ...) about type of stimulation can be found in ExperimentsOverview.xlsx
+Each row represents one stimulation
+Information is strucutred as follows (columns) (times and samples refer to start of recording as 0 ms / sample 1)
+{1} StimulationStart (in ms)
+{2} StimulationEnd (in ms)
+{3} StimulationDuration (in s)
+{4} Number of pulses (1 for ramp stimulation)
+{5} Duration per pulse (in ms)
+{6} Pulse frequency (in Hz)
+{7} Laser power (set manually on device for ramp stimulations, see inforamtion in ExperimentsOverview.xlsx)
+{8} Type of stimulation
+{9} Start of individual pulses (in ms)
+{10} StimulationStart (in samples)
+{11} StimulationEnd (in samples)
+{12} tart of individual pulses (in samples)
+
+
+--------------------------------------------------------
+--------------------------------------------------------
+--- LFPdata
+
+folder structure containing local field potential data segments in subfolders RampStimulation and Baseline with .mat files for each recording (subsubfolders named by animalID from ExperimentsOverview.xlsx)
+
+-- Baseline_LFP.mat
+contains LFP data from baseline period of spontaneous activity (without stimulation) for all recording sites (see ExperimentsOverview.xlsx for area)
+- LFP, int16, contains LFP data for baseline period in microvolts (-10 to 0 min from BaselinEnd). Data is filtered 1 to 100 Hz and downsampled to fs=200 Hz
+- fs, double, contains downsampled sampling frequency (200 Hz)
+
+-- AcuteStim1_LFP.mat
+contains LFP data from 30 repetitions of ramp light stimulations (AcuteStim1, 473 nm) for all recording sites (see ExperimentsOverview.xlsx for area and stimulation info)
+- LFP, int16, contains LFP data for stimulation periods in microvolts (-6 to 3 s from StimulationEnd). Data is filtered 1 to 100 Hz and downsampled to fs=200 Hz
+- fs, double, contains downsampled sampling frequency (200 Hz)
+
+- AcuteStim2_LFP.mat
+contains LFP data from 30 repetitions of control ramp light stimulations (AcuteStim2, 594 nm) for all recording sites (see ExperimentsOverview.xlsx for area and stimulation info)
+LFP contains LFP data for stimulation periods (-6 to 3 s from StimulationEnd). Data is filtered 1 to 100 Hz and downsampled to fs=200 Hz
+fs contains downsampled sampling frequency (200 Hz)
+
+
+--------------------------------------------------------
+--------------------------------------------------------
+--- sp.mat
+
+structure
+single unit data for 3554 single units
+
+- sp.st
+cell
+spike times per single unit in samples (sampling rate 32000 Hz)
+(times and samples refer to start of recording as sample 1)
+
+- sp.Nexp
+double
+experiment number per single unit (see column B in file ExperimentsOverview.xlsx)
+
+- sp.area
+double
+area per single unit
+1, for sp.peakchannel 17:20, ipsilateral mPFC hemisphere to stimulation, shank 1 (most medial)
+2, for sp.peakchannel 21:24, ipsilateral mPFC hemisphere to stimulation, shank 2
+3, for sp.peakchannel 25:28, ipsilateral mPFC hemisphere to stimulation, shank 3
+4, for sp.peakchannel 29:32, ipsilateral mPFC hemisphere to stimulation, shank 4 (most lateral)
+5, for sp.peakchannel 1:4, contralateral mPFC hemisphere to stimulation, shank 1 (most medial)
+6, for sp.peakchannel 5:8, contralateral mPFC hemisphere to stimulation, shank 2
+7, for sp.peakchannel 9:12, contralateral mPFC hemisphere to stimulation, shank 3
+8, for sp.peakchannel 13:16, contralateral mPFC hemisphere to stimulation, shank 4 (most lateral)
+
+- sp.peakchannel
+double
+peak channel (recording site) per single unit
+
+- sp.wf
+double
+average waveform per single unit (97 samples per single unit centered around negative peak, sampling rate 32000 Hz)
+
+- sp.age
+double
+age of recorded mouse per single unit
+
+-sp.FS
+logical
+0 if regular spiking 1 if fast spiking
+per single unit