Plugins for phy1 and phy2

Plugins to Phy - additional features to Phy. There are two repositories:

plugins for phy1: https://github.com/petersenpeter/phy1-plugins

plugins for phy2: https://github.com/petersenpeter/phy2-plugins

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.
• Visualization for spikes violating the refractory period and a filter for the raw traces. (phy2)

All new features are accessible from the top menu labeled clustering.

ControllerSettings - Extra columns in ClusterView (only for phy1)

• 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 (phy1)

To install, place the content in your plugins directory (~/.phy/), replacing the existing files and plugins folder.

Installation (phy2)

• place the content in your plugins directory (~/.phy/), replacing the existing files and plugins folder.
• Installl the python package panda: write “pip install pandas” in the terminal from your phy environment.
• Copy 'tempdir.py' in "YourPhyDirectory/phy/utils". The exact path can be found in the error message from phy you will receive when this step has not been completed.

For the time being, you will also have to find the path to your phy installation and copy 'tempdir.py' to ~YourPhyPath/phy/utils.