README.md

MountainSort to Phy Extension

This repository provides tools to integrate

• MountainSort spike sorting
• with the Phy curation environment.

Table of Contents

• Installation
• Usage
• Modules
• Configuration
• Contributing
• License

Installation

1. Clone the repository:

   git clone https://github.com/yourusername/mountainsort-to-phy.git
   cd mountainsort-to-phy

2. Install dependencies:

   pip install -r requirements.txt

3. Add the Phy plugins: Copy the plugins to your Phy plugins directory. This is typically located at ~/.phy/plugins/.

   mkdir -p ~/.phy/plugins
   cp plugins/* ~/.phy/plugins/

4. Update your Phy configuration: Edit your ~/.phy/phy_config.py to include the new plugins:

   c.TemplateGUI.plugins = ['MSCurationTagsPlugin', 'WaveformUMAPPluginComplete', 'TetrodeMetrics', 'MSCurationSave']

Usage

Converting Phy Clusters to MountainSort Format

To convert Phy clusters back to the MountainSort format, run:

python phy_to_mountainsort.py /path/to/phy/folder

Converting MountainSort to Phy

To convert MountainSort data for use in Phy:

1. Ensure your MountainSort data is organized in the specified directory structure.
2. Run the conversion script:

   python mountainsort_to_phy.py

Adding Behavioral Data to Phy

Use the provided MATLAB scripts to add behavioral data to Phy:

1. Update the configuration in makeNPYfiles.m and atomicNPYfile.m as needed.
2. Run the MATLAB scripts to generate the NPY files for behavioral data.

Modules

phy_to_mountainsort.py

Converts Phy clusters back to the MountainSort format. The script expects a folder containing Phy output and converts it to a format compatible with MountainSort.

mountainsort_to_phy.py

Processes MountainSort output to prepare it for use with Phy. This includes extracting waveforms, spike sorting, and exporting to Phy format.

Plugins

• umap_plugin.py: Adds a custom UMAP view for dimensionality reduction and visualization in Phy.
• MSclusterPlugins.py: Integrates MountainSort cluster metrics with Phy for enhanced curation capabilities.

MATLAB Utilities

• constructheader.m: Constructs headers for NPY files.
• write.m: Writes MATLAB arrays to NPY files.
• makeNPYfiles.m: Generates NPY files for behavioral data to be used in Phy.
• atomicNPYfile.m: Helper function to write behavioral data to NPY files.

Configuration

Configuration Options in mountainsort_to_phy.py

• filtered: Use filtered MDA files instead of raw MDA files.
• toleratemissing: Skip folders with missing tetrodes.
• skipproc: Skip already processed folders.
• parent_path: Directory containing MountainSort data.

Example Configuration

Update the configuration variables in mountainsort_to_phy.py as needed:

config['filtered'] = True
config['toleratemissing'] = True
config['skipproc'] = True
config['parent_path'] = '/mnt/data/MountainSort'

Contributing

Contributions are welcome! Please fork the repository and submit a pull request with your changes.

License

This project is licensed under the MIT License. See the LICENSE file for details.