Electromagnetic Stimulation Platform

This repository contains the code and documentation for the stimulation controller used in the paper Bioelectromagnetic Platform for Cell, Tissue, and In Vivo Stimulation.

Documentation

Detailed documentation of both the coils and stimulation controller can be found in the manuals in the docs folder.

Additionally, the following three figures show the use cases, physical and electromagnetic properties, and the assembled coils and stimulation controller.

Data Collection

The following video gives an overview of the process used to collect experimental data from coils to validate performance. The process consisted of 3D prinint custom mounts to attach a magnetometer sensor to a 3-axis robotic arm, which was then configured to scan over the region of interest near the coils both while they were operating and off to obtain both active and sham conditions.

Initial Setup

ELEGOO Nano Setup

To get started, first install the ELEGOO Nano driver

Next, configure the ELEGOO Nano to communicate with the host PC's python application. Load the prototype.ino sketch from the Arduino-Python3-Command-API github repository to the ELEGOO Nano using the Arduino IDE or some other microcontroller programmer.

Environment

Install virtualenv for creating virtual python environments. Then create and activate an environment.

Windows (command prompt)

Install virtualenv:

> python -m pip install virtualenv

Create an environment:

> python -m venv env_location\controller

Activate the environment:

> env_location\Scripts\activate.bat

Linux

Install virtualenv:

$ python3 -m pip install virtualenv

Create an environment:

virtualenv controller

Activate the environment:

source env_location/stim_controller/bin/activate

Python Environment

Install the python package dependencies either manually or automatically using the requirements.txt file.

Automatic:

pip3 install -r ./requirements.txt

Manually:

pip3 install pyserial arduino-python3 pyside2 pyqtgraph keyboard PyInstaller

Running the stimulation controller

Simply run the stimulation_controller.py python script when the stimulation controller is plugged in to the host computer to launch the GUI.

Windows (command prompt)

> python stimulation_controller.py

Linux

$ python3 stimulation_controller.py

Bundling program into a single package

Use PyInstaller to bundle all of the necessary files into a single folder or executable so that it can be easily installed on a computer without configuring and setting up a Python environment. This reduces setup time for computers that simply need to use the stimulation controller, but otherwise do not need to do any development.

Navigate to the stimulation-controller folder:

cd path/to/stimulation-controller/

Run PyInstaller to bundle the application

pyinstaller stimulation_controller.py

Run the program from bundled package:

Windows:

C:\path\to\stimulation-controller\Windows\dist\stimulation_controller\stimulation_controller.exe

CentOS:

/path/to/stimulation-controller/CentOs/dist/stimulation_controller/stimulation_controller

Cite

@article{ashbaugh2021bioelectromagnetic,
  title={Bioelectromagnetic platform for cell, tissue, and in vivo stimulation},
  author={Ashbaugh, Ryan C and Udpa, Lalita and Israeli, Ron R and Gilad, Assaf A and Pelled, Galit},
  journal={Biosensors},
  volume={11},
  number={8},
  pages={248},
  year={2021},
  publisher={MDPI}
}