GSoC 2022 Project Idea 12.2: Implement methods to calculate and visualize current source density signals (350 h)

Human Neocortical Neurosolver (HNN) is a software for interpreting the neural origin of macroscale magneto-/electro-encephalography (MEG/EEG) data using biophysically-detailed microcircuit simulations. HNN can be run through a user-friendly graphical user interface or through a Python interface HNN-core.

Mailing list(s):

Goal: The aim of this project is to enhance HNN functionality with tools to simulate and visualize current source density (CSD) signals from the HNN neocortical model, beginning with the HNN-core API for simulating local field potential signals (LFPs).


Related issue:

  • Understand the LFP example and code
  • Decide on CSD methods and API. For example: standard difference of LFP, spline, step etc. See the iCSD package
  • Develop the code for documenting CSD tools following the current examples for simulation event relate potentials and low frequency rhythms
  • Write tests for the CSD functionality. For example, by computing the CSD on artificial “sinusoidal” LFP pattern, or checking that the peaks are roughly the same with different methods.
  • Bonus: Build local fields potential and CSD visualization into the next generation HNN GUI components in Begin implementation of comparison of simulated LFP/CSD to empirically recorded data.

Difficulty: Medium

Duration: 350 hours (full time)

Skills: Some experience in neuroscience and Python. Experience in simulating neural activity with NEURON is helpful but not required.

Possible mentors: Nicholas Tolley, Stephanie Jones @Stephanie_Jones, Mainak Jas, Ryan Thorpe

Tech keywords: Python

Hi @malin and @Stephanie_Jones, I’m currently a phd student in computational neuroscience and I am focusing on neural stimulation simulation. I’m pretty interested in this project and just made a minimal working implementation of the CSD visualization with the LFP data generated by HNN simulations:

Could we discuss this more, like, the possible ways to introduce the API to hnn-core? I tried to use the google group but found having no access to it.

Hi @chenghuzi , that sounds exciting! Would you mind opening a WIP (work in progress) pull request on hnn-core github so we can discuss this further? I understand it’s premature but it helps us understand where you’re at and to start discussing further.

We should also look into what’s going on with the google group.


Sure! Will do it asap!

I created a PR here, have a look and let me know if you’re interested in letting me to use this as the starting point of the GSOC 2022 project.