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Achievement: Starstruckx2Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: YOLOAchievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

Achievements

Achievement: Starstruckx2Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: YOLOAchievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

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smestern/readme.md

Hi, I'm Sam Mestern

Neuroscientist and developer working on electrophysiology data analysis, neural modeling, and open-source scientific software.

Researcher at the University of Western Ontario.

Website Google Scholar Twitter

Neuroscience Stuff

Project Description
ni_dynamicclamp A high-throughput dynamic clamp system for biohybrid networks of up to 1000 neurons, connecting living neurons with computational models. Supports Brian2 and PyTorch. C/C++ Python Brian2
pypatchOTDA 🏆 Corrects for batch effects and experimental variability in electrophysiology data using optimal transport, enabling cross-dataset comparisons. Winner of the Allen Institute MapMySpikes Challenge. Python Optimal Transport
gigaseal Extracts action potentials and their features from neural time-series, with dashboarding and visualization for patch-clamp data. Python Signal Processing
sNMO Fits single-neuron models (AdEx, LIF, CAdEx, and others) to in vitro recordings using genetic algorithms, Bayesian optimization, and neural-network posterior modeling. Python Optimization
pyCEDFS Extracts and converts data from the CFS neuroscience format, including conversion to NWB. Python NWB
DANDI Intracellular Ephys Dashboard A unified dashboard for intracellular electrophysiology datasets on the DANDI Archive, covering 12,000+ recordings across species and brain regions. Blog post on building it. Python Dashboard
Primate Cell Type Database Backend developer for the JMT Primate Cell Type Database; built the data dashboard for the intracellular ephys table. Python Dashboard

LLM Things

Project Description
SciAgent A framework for building scientific data analysis agents with rigor guardrails. Includes a self-assembly wizard for generating domain-specific agents and a plugin architecture. Runs from the CLI, web UI, or IDE. MIT licensed. Python LLM
treepilot An agentic framework and frontend for genealogy research. Automates family tree construction and data extraction from genealogical records. Python LLM

Skills & Technologies

  • Languages: Python · JavaScript · MATLAB · R · SQL · C/C++
  • Neuroscience: Electrophysiology · Patch Clamp · Signal Processing · NWB Format
  • Machine Learning: PyTorch · Scikit-learn · Neural ODEs · Bayesian Optimization
  • Tools: Git · Docker · Plotly · Pandas · NumPy

Feel free to explore my repos or reach out. Always happy to talk neuroscience, open-source tools, or anything in between.

Pinned Loading

  1. 2D Histogram Sliced Wasserstein Dist... 2D Histogram Sliced Wasserstein Distance via Scipy.stats
    1 
    """
    2 
    Original Docstring -
    3
    4 
    Programmer: Chris Tralie
    5 
    Purpose: To use the POT library (https://github.com/rflamary/POT)
  2. sNMO sNMO Public

    sNMO : single neuron model optimzier (SNMO)

    Python

  3. pypatchOTDA pypatchOTDA Public

    Jupyter Notebook 3

  4. ni_dynamicclamp ni_dynamicclamp Public

    Dynamic Clamp interface for brian2 <-> NI daq systems

    C 2

  5. pyAPisolation pyAPisolation Public

    [DEPRECATED] Feature Extraction and Other tools for Patch-Clamp electrophysiology data

    HTML 2

  6. treepilot treepilot Public

    A hacky / vibecoded AI family tree researcher

    Python 151 4