ephys_pipeline:1_pipeline_overview
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ephys_pipeline:1_pipeline_overview [2021/12/14 15:17] – lukas.schneider | ephys_pipeline:1_pipeline_overview [2022/12/29 07:15] (current) – external edit 127.0.0.1 | ||
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====== Ephys pipeline overview ====== | ====== Ephys pipeline overview ====== | ||
+ | monkeypsych <-> TDT => https:// | ||
===== Folder structure ===== | ===== Folder structure ===== | ||
- | * Y: | + | ^Inputs |
- | | + | |Y: |
- | | + | |Y: |
- | | + | |Y: |
- | | + | |\Dropbox\DAG\phys\Monkey_phys_dpz\Electrode_depths.mat| electrode depths documentation| |
- | | + | |\Dropbox\DAG\phys\Monkey_phys_dpz\Same_cells.mat| same cells across blocks assignment| |
- | | + | ^Outputs |
- | | + | |Y: |
- | | + | |Y: |
- | -plx files excel table | + | |Y: |
- | | + | |\Dropbox\DAG\phys\Monkey_phys_dpz\plx_files.xls| (for multiple sortings:) used plx file documentation| |
+ | |\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|block/ | ||
===== General Workflow ===== | ===== General Workflow ===== | ||
- | * Update | + | |
- | | + | - Fill in [[ephys_pipeline: |
- | | + | - WC: Create waveclus pre-clustering files (implemented in [[ephys_pipeline: |
- | * (Optional - WC only) manually refine WC sorting | + | - WC: Run waveclus |
- | * (Optional | + | * Preferentially separate spike shapes |
- | * (Optional | + | - Create plxfiles (implemented in [[ephys_pipeline: |
- | | + | - Check and clean PLX file and **TAKE NOTES** (single/ |
- | | + | - Now we need to assess which units are the same within and across blocks |
- | | + | |
- | | + | |
- | | + | * Plot single unit tuning assuming cells are unique in every block (implemented in [[ephys_pipeline: |
- | * Update | + | |
- | Most of the steps above are automatized, | + | |
+ | - Complete [[ephys_pipeline: | ||
+ | | ||
+ | - Copy the automatic_soting entries to the final_sorting sheet of the [[ephys_pipeline: | ||
- | ===== Synchronization ===== | ||
- | * TDT data is stored as a continuous data (starting from start of recording) | ||
- | * behavioral data is stored per trial (starting from first trial) | ||
- | For combining both, we first convert TDT data to trial format (function TDT_trial_struct.m) preferentially using epocs store (Tnum and SVal) information. | ||
- | \\ Note: There is a flag for using the continous state information stream (stream_state_info), | ||
- | \\ Importantly, | ||
- | \\ Therefore, ITI between trial 1 and 2 as well as STATE 1 (initiation) of trial 2 are found at the end of trial 1. | ||
- | \\ This also means that data recorded before 1st trial' | ||
===== Associated code ===== | ===== Associated code ===== | ||
+ | For loading and writing plx files we use an external toolbox located in Github External_unmodified/ | ||
+ | |||
+ | The remaining code related to phys preprocessing (not including Waveclus and Plexon) can be found on Github Phys_preprocessing repository | ||
+ | * Data conversion functions | ||
+ | - TDTbin2mat_working.m | ||
+ | - SEV2mat_working.m | ||
+ | - PLX2SPK.m | ||
+ | - SPK2PLX.m | ||
+ | - WC32SPK.m | ||
+ | - WC32SPK_concatenated.m | ||
+ | - WC32SPK_directly.m | ||
+ | * Core functions | ||
+ | - phys_gui_working.m | ||
+ | - phys_gui_execute.m | ||
+ | - TDT_trial_struct.m | ||
+ | - ph_combine_MP_and_TDT_data | ||
+ | - DAG_update_sorting_table.m | ||
+ | * Waveclus pipeline specific | ||
+ | - DAG_WC3_preprocessing.m | ||
+ | - DAG_parse_data_tdt.m | ||
+ | - DAG_SpikefilterChan.m | ||
+ | - WC32SPK_directly.m | ||
+ | - ph_readout_broadband_lag.m | ||
+ | * Plexon pipeline specific | ||
+ | - DAG_create_PLX.m | ||
+ | - DAG_update_plx_file_table.m | ||
+ | - ph_get_new_plx_extension.m | ||
+ | * Extra standalone functions | ||
+ | - DAG_derive_TDT_streamer_broadband_lag.m | ||
+ | - ph_debugging_GUI.m | ||
+ | - DAG_take_over_sortcode_PLX2PLX.m | ||
+ | * Only of historical relevance (legacy subfolder) | ||
+ | - DAG_move_sorting_files.m | ||
+ | - ph_derive_electrode_depth.m | ||
+ | - ph_derive_same_cells.m | ||
+ | - ph_simulate_history.m | ||
+ | - PLX2TDT.m | ||
+ | - TDT2PLX.m | ||
+ | |||
+ |
ephys_pipeline/1_pipeline_overview.1639495076.txt.gz · Last modified: 2022/12/29 07:15 (external edit)