Microstim: Axonal and Cellular Dynamics Simulation

Microstim is a scientific Python package for simulating and analyzing axonal and cellular responses to electrical stimulation. It provides a flexible framework for running a variety of models, generating plots, and exploring the effects of stimulation parameters on neural cortical tissue.

Features

• Cellular and Axonal Models
  Simulate both cell and axon responses using customizable parameters.

• Configurable via YAML
  All global parameters are managed in a single config.yaml file for easy reproducibility and experimentation.

• Modular Functions
  Run specific analyses (e.g., heatmaps, radii, intensity plots) for both cell and axon domains.

• Command-Line Interface
  Launch any simulation or plot directly from the command line with flexible flags.

• Automated Plot Generation
  Produce publication-ready figures and animations.

• Extensible Architecture
  Easily add new models or analysis functions as the project grows.

Installation

1. Clone the repository

    git clone https://github.com/yourusername/microstim.git
    cd microstim

2. Create and activate a virtual environment

    python -m venv venv
    source venv/bin/activate   # On Linux/Mac
    venv\Scripts\activate      # On Windows

3. Install dependencies

    pip install -r requirements.txt

Configuration

All simulation parameters are stored in config.yaml at the project root. Edit this file to change model settings, stimulation parameters, or analysis options.

Usage

Run any function using the script:

python run.py {function} --is_depol --is_production --position 

Available functions

{
  "cell": [
    "heatmap",
    "radii",
    "boostHeatmap",
    "gif",
    "heatmapRadiusPot",
    "intensityPotential",
    "intensityRadius",
    "maxpotPosition",
    "maxpotDistance",
    "weightsHeatmap"
  ],
  "axon": [
    "ratios",
    "distributions",
    "EI",
    "intensity",
    "map",
    "mapintensity",
    "intensitygif",
    "mapgif"
  ]
}

flags

--is_depol # depolarization flag
--is_production # ready to produce plots flag
--position # distance between stim and cell

Example

python run.py maxpotPosition --is_depol --is_prod --position 500

Output

Results and plots are saved in the results/ directory. Animations and figures are automatically generated for supported functions.

Project Structure

microstim/
│── axon.py
│── utils.py
│── config.yaml
│── run.py
│
├── cell/
│   ├── heatmap.py
│   ├── radii.py
│   └── ...
│
├── axon/
│   ├── distributions.py
│   └── ...
│
└── plot/
    └── results/

Assets