====== 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: ... INDEED :)

===== Associated code =====

...