spike_analysis_pipeline:interaction_with_other_pipelines

### Table of Contents

## 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 | {3×1 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 | [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/interaction_with_other_pipelines.txt · Last modified: 2023/11/13 17:01 by i.kagan