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ephys_pipeline:pipeline_overview [2017/10/25 13:41] – [Plexon file naming] lukas.schneiderephys_pipeline:pipeline_overview [2021/12/14 13:42] (current) – delete lukas.schneider
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-====== Ephys pipeline overview ====== 
- 
-===== Folder structure ===== 
-  * Y:\Data\TDTtanks contains the Raw data and sorting related files 
-  * Y:\Data\Monkey_phys contains the behavioral data 
-  * Y:\Data\Monkey_phys_mat_from_TDT contains recorded data, arranged in the same trial structure as the behavioral data 
-  * Y:\Data\Monkey_phys_combined_monkeypsych_TDT contains trial structures with combined behavioral and ephys data 
- 
-===== Plexon file naming ===== 
-\\ Session_blocks_N.plx are based on online snippets 
-\\ Session_realigned_blocks_N.plx are based on realigned online snippets 
-\\ Session_from_BB_blocks_N.plx are based on waveclus clustering 
-\\ Importantly, when you save a plx file, it never overwrites an exisitng file, but rather appends "-01" to the file name. If that filename already exists as well, it will append "-02" instead. That means, all files with "-NN" affixes are manually saved. Because of that, for all steps after sorting, we use plx files with the "-01" affix. 
-    
-===== Waveclus pipeline ===== 
- 
-  - Fill in [[ephys_pipeline:electrode_depth_file|Electrode depth file]] 
-  - Create waveclus pre-clustering files (implemented in [[ephys_pipeline:phys_gui|phys_gui]]) 
-  - Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, MATLAB 2014+) 
-    * Preferentially separate spike shapes in difficult cases 
-  - Create plxfiles from WC (implemented in [[ephys_pipeline:phys_gui|phys_gui]]) 
-  - Check and clean PLX file AND TAKE NOTES (single/SNR/stability rating) 
-  - Create combined (phys+behavior) files (implemented in [[ephys_pipeline:phys_gui|phys_gui]]) 
-  - Plot single unit tuning assuming cells are unique in every block (implemented in [[ephys_pipeline:phys_gui|phys_gui]])   
-    * Optional, this is meant to help assessing if two "units" in the same block are actually the same 
-  - 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)  
-  - Re-sort PLX file (combining same cells sort codes of same block same channel) 
-    * Optional for cases where it was not clear if the "units" are the same 
-  - Fill in [[ephys_pipeline: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]] 
-  - Copy the automatic_soting entries to the final_sorting sheet of the [[ephys_pipeline:excel_table|Excel sorting table]] and complete with manual entries. 
- 
  
ephys_pipeline/pipeline_overview.1508938904.txt.gz · Last modified: 2022/12/29 07:15 (external edit)