Differences

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--- spike_analysis_pipeline:pipeline_overview [2022/01/10 17:17] – lukas.schneider
+++ spike_analysis_pipeline:pipeline_overview [2023/11/13 22:00] (current) – i.kagan
@@ Line 2: / Line 2: @@
 ===== Folder structure =====
-  * Y:\Projects\project\ephys\version
-    *
+^Inputs  ^Info|
-  * Y:\Data\Sortcodes\Monkey_phys contains sorting related files
+|\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|electrode locations, unit/site IDs,SNR/Stability/single ratings|
-  * Y:\Data\Monkey contains the behavioral data
+|\GitHub\Settings\spike_analysis\project|project and version specific settings (keys)|
-  * Y:\Data\Monkey_phys_mat_from_TDT contains recorded data, arranged in the same trial structure as the behavioral data
+|Y:\Data\Monkey_phys_combined_monkeypsych_TDT|raw data|
-  * Y:\Data\Monkey_phys_combined_monkeypsych_TDT contains trial structures with combined behavioral and ephys data
-  * Y:\Data\All_phys_preprocessing_log\Monkey_phys contains automatically created log files of all preprocessing performed
+Outputs in Y:\Projects\project\ephys\version:
-  * \Dropbox\DAG\phys\Monkey_phys_dpz\Sorted_neurons excel table
+^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,...})
-  * ph_initiate_populaiton_analysis
+  * 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
+  * Very important: ... INDEED :)
 ===== Associated code =====
-Data conversion functions are located in Github External_modified/PLXTDT repository
-  * PLX2SPK
+...
-  * PLX2TDT
-  * SEV2mat_working
-  * SPK2PLX
-  * TDT2PLX
-  * TDTbin2mat_working
-  * WC32SPK
-  * WC32SPK_concatenated
-  * WC32SPK_directly
-The remaining code related to phys preprocessing (not including Waveclus and Plexon) can be found on Github Phys_preprocessing repository
-  * Core functions
-    - phys_gui_working.m
-    - phys_gui_execute.m
-    - TDT_trial_struct.m
-    - ph_combine_MP_and_TDT_data
-    - DAG_update_sorting_table.m
-  * Waveclus pipeline specific
-    - DAG_WC3_preprocessing.m
-    - DAG_parse_data_tdt.m
-    - DAG_SpikefilterChan.m
-    - WC32SPK_directly.m
-    - ph_readout_broadband_lag.m
-  * Plexon pipeline specific
-    - DAG_create_PLX.m
-    - DAG_update_plx_file_table.m
-    - ph_get_new_plx_extension.m
-  * Extra standalone functions
-    - DAG_derive_TDT_streamer_broadband_lag.m
-    - ph_debugging_GUI.m
-    - DAG_take_over_sortcode_PLX2PLX.m
-  * Only of historical relevance
-    - DAG_move_sorting_files.m      Was used to transfer sortcodes to their current destination
-    - ph_derive_electrode_depth.m   Was used to create the first electrode_depths file extracting from sorted_neurons table
-    - ph_derive_same_cells.m        Was used to create the first same_cells file extracting from sorted_neurons table
-    - ph_simulate_history.m         Was used to create the first log files