spike_analysis_pipeline:pipeline_overview
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spike_analysis_pipeline:pipeline_overview [2022/01/10 18:33] – [Folder structure] lukas.schneider | spike_analysis_pipeline:pipeline_overview [2023/11/13 22:00] (current) – i.kagan | ||
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===== Folder structure ===== | ===== Folder structure ===== | ||
- | ^File ^Info ^ | + | |
- | | Y: | + | ^Inputs |
- | | population_monkey_session.mat | spike data sorted by unit for each session | + | |\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|electrode locations, unit/site IDs, |
- | | sites_monkey_session.mat | + | |\GitHub\Settings\spike_analysis\project|project and version specific settings (keys)| |
- | | by_block_monkey_session.mat | + | |Y: |
- | | Mon_sorted_neurons.xls | + | |
- | | keys_Monkey.mat | + | Outputs in Y: |
- | | tuning_table_combined.mat | + | |
- | | tuning_table_combined_CI.mat | + | ^File ^Info| |
- | | tuning_table_combined.xls | + | |population_monkey_session.mat|spike data sorted by unit for each session |
- | | seed.mat | + | |sites_monkey_session.mat |
- | | Subfolders: | + | |by_block_monkey_session.mat |
- | | spike_shapes | + | |Mon_sorted_neurons.xls |
- | | single_cell_examples | + | |keys_Monkey.mat |
- | | cell_counts | + | |tuning_table_combined.mat |
- | | scatter | + | |tuning_table_combined_CI.mat |
- | | population_analysis | + | |tuning_table_combined.xls |
- | | response timing | + | |seed.mat |
- | | ... | + | ^Subfolder |
- | | \Dropbox\DAG\phys\Monkey_phys_dpz\Sorted_neurons excel table|| | + | |spike_shapes |
+ | |single_cell_examples | ||
+ | |cell_counts | ||
+ | |scatter | ||
+ | |population_analysis | ||
+ | |response timing | ||
+ | |… | ||
===== General Workflow ===== | ===== General Workflow ===== | ||
- | | + | |
- | - loop per monkey | + | |
- | | + | - read in general settings |
- | - run ph_session_processing (core function) | + | - loop per monkey: |
* read in data from Y: | * read in data from Y: | ||
* run monkeypsych_analyze for saccade detection etc. | * run monkeypsych_analyze for saccade detection etc. | ||
* run ph_run_state_alignment_per_trial | * run ph_run_state_alignment_per_trial | ||
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
* resort data by unit/ | * resort data by unit/ | ||
* plot waveforms/ | * plot waveforms/ | ||
* exclude units dependent on excel entries (SNR/ | * exclude units dependent on excel entries (SNR/ | ||
* plot waveforms/ | * plot waveforms/ | ||
- | * run ANOVAs (ph_ANOVAS) | + | * run ANOVAs (ph_ANOVAS) |
* create single cell plots (ph_plot_unit_per_condition) | * create single cell plots (ph_plot_unit_per_condition) | ||
* save files per session | * save files per session | ||
- | | + | |
- | - 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 ===== | ===== Synchronization ===== | ||
- | | + | |
+ | | ||
===== Associated code ===== | ===== Associated code ===== | ||
- | hmm | + | |
+ | ... | ||
+ |
spike_analysis_pipeline/pipeline_overview.1641839592.txt.gz · Last modified: 2022/12/29 07:15 (external edit)