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Neuron-Simulation

This project explores various computational models of neuronal stimulation, culminating in an algorithm designed for the stimulation of current cochlear implants.
Originally developed in Matlab for a master's program in Neuroscience, the project has been reimagined in Python and formatted into a Jupyter lab notebook for enhanced readability. This transition not only showcases my scientific background but also reflects my approach to working with data and visualization. For a more in-depth understanding of the underlying mathematical and neurobiological details, refer to my written report.

Installation

You can view a rendered version of the notebook here.

Prerequisites

  • Python: Ensure that Python is installed on your machine. You can download it from python.org.
  • Jupyter Lab: Install Jupyter Lab using the following command in your terminal or command prompt: 
    pip install jupyter lab
  • External Libraries: Use pip install for library installation. 
    pip install pandas numpy matplotlib ipywidgets scipy

Steps

  1. Download: Download the Jupyter notebook file Neuron-Simulation.ipynb from this repository to your local machine.

  2. Run Jupyter Lab Server:

  • Open a terminal or command prompt.
  • Navigate to the directory where you saved the notebook file.
  • Run the following command: 
    jupyter lab
  1. Access the notebook:
  • Open your web browser and go to the URL displayed in the terminal.
  • Navigate to the notebook file and click on it to open.
  1. Interact with the Notebook:
  • Execute code cells using the "Run" button or by pressing Shift + Enter.

Usage

It is recommended to Run all cells as this ensures all cells to execute properly. The project is seperated into different models that can be run seperately, but within a model some calculations require the execution of preceeding cells.

Structure

  1. Neuron-Simulation.ipynb: Jupyter notebook containing the computational models of neuronal stimulation and cochlear implant algorithms.

  2. Neuroprothetics-report-Y-Karsten.pdf: Written report providing a more in-depth understanding of the underlying mathematical and neurobiological details.

  3. README.md: Instructions on how to get started, install dependencies, and use the Jupyter notebook.

Dependencies

  • Python: Version 3.10.12
  • Jupyter Lab: Version 4.0.5
  • Libraries:
    • NumPy: Version 1.25.2
    • pandas: Version 2.0.3
    • matplotlib: Version 3.7.2
    • ipywidgets: Version 8.1.0
    • scipy: Version 1.11.2

License

This project is licensed under the MIT License - see the LICENSE file for details.

References

This project was originally developed for the 'Neuroprosthetics' class in my master's program in Neuroscience, supervised by Mathias Dietz and Sven Hermann.
Relevant scientific references can be found in the Publication bibliography section of my written report.

Acknowledgments

I am grateful for the valuable guidance provided by Sven Hermann, who served as a tutor during the university class. His assistance was particularly instrumental in the development of the initial Matlab version of this project.