Plugins to Phy1
These plugins add additional features to Phy1
Features
- Reclustering. Reclustering with KlustaKwik 2.0 - dependent on a local version of KlustaKwik, which is provided in the zip file for Windows 10) and python package: pandas. To install write “pip install pandas” in the terminal in your phy environment.
- Outlier removal using the Mahalanobis distance. Standard threshold is 16 standard deviations (adjustable threshold).
- K-means clustering. Standard separation into clusters (adjustable number).
- Export shank info for each unit. This is necessary if you want to know which shank a given unit was detected on.
All new features are accessible from the top menu labeled clustering.
ControllerSettings - Extra columns in ClusterView
- Firing rate
- Horizontal position
- Shank number (dependent on the rezToPhy.m version in the KiloSortWrapper)
ControllerSettings also allows you to adjust the number of spike displayed i FeatureView (increased to 15,000) and WaveformView (standard: 300). I recommend to delete the local .phy folder in your data folder, when adjusting these parameters.
Installation
To install, place the content in your plugins directory (~/.phy/), replacing the existing files and plugins folder.
How to cite
Please use below DOI for citing these plugins.
