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spike_analysis_pipeline:intermediate_output

Interactions with other pipelines

because spike_analysis incorporates the sorted_neurons table (f.e. unit_IDs and site_IDs) into behavior and ephys data, it is used as a first step in all ephys analysis.

Outputs in Y:\Projects\project\ephys\version:

File Info
population_monkey_session.mat spike data sorted by unit for each session
sites_monkey_session.mat LFP data sorted by site for each session
by_block_monkey_session.mat body signals sorted by block for each session
Mon_sorted_neurons.xls copies of the used sorted neurons tables from dropbox
keys_Monkey.mat copy of the keys used when running ph_initiation
tuning_table_combined.mat Anova results stored in a table
tuning_table_combined_CI.mat Anova results restructured according to contra/ipsi definitions
tuning_table_combined.xls simplified excel table
spike_shapes Spike shapes, firing rates over time, and ISI plots for re-assessing spike sorting

The three main files come in a specific data structure, which contain the same fields except for the respective data:

  • by_block(body signals) - only trial information and body signals
  • sites (LFP) - additional site information and LFP, no body signals
  • population (spikes) - additional unit information and spike_arrival times, no LFP, no body signals

Trial structure subfields (By_block files)

to be removed:

                     cue_pos: NaN
                   cue_shape: NaN
                 all_tar_pos: [2x1 double]
                     col_dim: [2x3 double]
                     col_bri: [2x3 double]
Condition infoFormatInfo
typescalar from data
effectorscalar from data
reach_handscalar from data
choicescalar from data
successscalar from data
completedscalar from data
correct_targetsscalar from data
target_selectedscalar from data
n_nondistractorsscalar from data
n_distractorsscalar from data
difficultyscalar from data
stimuli_in_2hemifieldsscalar from data
perturbationscalar using perturbation_groups key ??
datasetscalar Dataset from sorted_neurons (only in spikes so far ??)
Timing infoFormatInfo
datescalar from data
blockscalar from data
runscalar from data
nscalar from data
trial_onset_timescalar from data
run_onset_timescalar from data
statesarray array of events marked in this trial
states_onsetarray [s] corresponding onset times (relative to state 2)
Spatial infoFormatInfo
fix_poscomplex x is real, y is imaginary (already preprocessed?)
tar_poscomplex x is real, y is imaginary
stm_poscomplex x is real, y is imaginary
Response infoFormatInfo
rea_offcomplex x is real, y is imaginary
sac_offcomplex x is real, y is imaginary
sac_latscalar Saccade RT (in seconds)
rea_latscalar Reach RT (in seconds)
Specific data FormatInfo
TDT_ECG1array Body signal Data (ECG1,CAP1,POX1)
TDT_ECG1_SRscalar Sampling rate
TDT_ECG1_t0_from_rec_startscalar state 2 onset relative to start of the recording (block?)
TDT_ECG1_tStartscalar (usually negative) how much of the stream is before state 2 - due to shift!!
LFParray LFP data, not called TDT_LFPx any more, but SR,t0,andtStart are…
arrival_timesarray in seconds, relative to this trial's state 2
FR_averagescalar average firing rate for this unit in this trial
acceptedscalar trial accepted for this unit
FRscalar ??
stability_ratingscalar why is this here ??

Additional Site files fields

FieldnameExampleInfo
site_ID'Bac_20210706_Site_01 as assigned in sorted_neurons, in population files this is the corresponding site for this unit
target'dPul_R' recording target from sorted_neurons
perturbation_site'NA' perturbation target from sorted_neurons
grid_x3 grid location from sorted_neurons
grid_y-4.5 grid location from sorted_neurons
electrode_depth45 Aimed_electrode_depth from sorted_neurons
monkey'Bacchus_phys' as assigned in sorted_neurons (?)

Additional Population file fields

FieldnameExampleInfo
unit_ID 'Bac_20210706_01' as assigned in sorted_neurons
channel2 channel the unit was recorded in
block_unit{3×1 cell} which cluster in which block are combined in this unit
SNR_rating2 SNR rating (either from sorted_neurons or automatic?)
Single_rating1 Single rating (either from sorted_neurons or automatic?)
stability_rating2 stability rating (either from sorted_neurons or automatic?)
quantSNR 11.5 KK automatic SNR
n_waveforms0 apparently bugged
waveform_average [1×30 single] average waveform of this unit
waveform_std [1×30 single] std of waveform for each bin
waveform_width 3.0224e-04 width (in time?)
waveform_amplitude 173.2376 amplitude (?)
FR 2.68 average firing rate across all data
spike_analysis_pipeline/intermediate_output.txt · Last modified: 2022/05/17 14:47 by lukas.schneider