Neuron Demonstration

Luke Campagnola, 2015

This is an educational simulation of a simple neuron.

• Hodgkin & Huxley channels
• Lewis & Gerstner (2002) cortical channels
• Destexhe 1993 Ih channel
• Current/voltage clamp electrode with access resistance
• Diagram of cell membrane with circuit schematic
• Realtime simulation and plotting of voltages, currents, open probabilities, etc.
• Analysis tool for generating I/V curves and similar analyses.

Requirements

• Python 3.10 or higher
• NumPy, SciPy
• PyQt5 or 6
• PyQtGraph
• lmfit

Installation

There are multiple ways to install:

1. Using Anaconda/miniconda:

   a. Experienced Python users can install the requirements listed above, then download the neurodemo code and run demo.py. For everybody else, I recommend installing the [Anaconda Python distribution] (http://continuum.io/downloads). Download and run the installation package for your platform. To keep the size down, you can instead install [miniconda] (http://conda.pydata.org/miniconda.html). When you run the installer, take note of the location it is installing to.

   b. If you installed miniconda, then it is necessary to manually install numpy, scipy, and pyqt6 (if you installed Anaconda, then these packages are already installed and you can skip this step, except for lmfit). This can be done from a terminal:

   > conda install numpy scipy pyqt pyqtgraph lmfit
   

   c. Install pyqtgraph (this is required regardless of which python distribution you installed):

   > pip install pyqtgraph
   

   d. Download the [neurodemo source code] (https://github.com/campagnola/neurodemo/archive/master.zip). You can find this by going to http://github.com/campagnola/neurodemo and clicking the "Download ZIP" button on the right side of the page. Unzip the file and you are ready to begin!

2. To get the latest version that runs with Python 3.10 and PyQt6 you can follow these steps, depending on your system. Note that these all create and use Python virtual environments rather than conda/mminiconda environments.

   a. Windows

   • Git clone the repository.
   • In the main directory, under the windows cmd terminal, run win_install.bat.
   • Create a shortcut on the desktop to the file win_start_demo.bat, and set the "window" to minimized. Clicking on the shortcut should start the program.
   • There is no working way to make an exe file at the moment - the .spec file are getting close but not working yet (missing a windows dll).

   b. macOS

   • Git clone the repository.
   • In the main directory, using a zsh or bash terminal, run ./make_local_env.sh. This should create the environment, install all the required packages, and leave you with the environment activated.
   • type "python demo.py" to run the program.
   • To make an installable file (dmg), run the shell script that is appropriate for the processor: make_M1_dmg.sh or make_x86_64_dmg.sh. The resulting dmg file will be in the folder dist/demo_(architecture).dmg. You can then install the app as you would with any other dmg file.

Running the Demo

You can launch the demo from the terminal by navigating to the location where you extracted the source code (eg, cd Downloads\neurodemo\) and then typing python demo.py.

Windows: Open the folder where you extracted the neurodemo source code. Right click demo.py and select "Open with..". Navigate to the location where you installed anaconda or miniconda (you may need to click something like "browse" or "choose another application" depending on your version of windows). Select python.exe.

macOS: You can launch as above, or install the dmg file and just start the app.