CN2 Simulator

Computational Neuroscientists' Comprehensive Neuronal Simulator including

• electrophysiological recording
• calcium imaging
• voltage imaging
• motif simulation

Features

• Camera settings
  • recording time / frame rate / exposure time
  • Field of View
  • pixel size
• Various microscopy simulation
  • SPIM
  • XLFM
• Neuron physiological parameters
  • refractory period
  • photobleaching
  • protein expression rate
  • GECI
    • rise/decay time
    • dF/F0
• Recording proteins
  • GEVI/GECI
  • H2B(NLS), cytosolic, soma targeted, membrane targeted
• Various motif types
  • synchronous firing
  • sequentially firing
  • arbitrary pattern of firing
  • synchronous firing rate increase
  • sequential firing rate increase

Applications

• benchmarks
  • computational microscopy
  • cell extraction
  • spike deconvolution
  • motif mining

How to use

For package use

• pip install git+https://github.com/NICALab/CN2-Simulator.git

For development

• Install dependencies through conda env create -f environment.yml.

• Activate the conda environment through conda activate CN2Simulator.

• Follow tutorials

  • Follow tutorials/example.ipynb to simulate neuron motif.
  • Follow tutorials/imaging.py to simulate calcium imaging.

• One can change params.yaml for different simulation settings.

• Check the data inside \generated_data folder.

• Visualize motifs with SimulMotif/visualize.m, which is a Matlab script.

Figures