notebook improvements

[MSenden]

Here are some suggestions:

1. Enhance Documentation:

   • Use markdown cells to provide explanations before code cells.
   • Explain the rationale and purpose behind each significant block of code.
   • Add comments within code cells for complex lines or functions.

2. Introduce a Table of Contents:

   • Begin the notebook with a table of contents that links to the key sections. This helps users navigate large notebooks and quickly access the information they need.

3. Clean Up:

   • Before finalizing, clear all cell outputs and run the notebook from the start to ensure everything works in sequence.
   • Remove any redundant or unused code cells or imports (e.g., set_stimulation, fit_gamma and running_mean are not used).

4. Interactive Widgets:

   • ipywidgets are imported bu never used.
   • It could be nice to create interactive sliders, buttons, and dropdown menus. This is particularly useful for adjusting model parameters and instantly visualizing the effects.

5. Modularize Code:

   • Break down long code cells into smaller, more manageable chunks.
   • Consider moving utility functions or repetitive code blocks to external Python files and import them. This cleans up the notebook and makes code reusable.