Kilosort Batch Runner

This repository contains a set of MATLAB scripts for automated and manual spike sorting using Kilosort and Phy.

Scripts

Script	Description
runKs2.m	Automated spike-sorting using Kilosort2
runKs3.m	Automated spike-sorting using Kilosort3
runPhy.m	Manual spike-sorting using Phy (Windows only)
saveKs.m	Save Phy format as a MATLAB struct
viewRaw.m	Raw binary data viewer for SpikeGLX bin files

Usage

1. Ensure Kilosort2/3 and npy-matlab are in your MATLAB path.
2. Run the desired script (e.g., runKs2) with the data directory as an argument.
3. Follow the prompts to select files and start the sorting process.

• [New] You don't need to have a separate channel map file, as these scripts read the SpikeGLX meta file to parse the channel map information. 🗺️

>> runKs2('/mnt/data')
*****************************************
******** Batch Kilosort2 sorting ********
*****************************************

1: ...imec0/ANM480363_20210524_pfc301_hpc200_g0_t0.imec0.ap.bin
2: ...imec1/ANM480363_20210524_pfc301_hpc200_g0_t0.imec1.ap.bin

[1] Add folder
[2] Add file
[3] Delete file selection
[4] Set channel to exclude
[5] View raw data
[s] Start
[q] Quit
>> s