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--- spike_analysis_pipeline:1_pipeline_overview [2023/11/13 16:53] – i.kagan
+++ spike_analysis_pipeline:1_pipeline_overview [2023/11/13 16:59] (current) – removed i.kagan
@@ Line 1: / Line 1: @@
-====== Spike analysis pipeline overview ======
-===== Folder structur =====
-^Inputs  ^Info|
-|\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|electrode locations, unit/site IDs,SNR/Stability/single ratings|
-|\GitHub\Settings\spike_analysis\project|project and version specific settings (keys)|
-|Y:\Data\Monkey_phys_combined_monkeypsych_TDT|raw data|
-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 accroding to contra/ipsi definitions  |
-|tuning_table_combined.xls  |simplified excel table  |
-|seed.mat  |a saved seed to make randomizations reproducable  |
-^Subfolder  ^Info|
-|spike_shapes  |Spike shapes, firing rates over time, and ISI plots  |
-|single_cell_examples  |Single cell plots  |
-|cell_counts  |Anova results as pie plots  |
-|scatter  |Anova results as scatter plots (one column versus another)|
-|population_analysis  |population PSTHs  |
-|response timing  |tuning over time plots  |
-|…  |   |
-===== General Workflow =====
-  * ph_initiation(project,{version1,version2,…})
-      - read in general settings → project settings → version settings
-      - loop per monkey: ph_session_processing (core function)
-        * read in data from Y:\Data\Monkey_phys_combined_monkeypsych_TDT
-        * run monkeypsych_analyze for saccade detection etc.
-        * run ph_run_state_alignment_per_trial
-          * takes over relevant trial and state (event) information from monkeypsych_analyze output (TDT_states and saccade/reach initiation)
-          * combines it with Sorted Neuron table information
-          * !! Copies last 1 second of spikes to beginning of next trial
-          * !! Cuts and appends last 1 second of streams to beginning of next trial
-          * !! excludes trials without physiology data And/or NOT matching condition
-        * resort data by unit/site/block
-        * plot waveforms/ISI/FR_across time per unit
-        * exclude units dependent on excel entries (SNR/stability/single rating)
-        * plot waveforms/ISI/FR_across time per unit again for remaining units
-        * run ANOVAs (ph_ANOVAS) and create tuning table
-        * create single cell plots (ph_plot_unit_per_condition)
-        * save files per session
-      - format tuning table (create tuning_table_combined_CI.mat and tuning_table_combined.xls)
-      - ph_get_filelist for crossreferencing with behavior
-      - ph_initiate_population_analysis also runs population analysis
-  *
-===== Synchronization =====
-  * Very important: ... INDEED :)
-===== Associated code =====
-...