spike_analysis_pipeline:pipeline_overview
This is an old revision of the document!
Table of Contents
Spike analysis pipeline overview
Folder structure
^File ^Info | Y:\Projects\project\ephys\version main folder contains: || | 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 | | Subfolders: || | 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 | | ... | | * \Dropbox\DAG\phys\Monkey_phys_dpz\Sorted_neurons excel table
General Workflow
- ph_initiation(project,{version1,version2,…})
- loop per monkey
- read in general settings → project settings → version settings
- run 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
- 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)
- 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
spike_analysis_pipeline/pipeline_overview.1641839446.txt.gz · Last modified: 2022/12/29 07:15 (external edit)