Enhanced Motor Unit sorter (EMUsort)

A command line tool for high performance spike sorting of multichannel, single unit electromyography

• Perform spike sorting with a modified version of Kilosort4 specifically tailored to MUAP data for improved performance (see paper for performance comparison results)
• Use a central configuration file to control all parameters and perform parameter sweeps
• Capable of automatically handling Intan, OpenEphys, NWB, Blackrock, and Binary datasets
• Combine recordings into single object for unified processing
• Remove broken or noisy channels automatically
• Export results and easily view in Phy

Installation

Requirements

• Currently, using a Linux-based OS is recommended. The code has been tested on Ubuntu. Windows is supported, but may require additional configuration steps as specified below. MacOS is not supported, but might work if it is macOS version >=12.3 and has an Apple silicon or AMD GPU, however, it is untested and tailored instructions are not provided.
• GPUs with compute capability >=5.0 are supported
• Nvidia Driver:
  • Linux: >=450.80.02
  • Windows: >=452.39
• CUDA Toolkit (Automatically installed with the environment):
  • >=11.3

Cloning from GitHub

Clone the repository recursively onto your machine (for example, in the home directory)

git clone --recurse-submodules https://github.com/snel-repo/EMUsort.git

If you accidentally ran git clone without --recurse-submodules, just delete the entire EMUsort folder and rerun the above command

After cloning is complete, you will need to configure a uv, micromamba, or conda environment.

Pulling Updates from GitHub

To update your EMUsort clone to the latest version, you can pull updates from the main repository. To do so, navigate into the folder where EMUsort was cloned and run:

git pull --recurse-submodules
git submodule update

If you used the uv method to install previously, and the submodules have been changed in the latest updates, you may need to run the below commands to update the submodules and reinstall those:

Windows only: Replace the sync command below with uv sync --extra full --python 3.9

uv cache clean
uv pip uninstall kilosort spikeinterface
uv sync --extra full

If you are updating a previous EMUsort installation, you may encounter issues with the configuration file (if it's structure changed in the latest update). If this happens, you may want to backup your configuration file somewhere, then you can reset it to the new default configuration file by running:

emusort --reset-config --folder /path/to/session_folder

Python Environment Creation

Before following the below steps, make sure to navigate into the folder where EMUsort was cloned.

Option 1: uv

Recommended for Windows and Linux (see Option 2 if using Linux over RDP)

Follow the steps and execute the commands below to install and manage EMUsort with uv, a high performance Python package and project manager:

Windows only: Install GitBash first with default settings and use its shell to use EMUsort.

curl -LsSf https://astral.sh/uv/install.sh | sh

Then either restart the terminal or execute the command suggested in the terminal to enable using uv in the terminal. Next, create the environment and install all dependencies including Phy, using uv:

cd /path/to/repo_folder # go into the EMUsort clone location  

Windows only: Windows seems most stable using Python version 3.9, so be sure to use the --python 3.9 option with the below command. For example: uv sync --extra full --python 3.9. Other Python versions can be tried afterwards, if necessary.

Use uv to execute the installation with the "full" option, which will install Kilosort4 (with modifications), SpikeInterface, PyTorch, and Phy GUI. See pyproject.toml for more "--extra" options.

uv sync --extra full

If the install finished successfully, proceed to the Usage section next.

Option 2: micromamba

Recommended for Linux (remote, e.g., for use over Remote Desktop with X11 on remote system)

To install micromamba and set up a micromamba environment, follow the steps and execute the commands below:

Windows only: Install GitBash first with default settings and use its shell to use EMUsort.

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

If this errors out, you can simply download the script from micro.mamba.pm/install.sh and run a file with those contents manually with bash ./install.sh. Afterwards, make sure to either restart the terminal or initialize micromamba directly, then run the below commands:

cd /path/to/repo_folder # go into the EMUsort clone location
micromamba env create -f environment.yml

Windows only: During micromamba environment creation, the conda packages usually work, but you may get an error at the end related to the pip packages not install installing. If this happened, it's likely micromamba worked, but the pip packages need manual installation. This is a Windows problem. So, go ahead and activate the micromamba environment you just created (micromamba activate emusort), and run the following, one by one: pip install -e ./src/emusort/spikeinterface pip install -e ./src/emusort/Kilosort4 pip install "git+https://github.com/cortex-lab/phy.git@7a2494b" pip install -e . If you encounter errors installing spikeinterface or Kilosort4, try navigating into each submodule folder and running pip install -e . to install the packages manually. Then pip install -e . in the main folder again to install the main EMUsort package.

If the install finished successfully, proceed to the Usage section next.

Option 3: anaconda/miniconda

Fallback Method, No Longer Recommended

To install miniconda, follow the link below, making sure to select the correct option for your OS:

• https://www.anaconda.com/docs/getting-started/miniconda/install#quickstart-install-instructions

Windows only: Open Anaconda Prompt from the Start Menu, and proceed with the below commands

Make sure restart the terminal or initialize conda in the terminal, then run the below commands:

cd /path/to/repo_folder # go into the EMUsort clone location
conda env create -f environment.yml

Usage

Python Environment Activation

Every time you open a new terminal, the environment must be activated, whether manually or automatically (see Advanced Usage for automatic activation).

Option 1: uv

Linux only:

source /path/to/repo_folder/.venv/bin/activate

Windows only:

source /path/to/repo_folder/.venv/Scripts/activate

Option 2: micromamba

micromamba activate emusort

Option 3: anaconda/miniconda

conda activate emusort

Session Folder Structure

EMUsort relies on a main "session folder", which contains the below 4 items.

• For Intan, NWB, Blackrock, or Binary datasets, all you need to do is create a new session folder to contain your desired dataset files (Item #1 below).
• For Open Ephys, the session folder itself (dated folder containing 'Record Node ###') will act as the session folder. The original dataset files will not be modified.

Items #2-4, will be generated automatically inside the provided session folder.

1. Data files (several dataset formats are supported)
   • Intan RHD/RHS files
   • NWB files
   • Blackrock files
   • Binary recording files
   • Record Node ### (if using OpenEphys session folder)
2. emu_config.yaml file
   • will be automatically generated and should be updated to make operational changes to EMUsort using the --config (or -c) command line option. Within the configuration file, please note that you will have to change the dataset_type attribute to match your desired dataset type. Once you generate the default config template, please review it and utilize the comments as documentation to guide your actions
3. sorted_yyyyMMdd_HHmmssffffff_g#_<session_folder>_P1_#_P2_#... folders, which are tagged with a datetime stamp, a channel group ID (if used), session folder name, and parameters used in a sweep in the same order as they appear under KS_params_to_sweep (if used)
   • Each time a sort is performed, a new folder will be created in the session folder with the date and time of the sort. Inside this sorted folder will be the sorted data, the phy output files, and a copy of the parameters used to sort the data (ops.npy includes channel delays under ops['preprocessing']['chan_delays'] and which channel was used as the reference for applying the delays under ops['preprocessing']['reference_chan'], which can be used as an index into ops['preprocessing']['chan_delays'] or emg_chans_used). The corresponding channel indexes for each sort are saved as emg_chans_used.npy. In each new sort folder, the emu_config.yaml is also dumped for future reference, which also includes channel indexes used in each sort as emg_chans_used.
4. concatenated_data folder
   • will be automatically created if the emg_recordings field has more than one entry, such as [0,1,2,7] or [all], which automatically includes all recordings in the session folder

Example Folder Tree

Intan, NWB, Blackrock, and Binary datasets:

Open Ephys datasets:

EMUsort Commands

To show a helpful summary of EMUsort commands:

emusort --help

To simply generate a configuration file (if it doesn't exist), run the below command:

Note: Absolute and relative paths are both acceptable.

emusort --folder /path/to/session_folder

Editing the main configuration file, emu_config.yaml, can be done by running the command below (will be generated from configs/config_template_emu.yaml if it doesn't exist):

emusort --config --folder /path/to/session_folder

If a problem occurs with your emu_config.yaml file and you would like to reset it to the default at configs/config_template_emu.yaml, you can run:

emusort --reset-config --folder /path/to/session_folder

To run a sort directly with the current emu_config.yaml on the dataset(s) in the session folder, run:

emusort --sort --folder /path/to/session_folder

For Kilosort4 emulation runs, you can include the --ks4 flag. See Running EMUsort As If Default Kilosort4 for more details.

If you want to specify multiple settings at the same time, you can append any combination of the below commands to the command line after emusort.

Note: For all commands, there is a short-form equivalent. The flags can be used in any order, but the path must always follow directly after the --folder flag.

--help, -h
--folder /path/to/session_folder, -f ./session_folder
--config, -c
--reset-config, --r
--sort, -s
--ks4, -k

As an example of using multiple commands, if you want to reset to the default configuration file, edit the new emu_config.yaml, and also spike sort immediately after saving, you can run the below:

emusort --reset-config --config --sort --folder /path/to/session_folder

Inspecting and Curating with phy

To view and analyze the latest sort with Phy GUI, you can either copy and paste the suggested phy command in the terminal output, or navigate into the latest sorted_### folder, and execute:

phy template-gui params.py

For more information on phy, see the documentation at the main GitHub repository: https://phy.readthedocs.io/en/latest/

Advanced Usage

Automatically Activate the Environment

To automatically activate the environment each time you open a new terminal, append to the end of your ~/.bashrc file the activation command, depending on which environment manager you are using, execute:

Windows only: If using GitBash (recommended), you may need to replace ~/.bashrc with ~/.bash_profile in the below commands. For uv, you must also swap to "source /path/to/repo_folder/.venv/Scripts/activate".

uv:

echo "source /path/to/repo_folder/.venv/bin/activate" >> ~/.bashrc # USING YOUR VALID PATH

micromamba:

echo "micromamba activate emusort" >> ~/.bashrc # USING YOUR VALID PATH

conda:

echo "conda activate emusort" >> ~/.bashrc # USING YOUR VALID PATH

Parameter Sweeping Over Multiple Kilosort Parameters to Find the Best Configurations for Your Dataset

EMUsort can now perform parameter sweeps across all parameters under the KS section of the configuration file.

Initial Set Up and Managing Jobs for a Parameter Sweep

If you want to explore different settings for multiple parameters and find the best parameter combinations for your dataset, you can edit the emu_config.yaml file under the Sorting section to enable a parameter sweep. First, you should decide which GPU(s) you want to use during processing. This is usually determined by how much memory each GPU has, and how many sorting processes can fit on a single GPU. You can test empirically to see what arrangement of job loads runs fastest on your system.

To set the selected GPU(s), modify the GPU_to_use list to include the indexes of the GPU(s) that should be used. Next, modify num_KS_jobs to specify how many total jobs to distribute evenly across all chosen GPUs. This num_KS_jobs parameter determines how many jobs will be running in parallel, so if you set num_KS_jobs: 1, any parameter combinations to be tried will be run sequentially on the first GPU specified in the GPU_to_use list.

For example, if you set GPU_to_use: [0,1] and num_KS_jobs: 1, the jobs would be run one after the other on GPU 0, but if you instead set num_KS_jobs: 10, this would allow up to 5 sort jobs to be run on each of GPU 0 and GPU 1.

Managing Parameter Combinations and Executing a Parameter Sweep

In order to activate the parameter sweep, you must set the do_KS_param_sweep field to true. However, if do_KS_param_sweep is false, then num_KS_jobs must be 1 to reflect that only 1 sort job will be performed. Next, the KS_params_to_sweep field controls which parameters are going to be explored during the parameter sweep. Each field under KS_params_to_sweep must be a Kilosort parameter as listed under the KS section. The values corresponding to each Kilosort parameter under KS_params_to_sweep must be a list, which will be iterated across during the sweep.

The linked_params_for_sweep parameter controls how the sweep combinations are explored by using only matched indexes for linked parameters. If no linked parameters are specified (e.g., if linked_params_for_sweep is left blank), the Kilosort parameter combinations will be explored in full, so that the product of the number of elements in each Kilosort parameter list defined in KS_params_to_sweep is the total number of combinations. In this case, beware of the combinatorics so you don't generate more sorts than you expected (e.g., NxM combinations for N of param1, M of param2, etc.). With linked_params_for_sweep, you can specify lists of linked parameters where each element is a list of parameter keys, such as linked_params_for_sweep: [[Th_universal, Th_learned]] for a single linkage, or linked_params_for_sweep: [[Th_universal, Th_learned], [nt, nt0min]] for two different linkages. When parameters are linked, the first element of each parameter will be used with the first element of all other parameters in the group, the second elements of linked parameters are used together, and so on. This means each Kilosort parameter list for linked parameters must be equal length. If you want, you may also link more than 2 parameters together, such as linked_params_for_sweep: [[Th_universal, Th_learned, Th_single_ch]].

By using linked_params_for_sweep, you get explicit control of some Kilosort parameter combinations to avoid bad combinations and reduce the overall number of runs to be performed. To determine the total number of combinations for a given sweep when using linked_params_for_sweep, you can treat the linked parameters as a single parameter in the combinatorics multiplication.

For example, the default configuration file specifies 5 settings each for Th_universal, Th_learned, and Th_single_ch. If no parameters were linked, the number of combinations would by 5*5*5=125, which is a very large number of combinations. So, instead, Th_learned, and Th_single_ch are linked by adding a sublist with the two keys: linked_params_for_sweep: [[Th_universal, Th_learned]]. In this case, because the linked parameters are treated as a single parameter in the combinatorics multiplication, the number of combinations will be 5*5=25.

Running EMUsort As If Default Kilosort4 (v4.0.11)

In order to run EMUsort exactly like a default Kilosort4 (v4.0.11) installation for comparison of performance, you can use the short-form command emusort -kcsf . to run it in the current folder, or use the below, longer-form command:

emusort --ks4 --config --sort --folder /path/to/session_folder

This will generate a default Kilosort4 configuration file and run the sort with it. It does not interfere with the main emu_config.yaml file because it is a separate configuration file named ks4_config.yaml.

To only adjust the ks4_config.yaml in the session folder without performing spike sorting, you can run:

emusort --ks4 --config --folder /path/to/session_folder

To reset the ks4_config.yaml file to default from configs/config_template_ks4.yaml and edit it, run:

emusort --reset-config --ks4 --config --folder /path/to/session_folder

To run Kilosort4 emulation, reset ks4_config.yaml to default settings, edit the new ks4_config.yaml, and perform spike sorting in the current folder, all in one compact command, you can run the below command:

emusort --r -kcsf .

This emulation capability is useful for comparing the performance of EMUsort vs. Kilosort4.

Final Notes

If there are any discrepancies in the instructions or any problems with the comments/code, please submit an issue on GitHub so we can try to address the issue ASAP.

Thank you for trying out EMUsort! If you find it helpful, enjoy it, or love emus, give us a ⭐️ on GitHub!