# Workflow for spike sorting [![hackmd-github-sync-badge](https://hackmd.io/Cv9EWPSqT12RkovOfMVXaQ/badge)](https://hackmd.io/Cv9EWPSqT12RkovOfMVXaQ) Say we are going to sort animal `DS_15` session 1 region AC data. 1. Create a folder on your local computer, say `D:/DualRecording/DS_15/DS_15 1/` 2. Copy the recording files to the folder, here I got the following files under the directory `P:\Electrophysiology\DS_15` on NAS. - `Apr 8 2021 Dual DS_15_1001.ccf` - `Apr 8 2021 Dual DS_15_1001.nev` - `Apr 8 2021 Dual DS_15_1001.ns5` - `Apr 8 2021 Dual DS_15_1001.ns6` - `Apr 8 2021 Dual DS_15_1002.ccf` - `Apr 8 2021 Dual DS_15_1002.nev` - `Apr 8 2021 Dual DS_15_1002.ns5` - `Apr 8 2021 Dual DS_15_1002.ns6` - `Apr 8 2021 Dual DS_15_1003.ccf` - `Apr 8 2021 Dual DS_15_1003.nev` - `Apr 8 2021 Dual DS_15_1003.ns5` - `Apr 8 2021 Dual DS_15_1003.ns6` Note: make sure you have 4 files for each block of the session, `ccf`, `nev`, `ns5`, `ns6`. 3. Open Matlab, and run the scripts from `EphysAnalysis/Matlab Code/` in the following order: - Run `repackage.m`, enter the number of blocks in the session, and open each block file ended with `.ns5` from the window that pops up. - Run `saveTrials.m`, enter the number of trials in the session, and open each block file ended with `.ns6` from the window that pops up. 4. Run Kilosort in matlab: - Run `kilosort.m`, select the correct `.bin` file (generated by the previous step) from the window that pops up. - After running, three figures will pop up, align them together, take a screenshot, and save it as `DS_15 1 AC Drift Map.png` 5. Run Phy in terminal: - Open terminal, navigate to the folder `D:/DualRecording/DS_15/DS_15 1/` - Activate the conda environment by running `conda activate phy2` - Run `phy template-gui params.py` to open the Phy GUI - After sorting, save the results and close the GUI 6. Run `EphysAnalysis/Matlab Code/packageMetadata.m` in Matlab, look for the information required from the [lab notebook](https://docs.google.com/spreadsheets/d/1PHQ9fQUMWEAgZIQ-V3ok8NXkPfBXMZ74ZKpdqTZjT9s/edit?pli=1&gid=0#gid=0) and enter them when prompted. --- A few tips when using Phy to sort: 1. Units with firing rate less than 0.2 spikes/s can be considered as noise 2. Sort by KiloSort labels and look at the good units first