spike_analysis_pipeline:intermediate_output
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spike_analysis_pipeline:intermediate_output [2023/11/02 11:15] – [Additional Population file fields] lvasileva | spike_analysis_pipeline:intermediate_output [2023/11/13 17:05] (current) – removed i.kagan | ||
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- | ===== 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. | ||
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- | Outputs in Y: | ||
- | ^File ^Info ^ | ||
- | | population_monkey_session.mat | spike data sorted by unit for each session | ||
- | | sites_monkey_session.mat | ||
- | | by_block_monkey_session.mat | ||
- | | Mon_sorted_neurons.xls | ||
- | | keys_Monkey.mat | ||
- | | tuning_table_combined.mat | ||
- | | tuning_table_combined_CI.mat | ||
- | | tuning_table_combined.xls | ||
- | | spike_shapes | ||
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- | 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 | ||
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- | ==== Trial structure subfields (By_block files) ==== | ||
- | to be removed: | ||
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- | ^Condition info^Format^Info ^ | ||
- | | type|scalar| from data| | ||
- | | effector|scalar| from data| | ||
- | | reach_hand|scalar| from data| | ||
- | | choice|scalar| from data| | ||
- | | success|scalar| from data| | ||
- | | completed|scalar| from data| | ||
- | | correct_targets|scalar| from data| | ||
- | | target_selected|scalar| from data| | ||
- | | n_nondistractors|scalar| from data| | ||
- | | n_distractors|scalar| from data| | ||
- | | difficulty|scalar| from data| | ||
- | | stimuli_in_2hemifields|scalar| from data| | ||
- | | perturbation|scalar| using perturbation_groups key ??| | ||
- | | dataset|scalar| Dataset from sorted_neurons (only in spikes so far ??)| | ||
- | ^Timing info^Format^Info ^ | ||
- | | date|scalar| from data| | ||
- | | block|scalar| from data| | ||
- | | run|scalar| from data| | ||
- | | n|scalar| from data| | ||
- | | trial_onset_time|scalar| from data| | ||
- | | run_onset_time|scalar| from data| | ||
- | | states|array| array of events marked in this trial| | ||
- | | states_onset|array [s]| corresponding onset times (relative to state 2)| | ||
- | ^Spatial info^Format^Info ^ | ||
- | | fix_pos|complex| x is real, y is imaginary (already preprocessed? | ||
- | | tar_pos|complex| x is real, y is imaginary| | ||
- | | stm_pos|complex| x is real, y is imaginary| | ||
- | ^Response info^Format^Info ^ | ||
- | | rea_off|complex| x is real, y is imaginary| | ||
- | | sac_off|complex| x is real, y is imaginary| | ||
- | | sac_lat|scalar| Saccade RT (in seconds)| | ||
- | | rea_lat|scalar| Reach RT (in seconds)| | ||
- | ^Specific data ^Format^Info ^ | ||
- | | TDT_ECG1|array| Body signal Data (ECG1, | ||
- | | TDT_ECG1_SR|scalar| Sampling rate| | ||
- | | TDT_ECG1_t0_from_rec_start|scalar| state 2 onset relative to start of the recording (block?) | | ||
- | | TDT_ECG1_tStart|scalar| (usually negative) how much of the stream is before state 2 - due to shift!!| | ||
- | | LFP|array| LFP data, not called TDT_LFPx any more, but SR, | ||
- | | arrival_times|array| in seconds, relative to this trial' | ||
- | | FR_average|scalar| average firing rate for this unit in this trial| | ||
- | | accepted|scalar| trial accepted for this unit| | ||
- | | FR|scalar| ??| | ||
- | | stability_rating|scalar| why is this here ??| | ||
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- | ==== Additional Site files fields==== | ||
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- | ^Fieldname^Example^Info ^ | ||
- | | site_ID|' | ||
- | | target|' | ||
- | | perturbation_site|' | ||
- | | grid_x|3| grid location from sorted_neurons| | ||
- | | grid_y|-4.5| grid location from sorted_neurons| | ||
- | | electrode_depth|45| Aimed_electrode_depth from sorted_neurons| | ||
- | | monkey|' | ||
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- | ==== Additional Population file fields==== | ||
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- | ^Fieldname^Example^Info ^ | ||
- | | unit_ID |' | ||
- | | channel|2| channel the unit was recorded in | | ||
- | | block_unit|{3x1 cell}| which cluster in which block are combined in this unit| | ||
- | | SNR_rating|2| SNR rating (either from sorted_neurons or automatic? | ||
- | | Single_rating|1| Single rating (either from sorted_neurons or automatic? | ||
- | | stability_rating|2| stability rating (either from sorted_neurons or automatic? | ||
- | | quantSNR| 11.5| KK automatic SNR| | ||
- | | n_waveforms|36379| number of spikes| | ||
- | | waveform_average| [1x30 single]| average waveform of this unit, 30 datapoints per waveform| | ||
- | | waveform_std| [1x30 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| | ||
- | | monkey| ' | ||
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spike_analysis_pipeline/intermediate_output.1698923716.txt.gz · Last modified: 2023/11/02 11:15 by lvasileva