Available student projects

Would you like to contribute to our research? This is a list of projects available for interested students. Most are designed to be completed within 3 to 6 month, but some can be expanded into longer projects, even full PhD scope. If you are interested in working on any of the projects please contact Ján Antolík.

If you want to get to know us, stop by at the Computational neuroscience seminar NAIL128 and have a chat with us.

Simulation of cortical implants for vision restoration

  • Modeling electrical stimulation in the visual cortex for visual prosthetic (brain-computer interface) applications

  • Characterizing the spatiotemporal activation profile of different neuron types for optogenetic stimulation

  • Stimulation protocols for vision restoration using brain-machine-interface.

Machine Learning in Neuroscience

  • Transfer learning: from spiking models to DNNs.

  • Reimplement firing rate hebbian-driven development simulation framework in PyTorch

  • Capturing V1 spatio-temporal dynamics in deep neuralnetwork model

  • Novel DNN model for decoding visual stimuli from population recordings in primary visual cortex.

  • Determining maximally exciting and suppressive surround stimuli in a spiking model of primary visual cortex.

Spiking Network Models of Visual System

  • Modeling different inhibitory neural types in large-scale spiking model of V1.

  • Porting model of cortico-thalamic loop to latest version of Mozaik

  • Asymmetric On & Off responses in Retina, LGN and V1.

  • Model of monkey visual system.

  • Unified model of cat visual system.

  • OFF centred thalamic V1 convergence.

  • Embedding of detailed compartmental neuron models into large-scale model of primary visual cortex.

  • Local-field potentials (LFP) in a large-scale model of cat primary visual cortex.

  • Travelling waves.

Methods for analyzing experimental and simulated neural data

  • Impact of traveling waves on decoding of functional cortical organisation from spontaneous activity.

  • Relationship of traveling waves and oscillations in the cat primary visual cortex.

  • Topological analysis of population activity in a large-scale V1 model.

  • Fractal dimension of population activity in a large-scale V1 model.

Models of neural system development

  • Biologically plausible model of body representation development (collaboration with the robotics group of Matej Hoffman, CVUT).

  • Development of long-range correlations in spontaneous activity.

  • Reconciling activity driven development of orientation maps with ON/OFF V1 convergence.

  • Unifying retinal mozaik model with activity based development.

Software engineering projects

  • Mozaik dockerization.

  • Mozaik analysis parallelization.

  • Data-store module based on object oriented database for biological neural network simulator.

  • A 3D model visualization of detailed spiking neural network models.

  • Sumatra integration with Mozaik.

  • Parameter searches in Mozaik

Web development projects

  • Arkheia update & expansion.

  • Open Vision project.

  • Graphical user interface for biological neural network simulator.

  • Deployment of a biological neural network simulator on a HPC platrform.