Loading...

Primary Visual Pathway Simulation in Mouse Using NetPyNE

Waheed Al-Kaabi, Anwer Fadhil | 2021

346 Viewed
  1. Type of Document: M.Sc. Thesis
  2. Language: English
  3. Document No: 54438 (52)
  4. University: Sharif University of Technology, International Campus, Kish Island
  5. Department: Science and Engineering
  6. Advisor(s): Peyvandi, Hossein
  7. Abstract:
  8. Simulation of biophysical neural networks enables the interpretation and integration of fast-growing and different experimental datasets. The widely used NEURON simulator allows molecular-to-network simulation. However, it is still a very hard challenge to create large-scale models and operate parallel simulations applying NEURON. SUNY Downstate developed the NetPyNE means networks using Python and NEURON, which was funded by the New York State Department of Health and some other institutions. NetPyNE is a Python-based tool that enables the development of data-driven multi-scale network models in NEURON through both programmatic and graphical interfaces. It is a powerful tool for parallel simulation and analysis of large-scale models. Modelers can use NetPyNE to create NEURON networks, perform parallelized simulations efficiently, use built-in visualization and analysis functions (voltage traces, connectivity matrices, spike raster plots). The aim of this study is to understand the representation and transmission of information across the visual pathway and how the V1 receives and processes visual inputs using the NetPyNE tool. We constructed our model using an internal network (V1) composed of four biophysical neurons (Scnn1a, Rorb, NR5A1, and Pvalb). We assumed 900 simulated cells connected to an external network (LGN), which composed of 100 virtual cells. After simulation at a firing rate of 20.0 Hz, we got 265020 connections representing the pathway between 1000 cells (LGN-to-V1) with 984038 Synaptic contacts. In this study, we simulated a simple biophysically detailed model of mouse V1. The model was constructed with an acceptable degree of biological reality and simulated in the NetPyNE framework of a visual physiology analysis
  9. Keywords:
  10. Spiking Neurons ; Brain Modeling ; Scalable Open Network Architecture Template (SONATA) ; Visual Pathway ; NetPyNE Tools ; Brain Modeling Toolkit (BMTK)

 Digital Object List

 Bookmark

No TOC