Differences

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--- spike_analysis_pipeline:pipeline_overview [2022/01/10 18:28] – 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 main folder contains:                                        ||
-    | population_monkey_session.mat | spike data sorted by unit for each session                       |
+^Inputs  ^Info|
-    | sites_monkey_session.mat      | LFP data sorted by site for each session                         |
+|\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|electrode locations, unit/site IDs,SNR/Stability/single ratings|
-    | by_block_monkey_session.mat   | body signals sorted by block for each session                    |
+|\GitHub\Settings\spike_analysis\project|project and version specific settings (keys)|
-    | Mon_sorted_neurons.xls        | copies of the used sorted neurons tables from dropbox            |
+|Y:\Data\Monkey_phys_combined_monkeypsych_TDT|raw data|
-    | keys_Monkey.mat               | copy of the keys used when running ph_initiation                 |
-    | tuning_table_combined.mat     | Anova results stored in a table                                  |
+Outputs in Y:\Projects\project\ephys\version:
-    | tuning_table_combined_CI.mat  | Anova results restructured accroding to contra/ipsi definitions  |
-    | tuning_table_combined.xls     | simplified excel table                                           |
+^File  ^Info|
-    | seed.mat                      | a saved seed to make randomizations reproducable                 |
+|population_monkey_session.mat|spike data sorted by unit for each session  |
-    | ^Subfolders:                                                                              ||
+|sites_monkey_session.mat  |LFP data sorted by site for each session  |
-    | spike_shapes                  | Spike shapes, firing rates over time, and ISI plots        |
+|by_block_monkey_session.mat  |body signals sorted by block for each session  |
-    | single_cell_examples          | Single cell plots                                          |
+|Mon_sorted_neurons.xls  |copies of the used sorted neurons tables from dropbox  |
-    | cell_counts                   | Anova results as pie plots                                 |
+|keys_Monkey.mat  |copy of the keys used when running ph_initiation  |
-    | scatter                       | Anova results as scatter plots (one column versus another) |
+|tuning_table_combined.mat  |Anova results stored in a table  |
-    | population_analysis           | population PSTHs                                           |
+|tuning_table_combined_CI.mat  |Anova results restructured accroding to contra/ipsi definitions  |
-    | response timing               | tuning over time plots                                     |
+|tuning_table_combined.xls  |simplified excel table  |
-    | ...                           |                                                            |
+|seed.mat  |a saved seed to make randomizations reproducable  |
-  * \Dropbox\DAG\phys\Monkey_phys_dpz\Sorted_neurons excel table
+^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,...})
-    - loop per monkey
+  * ph_initiation(project,{version1,version2,…})
-    - read in general settings -> project settings -> version settings
+      - read in general settings → project settings → version settings
-    - run ph_session_processing (core function)
+      - 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
+          * 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
+          * combines it with Sorted Neuron table information
-          - !! Copies last 1 second of spikes to beginning of next trial
+          * !! Copies last 1 second of spikes to beginning of next trial
-          - !! Cuts and appends last 1 second of streams 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
+          * !! 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)
+        * 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)
+      - format tuning table (create tuning_table_combined_CI.mat and tuning_table_combined.xls)
-    - ph_get_filelist for crossreferencing with behavior
+      - ph_get_filelist for crossreferencing with behavior
-    - ph_initiate_population_analysis also runs population analysis
+      - ph_initiate_population_analysis also runs population analysis
   *
 ===== Synchronization =====
-  * Very important: In additi
+  * Very important: ... INDEED :)
 ===== Associated code =====
-hmm
+...