My open-source projects on github#

Outside my day job, I contribute to open-source projects. I made a few on my own time that are not used in the lab, but may help someone out there.

Overview#

https://github.com/mmyros

Some highlights#

  • Cluster quality: measurements of how well spikes were isolated from noise. Parallelized and packaged into a CLI interface.

  • Phy extras are enhancements to the popular Phy interface for inspecting clustering. Includes:

    • Alt+R to cycle through raw data and waveform views: raw, highpass, mean+highpass, median+highpass, highpass+median, highpass+mean

    • s for Scrub outliers using Local Outlier Factor (also implemented are Robust covariance, One-Class SVM, and Isolation Forest. See plugins/custom_split.py)

    • t for Time split using gaussian hierarchical model

    • x for k-means split

    • d for GAC split (Due to Swindale lab, gradient ascent clustering (GAC) algorithm, a variant of the mean-shift algorithm)

  • PulsePal port to Python 3: Port to Python 3 of a mainly-Matlab project from Sanworks LLC. They had some Python code, but it broke a while ago.