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ephys_pipeline:1_pipeline_overview [2022/01/11 20:28] – [Ephys pipeline overview] lukas.schneiderephys_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 ======
-e +monkeypsych <-> TDT => https://github.com/dagdpz/Phys_preprocessing
-e +
-e +
-e+
 ===== Folder structure ===== ===== Folder structure =====
 ^Inputs                         ^Info^ ^Inputs                         ^Info^
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 ===== General Workflow ===== ===== General Workflow =====
  
-  - Fill in [[ephys_pipeline:electrode_depth_file|Electrode depth file]] (required as first step for WC pipeline) +  - Fill in [[ephys_pipeline:5_Meta-info#electrode_depths file|Electrode depths file]] (required as first step for WC pipeline) 
-  - WC: Create waveclus pre-clustering files (implemented in [[ephys_pipeline:phys_gui|phys_gui]])+  - WC: Create waveclus pre-clustering files (implemented in [[ephys_pipeline:3_phys_gui|phys_gui]])
   - WC: Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, MATLAB 2014+)   - WC: Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, MATLAB 2014+)
     * Preferentially separate spike shapes in difficult cases     * Preferentially separate spike shapes in difficult cases
-  - Create plxfiles (implemented in [[ephys_pipeline:phys_gui|phys_gui]])+  - Create plxfiles (implemented in [[ephys_pipeline:3_phys_gui|phys_gui]])
   - Check and clean PLX file and **TAKE NOTES** (single/SNR/stability rating)   - Check and clean PLX file and **TAKE NOTES** (single/SNR/stability rating)
   - 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:phys_gui|phys_gui]]) +     * Create combined (phys+behavior) files (implemented in [[ephys_pipeline:3_phys_gui|phys_gui]]) 
-     * Assign same cells across blocks in [[ephys_pipeline:same_cells_file|Same cells file]] +     * Assign same cells across blocks in [[ephys_pipeline:5_Meta-info#same_cells file|Same cells file]] 
-     * Plot single unit tuning assuming cells are unique in every block (implemented in [[ephys_pipeline:phys_gui|phys_gui]]) - This is meant to help assessing if two "units" in the same block might actually be the same (if they have very similar tuning properties)+     * Plot single unit tuning assuming cells are unique in every block (implemented in [[ephys_pipeline:3_phys_gui|phys_gui]]) - This is meant to help assessing if two "units" in the same block might actually be the same (if they have very similar tuning properties)
      * 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:phys_gui|phys_gui]]) (yes, once again, now that you have a different amount of cells) +  - If you have finalized the sorting, create combined (phys+behavior) files (implemented in [[ephys_pipeline:3_phys_gui|phys_gui]]) (yes, once again, now that you have a different amount of cells) 
-  - Complete [[ephys_pipeline:same_cells_file|Same cells file]] +  - Complete [[ephys_pipeline:5_Meta-info#same_cells file|Same cells file]] 
-  - Automatically update the automatic_sorting sheet from the [[ephys_pipeline:excel_table|Excel sorting table]] using [[ephys_pipeline:phys_gui|phys_gui]] +  - Automatically update the automatic_sorting sheet from the [[ephys_pipeline:5_Meta-info#sorted_neurons table|Excel sorting table]] using [[ephys_pipeline:3_phys_gui|phys_gui]] 
-  - Copy the automatic_soting entries to the final_sorting sheet of the [[ephys_pipeline:excel_table|Excel sorting table]] and complete with manual entries.+  - Copy the automatic_soting entries to the final_sorting sheet of the [[ephys_pipeline:5_Meta-info#sorted_neurons table|Excel sorting table]] and complete with manual entries.
  
  
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 ===== Associated code ===== ===== Associated code =====
-Data conversion functions are located in Github External_modified/PLXTDT repository +For loading and writing plx files we use an external toolbox located in Github External_unmodified/Matlab Offline Files SDK repository 
-  * 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             Debugged and modified version of TDTbin2mat
 +    - SEV2mat_working.m                Debugged and modified version of SEV2mat
 +    - PLX2SPK.m                        For reading in PLX files (Stefan Schaffelhofer)
 +    - SPK2PLX.m                        For writing PLX files (Stefan Schaffelhofer)
 +    - 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 (legacy subfolder)
     - DAG_move_sorting_files.m      Was used to transfer sortcodes to their current destination     - DAG_move_sorting_files.m      Was used to transfer sortcodes to their current destination
     - ph_derive_electrode_depth.m   Was used to create the first electrode_depths file extracting from sorted_neurons table     - ph_derive_electrode_depth.m   Was used to create the first electrode_depths file extracting from sorted_neurons table
     - ph_derive_same_cells.m        Was used to create the first same_cells file extracting from sorted_neurons table     - ph_derive_same_cells.m        Was used to create the first same_cells file extracting from sorted_neurons table
     - ph_simulate_history.m         Was used to create the first log files     - ph_simulate_history.m         Was used to create the first log files
 +    - PLX2TDT.m                     Was used to create TDT sortcodes from PLX files
 +    - TDT2PLX.m                     Was used to create PLX files from TDT sortcodes
  
  
ephys_pipeline/1_pipeline_overview.1641932914.txt.gz · Last modified: 2022/12/29 07:15 (external edit)