obi_platform_analysis_notebooks

OBI Platform Analysis Notebooks

Notebook Folder Structure

The folder has been divided into 3 main subfolders, each corresponding to the level of analysis:

• Cellular

  • analyse_single_cell_sim: Notebooks to analyse single cell simulations

    • analyse_single_cell_sim: Plot recordings and extract spikecount

  • efeature_extraction: Notebooks of e-feature extraction

    • current_clamp_ephys_extraction: Extraction of e-features from voltage clamp experiments for analysing the firing behaviour of neurons, AP properties, subthreshold and suprathreshold voltage properties
    • voltage_clamp_ephys_extraction: Extraction e-features from whole cell patch voltage clamp data. Use for ion channel model building.

  • emodels: Notebooks on E-models. See this README for more details

    • parameter_plots: Compare parameters of an e-model across sections on Open Brain Institute Platform (OBP)
    • cadpyr_showcase: Demonstrates various properties of the OBP canonical cADPyr (continuos firing and adapting type pyramidal neuron) e-model
    • plot_iv_fi_curve: Computes and visualize IV and FI curves for a single-cell model using BlueCelluLab.
    • single_cell_currentscape_analysis: Currentscape analysis of single cells
    • single_cell_impedance_analysis: Impedance analysis of single cells
    • lfpy_simulations
      • LFPy_active_iclamp: Running an OBP e-model with current clamp: record and plot LFP on a microelectrode array
      • LFPy_active_synapse: Running an OBP active e-model with a synapse activation
      • LFPy_passive_synapse_1: Running a passive OBP e-model with a synapse activation: Plot LFP Heatmap
      • LFPy_passive_emodel_synapses_LFP: Running a passive OBP e-model with a synapse activation: Plot Local Field

  • morphologies: Notebooks on morphologies

    • display_morphology_population_features: Plot morphological features for a population of morphologies
    • morphology_quality_check: To test a list of morphologies against some common issues that may cause issues with tools and analyses using the morphologies.

• Circuit

  • adjacency_matrix: extracts and visualize the connectivity between all pairs of pre- and post-synaptic neurons
  • circuit_composition: displays the composition of a circuit model with respect to user-selected neuron properties, such as morphological types, electrical types, etc.
  • connectivity_matrix: extracts and visualizes a matrix of connection probabilities or #synapses per connection (mean/std/...), grouped by a selected neuron property (layer, m-type, ...).
  • synapse_properties_matrix: analyse, extract and visualize a matrix of a selected synapse property (conductance, delay, ...), grouped by a selected neuron property (layer, m-type, ...).

• Metabolism

  • Metabolism: Data-driven molecular model of the neuro-glia-vascular system allows exploration of the complex relationships between the aging brain, energy metabolism, blood flow, and neuronal activity.

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