spike_analysis_pipeline:1_pipeline_overview
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spike_analysis_pipeline:1_pipeline_overview [2023/02/16 16:01] – lschneider | spike_analysis_pipeline:1_pipeline_overview [2023/11/13 16:59] (current) – removed i.kagan | ||
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- | ====== Spike analysis pipeline overview ====== | ||
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- | ===== Folder structur ===== | ||
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- | ^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: | ||
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- | Outputs in Y: | ||
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- | ^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 | ||
- | |… | | | ||
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- | ===== General Workflow ===== | ||
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- | * 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 | ||
- | * | ||
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- | ===== Synchronization ===== | ||
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- | * Very important: In additi | ||
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- | ===== Associated code ===== | ||
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- | hmm | ||
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spike_analysis_pipeline/1_pipeline_overview.1676563302.txt.gz · Last modified: 2023/02/16 16:01 by lschneider