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--- spike_analysis_pipeline:1_pipeline_overview [2022/12/29 07:15] – external edit 127.0.0.1
+++ spike_analysis_pipeline:1_pipeline_overview [2023/11/13 16:59] (current) – removed i.kagan
@@ Line 1: / Line 1: @@
-====== Spike analysis pipeline overview ======
-===== Folder structure =====
-^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: In additi
-===== Associated code =====
-hmm