Plugins to Phy2

These plugins add additional features to Phy2. Originally created for Phy1 by Peter Petersen and made compatible with Phy2 by Thomas Hainmueller. Newly updated implementations made by Mingze Dou.

Features

Newly Updated Features

• ImprovedISIAnalysis (alt+i): Detects ISI conflicts using multiple metrics
• StableMahalanobisDetection (alt+x): Outlier detection with interactive visualization
• ReclusterUMAP (alt+k): Modern reclustering using UMAP and template matching
• GoodLabelsPlugin: Improved cluster organization that sorts by quality (good > mua > noise). Provides better workflow organization despite Phy's real-time update limitations.

Legacy Features

• Reclustering (alt+shift+k, alt+shift+t): KlustaKwik 2.0 based reclustering
• Mahalanobis Distance (alt+shift+x): Outlier detection (threshold: 16 std)
• K-means Clustering (alt+shift+q): Basic clustering with adjustable clusters
• ISI Violation (alt+shift+i): Visualize refractory period violations

Dependencies

pip install pandas numpy scipy scikit-learn umap-learn

Installation

1. Copy the plugin files from the plugins directory of this repository to your Phy user configuration directory, inside a plugins subfolder.
   • On Windows, this is typically C:\Users\<YourUserName>\.phy\plugins.
   • If the plugins folder doesn't exist, you will need to create it.
2. Copy other supporting files (e.g., phy_config.py, klustakwik.exe if used) from the root of this repository to your Phy user configuration directory (e.g., ~/.phy/ or C:\Users\<YourUserName>\.phy).
3. Install dependencies (see Dependencies section above).
4. Copy 'tempdir.py' (from the plugins directory of this repository) to *YourPhyDirectory*/phy/utils.

Authors

• Original Phy1: Peter Petersen
• Phy2 compatibility: Thomas Hainmueller
• New implementations: Mingze Dou

How to Cite