ephys_pipeline:1_pipeline_overview
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ephys_pipeline:1_pipeline_overview [2022/01/11 19:59] – [Synchronization] 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 | ||
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===== General Workflow ===== | ===== General Workflow ===== | ||
- | - Fill in [[ephys_pipeline: | + | - Fill in [[ephys_pipeline: |
- | - WC: Create waveclus pre-clustering files (implemented 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, | - WC: Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, | ||
* Preferentially separate spike shapes in difficult cases | * Preferentially separate spike shapes in difficult cases | ||
- | - Create plxfiles (implemented in [[ephys_pipeline: | + | - Create plxfiles (implemented in [[ephys_pipeline: |
- Check and clean PLX file and **TAKE NOTES** (single/ | - 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): | - 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: | + | * Create combined (phys+behavior) files (implemented in [[ephys_pipeline: |
- | * Assign same cells across blocks 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: | + | * 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) | * 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: | + | - If you have finalized the sorting, create combined (phys+behavior) files (implemented in [[ephys_pipeline: |
- | - Complete [[ephys_pipeline: | + | - Complete [[ephys_pipeline: |
- | - Automatically update the automatic_sorting sheet from the [[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: | + | - Copy the automatic_soting entries to the final_sorting sheet of the [[ephys_pipeline: |
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===== Associated code ===== | ===== Associated code ===== | ||
- | Data conversion functions are located in Github | + | For loading and writing plx files we use an external toolbox |
- | * PLX2SPK | + | |
- | * PLX2TDT | + | |
- | * SEV2mat_working | + | |
- | * SPK2PLX | + | |
- | * TDT2PLX | + | |
- | * TDTbin2mat_working | + | |
- | * WC32SPK | + | |
- | * WC32SPK_concatenated | + | |
- | * WC32SPK_directly | + | |
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 | ||
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- 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.1641931167.txt.gz · Last modified: 2022/12/29 07:15 (external edit)