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--- spike_analysis_pipeline:2_interactions_with_other_pipelines [2022/12/29 07:15] – external edit 127.0.0.1
+++ spike_analysis_pipeline:2_interactions_with_other_pipelines [2023/11/13 17:00] (current) – removed i.kagan
@@ Line 1: / Line 1: @@
-===== 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 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,CAP1,POX1)|
-| 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,t0,andtStart are...|
-| arrival_times|array| in seconds, relative to this trial's state 2|
-| 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 ??|
-==== Additional Site files fields====
-^Fieldname^Example^Info ^
-| 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_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|'Bacchus_phys'| as assigned in sorted_neurons (?) |
-==== Additional Population file fields====
-^Fieldname^Example^Info ^
-| unit_ID |'Bac_20210706_01'| as assigned in sorted_neurons |
-| 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|0| apparently bugged|
-| waveform_average| [1x30 single]| average waveform of this unit|
-| 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|