IntroNE

Code material for the interactive recitations and homeworks of the NYU course Introduction to Neural Engineering.

These recitations are based on Jupyter notebooks that can be executed either locally on your laptop (this will require some installations, see instructions below) or online in the following Binder environment (does not required any installation):

Local use instructions

Installation

• Download and install a Python distribution from https://www.anaconda.com/download/ using the Anaconda installer
• Open the Anaconda prompt
• Clone this repository: git clone https://github.com/tjjlemaire/IntroNE.git. To do this you will need to have Git installed on your computer. Alternatively, you can download the repo archive and unzip it (although the Git way is highly advised).
• Move to the repo folder: cd IntroNE
• Create a new anaconda environment: conda create -n introne python=3.8
• Activate the anaconda environment conda activate introne
• Install the code dependencies: pip install -r requirements.txt
• You're all set!

Notebook execution

• Open an anaconda prompt
• Activate the anaconda environment: conda activate introne
• Move to this repository
• Download the latest updates from the online repository: git pull
• Install the code dependencies: pip install -r requirements.txt
• Start a jupyter lab session: jupyter lab
• Open the notebook of interest by double-clicking on it
• In the upper right corner, make sure that jupyter is running with the right kernel (Python 3.8.12 64-bit ('introne': conda)). If not, click and select the appropriate kernel from the drop-down list.
• You're all set!

Recitations schedule

• 2025.01.30: the basics of action potential dynamics (recitation1_AP_basics.ipynb)
• 2025.02.06: extracellular action potentials and recordings (recitation2_ext_recording.ipynb)
• 2025.02.13: spike detection and classification (recitation3_spikesorting.ipynb) This tutorial uses a significant amount of RAM, hence execution in the Binder environment will be very slow. It is therefore highly advised to execute the notebook locally.
• 2025.02.20: extracellular electrical stimulation (recitation4_ext_stim.ipynb) For Windows users, you will to download and install a NEURON distribution if you want to run this notebook on your machine.

Homeworks schedule: T.B.D.

Questions

For any questions, you can contact me by email: theo.lemaire@nyulangone.org