spike_analysis_pipeline:pipeline_overview
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
spike_analysis_pipeline:pipeline_overview [2022/01/10 17:11] – created lukas.schneider | spike_analysis_pipeline:pipeline_overview [2023/11/13 22:00] (current) – i.kagan | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | j | + | ====== Spike analysis pipeline overview ====== |
+ | |||
+ | ===== Folder structure ===== | ||
+ | |||
+ | ^Inputs | ||
+ | |\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|electrode locations, unit/site IDs, | ||
+ | |\GitHub\Settings\spike_analysis\project|project and version specific settings (keys)| | ||
+ | |Y: | ||
+ | |||
+ | Outputs in Y: | ||
+ | |||
+ | ^File ^Info| | ||
+ | |population_monkey_session.mat|spike data sorted by unit for each session | ||
+ | |sites_monkey_session.mat | ||
+ | |by_block_monkey_session.mat | ||
+ | |Mon_sorted_neurons.xls | ||
+ | |keys_Monkey.mat | ||
+ | |tuning_table_combined.mat | ||
+ | |tuning_table_combined_CI.mat | ||
+ | |tuning_table_combined.xls | ||
+ | |seed.mat | ||
+ | ^Subfolder | ||
+ | |spike_shapes | ||
+ | |single_cell_examples | ||
+ | |cell_counts | ||
+ | |scatter | ||
+ | |population_analysis | ||
+ | |response timing | ||
+ | |… | | | ||
+ | |||
+ | ===== General Workflow ===== | ||
+ | |||
+ | * ph_initiation(project, | ||
+ | - read in general settings → project settings → version settings | ||
+ | - loop per monkey: ph_session_processing (core function) | ||
+ | * read in data from Y: | ||
+ | * 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/ | ||
+ | * 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/ | ||
+ | * plot waveforms/ | ||
+ | * exclude units dependent on excel entries (SNR/ | ||
+ | * plot waveforms/ | ||
+ | * 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 ===== | ||
+ | |||
+ | ... | ||
+ |
spike_analysis_pipeline/pipeline_overview.1641834683.txt.gz · Last modified: 2022/12/29 07:15 (external edit)