Differences

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--- ephys_pipeline:4_sorting [2022/03/17 14:07] – created lukas.schneider
+++ ephys_pipeline:4_sorting [2022/12/29 07:15] (current) – external edit 127.0.0.1
@@ Line 11: / Line 11: @@
 ===== Sorting pipeline =====
-  - Fill in [[ephys_pipeline:electrode_depth_file|Electrode depth file]] (required as first step for WC pipeline)
-  - WC: Create waveclus pre-clustering files (implemented in [[ephys_pipeline:phys_gui|phys_gui]])
+  - 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:3_phys_gui|phys_gui]])
   - WC: 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 (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)
   - 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)
-  - 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.