NeuronQuickStart

A wrapper to common functionality to work with Neuron package (https://www.neuron.yale.edu/neuron/)

Overview

Installation:

• git clone

• conda create --name neuron python=3.8

• conda activate neuron

• pip install -r requirements.txt

• pip install neuron==8.0.2 # in linux. maybe different in windows

• For windows, may requrire to manually install neuron separately: https://www.neuron.yale.edu/neuron/download

• Can updgrade for newer python & neuron version if needed (not validated against the code here)

Compile mod (mechanism) files:

• cd L5PC_Mouse_model_example
• nrnivmodl mods # Important: after conda activate neuron!

Usage example:

python main_example.py # or via IDE run the python code

• main_example.py / ipynb for a short overview of functionality
• Neuron's python tutorials: https://nrn.readthedocs.io/en/8.2.6/tutorials/index.html

Repository structure:

• Python files:
  • main_example.py & main_example.ipynb- show functionality in current repository
  • utils/neuron_model.py - NeuronCell wraps neuron h loading (common functionality and replacement for some hoc code)
  • utils/factory_neuron_model.py - wrap & refactor converters (swc, asc, NeuronCell)
  • utils/neuron_viewer.py - plot cell (with extensions of markers, electrodes and scalebars)
• Neuron models:
  • h01_Human_swc_example - contains downloaded examples from h01 data
  • L5PC_Mouse_model_example - commonly used neuron model (Etay Hay, 2011). Contains:
    • mods - folder with needed mechanisms (mod) files. Compile with: "nrnivmodl mods" (mods is the mechanisms' folder name). Will create output file within the folder you run the script from.
    • morphologies - *.ASC or *.SWC ascii (textual) description files with morphology description. ASC - tree-like structure. SWC - table-like structure with columns for: (id, type, x, y , z, diam, parent-id). Can be viewed with the following tool: https://neuroinformatics.nl/HBP/morphology-viewer/
    • hoc files - templates used when loading the model (can be a single generic template instead)
      • generic_template.hoc - common/basic hoc file for swc/asc neuron loading
      • hoc files can be re-written to use the python API (as in this repository) (NeuronCell complete additional functionality converted from hoc to python code)