ephys_pipeline:1_pipeline_overview
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ephys_pipeline:1_pipeline_overview [2022/01/10 19:28] – [Folder structure] 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 ===== | ||
^Inputs | ^Inputs | ||
Line 15: | Line 15: | ||
|\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|block/ | |\Dropbox\DAG\phys\Monkey_phys_dpz\Mon_sorted_neurons.xls|block/ | ||
===== General Workflow ===== | ===== General Workflow ===== | ||
- | * Update Electrode depths matfile. Only block/ | ||
- | * (Optional - Synapse only) Reformat Synapse tank folder format to match previous conventions | ||
- | * (Optional - WC only) Run waveclus automatic sorting (Channels with electrodes in the same depth across blocks will be combined across blocks) | ||
- | * (Optional - WC only) manually refine WC sorting | ||
- | * (Optional - Plexon only) Create Plexon sortcodes | ||
- | * (Optional - Plexon only) Manual Plexon sorting | ||
- | * Update plx files excel table | ||
- | * Combine TDT and behavioral data | ||
- | - Create TDT trial structure | ||
- | - Combine | ||
- | * Update Same_cells matfile | ||
- | * Update sorted_neurons excel table | ||
- | Most of the steps above are automatized, | ||
+ | - Fill in [[ephys_pipeline: | ||
+ | - WC: Create waveclus pre-clustering files (implemented in [[ephys_pipeline: | ||
+ | - WC: Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, | ||
+ | * Preferentially separate spike shapes in difficult cases | ||
+ | - 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 (based on channel, electrode depths, spike shapes and potentially tuning, carefully check notes for this). For that purpose you might want to do the following steps in any order (potentially even going back and forth): | ||
+ | * Create combined (phys+behavior) files (implemented in [[ephys_pipeline: | ||
+ | * Assign same cells across blocks in [[ephys_pipeline: | ||
+ | * Plot single unit tuning assuming cells are unique in every block (implemented in [[ephys_pipeline: | ||
+ | * Re-sort PLX file (combining same cells sort codes of same block same channel) | ||
+ | - If you have finalized the sorting, create combined (phys+behavior) files (implemented in [[ephys_pipeline: | ||
+ | - Complete [[ephys_pipeline: | ||
+ | - Automatically update the automatic_sorting sheet from the [[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 ===== | ||
- | Data conversion functions are located in Github External_modified/ | ||
- | * PLX2SPK | ||
- | * PLX2TDT | ||
- | * SEV2mat_working | ||
- | * SPK2PLX | ||
- | * TDT2PLX | ||
- | * TDTbin2mat_working | ||
- | * WC32SPK | ||
- | * WC32SPK_concatenated | ||
- | * WC32SPK_directly | ||
+ | |||
+ | ===== 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 | 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 | * Core functions | ||
- phys_gui_working.m | - phys_gui_working.m | ||
Line 73: | Line 67: | ||
- ph_debugging_GUI.m | - ph_debugging_GUI.m | ||
- DAG_take_over_sortcode_PLX2PLX.m | - DAG_take_over_sortcode_PLX2PLX.m | ||
- | * Only of historical relevance | + | * Only of historical relevance |
- DAG_move_sorting_files.m | - DAG_move_sorting_files.m | ||
- ph_derive_electrode_depth.m | - ph_derive_electrode_depth.m | ||
- ph_derive_same_cells.m | - ph_derive_same_cells.m | ||
- ph_simulate_history.m | - ph_simulate_history.m | ||
+ | - PLX2TDT.m | ||
+ | - TDT2PLX.m | ||
ephys_pipeline/1_pipeline_overview.1641842899.txt.gz · Last modified: 2022/12/29 07:15 (external edit)