Available Functions for CBGTC

Data Loading and Processing

Available functions:

• Parameters for CBGTC model and simulation
  • SignalAnalysisParams
  • SimulationParams
  • bin_size_by_rule()
• Loader class for CBGTC results (in respective files)
  • CommonLoader
    • CommonLoader.get_region_name()
  • FetchConnectionList
    • FetchConnectionList.bg_to_thalamus()
    • FetchConnectionList.cortex_to_bg()
    • FetchConnectionList.cortex_to_thalamus()
    • FetchConnectionList.thalamus_to_cortex()
    • FetchConnectionList.within_bg()
    • FetchConnectionList.within_cortex()
    • FetchConnectionList.within_thalamus()
  • LoadChannelIorG
    • LoadChannelIorG.get_measurables()
  • LoadMembraneVorI
    • LoadMembraneVorI.get_measurables()
  • LoadSpikeTimes
    • LoadSpikeTimes.extract_nucleus_name()
    • LoadSpikeTimes.get_spiketimes_subset()
    • LoadSpikeTimes.get_spiketimes_superset()
• Curate class for processing CBGTC results (in respective files)
  • get_binary_spiketrains()
  • get_desired_spiketimes_subset()

Statistics

Available statistical functions:

• Iter-Spiking Interval Statistics for CBGTC spike times
  • InterSpikeInterval
    • InterSpikeInterval.compute()
    • InterSpikeInterval.grand_mean_freq()
    • InterSpikeInterval.inst_rates()
    • InterSpikeInterval.mean_freqs()
    • InterSpikeInterval.pool_avg_inst_rates()
    • InterSpikeInterval.true_avg_inst_rates()
• Variation Statistics for CBGTC spike times
  • Variations
    • Variations.computeCV()
    • Variations.computeCV2()
    • Variations.computeLV()
    • Variations.grandCV()
    • Variations.grandCV2()
    • Variations.grandLV()
• Synchrony Statistics of CBGTC spike times
  • Synchrony
    • Synchrony.compute_basic()
    • Synchrony.compute_basic_slide()
    • Synchrony.compute_fano_factor()
    • Synchrony.compute_fano_factor_multibins()
    • Synchrony.compute_pairwise_ci()
    • Synchrony.compute_pairwise_corr()
    • Synchrony.compute_sync_index_from_PSTH()
• Rate Statistics of CBGTC spike times
  • Rate
    • Rate.get_count_rate_matrix()
    • Rate.mean_rate()
• Peri-Stimulus Time Histogram (PSTH) of CBGTC spike times
  • PSTH
    • PSTH.analyze_energy()
    • PSTH.analyze_rate()
    • PSTH.analyze_temporal()
    • PSTH.compute_avgPSTH()
    • PSTH.compute_poolPSTH()
• Population Activity of CBGTC spike times
  • PopAct
    • PopAct.compute_complexity_pdf()
    • PopAct.count_allspikes_per_bin()
• Power Spectrum of CBGTC spike times
  • PowerSpectrum
    • PowerSpectrum.compute_for_rate()
    • PowerSpectrum.compute_for_spike()
• PCA Statistics for CBGTC spike times
  • PCA
    • PCA.compute()
    • PCA.eigenspectrum()
    • PCA.get_spike_activity_matrix()
    • PCA.participation_ratio()
• Wavelet Transform of CBGTC spike times
  • ContinuousWaveletTransform
    • ContinuousWaveletTransform.compute_cwt_avg()
    • ContinuousWaveletTransform.compute_cwt_sum()
    • ContinuousWaveletTransform.freq_window_to_scales()
    • ContinuousWaveletTransform.scale_to_freq()
    • ContinuousWaveletTransform.smooth_signal()
• Shared computations
  • autocorr()
  • compute_grand_mean()
  • correlation_time()

Analytics

Available analytics functions:

• Sparsity Index of CBGTC spike times
  • Sparsity
    • Sparsity.analyze()
    • Sparsity.biointerpret_sparsity_index()
    • Sparsity.interpret_sparsity_index()
    • Sparsity.mathinterpret_sparsity_index()

Visualizers

Available visualization functions:

• Visualize Connection Statistics of CBGTC model
  • Conn
    • Conn.connections_bar_chart()
    • Conn.global_stats()
    • Conn.overall_connections_bar_chart()
    • Conn.plot_all_channel_projections()
    • Conn.plot_all_connectivity_matrices()
    • Conn.plot_all_density()
    • Conn.plot_channel_projection()
    • Conn.plot_connectivity_matrix()
    • Conn.plot_degree_distribution()
    • Conn.plot_density()
    • Conn.plot_global_connectivity()
    • Conn.plot_global_density()
    • Conn.plot_population_connectome()
• Membrane Voltage for CBGTC neurons
  • VoltageTrace
    • VoltageTrace.load_measurables()
    • VoltageTrace.plot()
    • VoltageTrace.plot_collection()
    • VoltageTrace.plot_collection_in_ax()
    • VoltageTrace.plot_in_ax()
    • VoltageTrace.volt_trace_collections()
• Marker Plots (Scatter, Raster, etc.) of CBGTC spike times
  • Marker Plotting
    • Raster Plot of Spike Times
      • 1. Pre-requisites
        • 1.1. Import Modules
        • 1.2. Load file and get spike times
      • 2. Cases
        • 2.1. Raster for all the neurons
        • 2.2. Raster for first 50 neurons
        • 2.3. Raster for second 50 neurons
    • Plot Rate Change Scatter
      • 1. Pre-requisites
        • 1.1. Import Modules
        • 1.2. Load file and get spike times
      • 2. Cases
        • 2.1. Plot Rate Change Scatter for all the neurons
  • plot_raster()
  • plot_raster_in_ax()
  • plot_ratechange()
  • plot_ratechange_in_ax()
• Visualize Rate Statistics of CBGTC spike times
  • Rate Plotting
    • Plot Mean Rate
      • 1. Pre-requisites
        • 1.1. Import Modules
        • 1.2. Load file and get spike times
      • 2. Cases
        • 2.1. Visualize Mean Rate with default setting
        • 2.2. Visualize Mean Rate in portrait mode
        • 2.3. Visualize Mean Rate in portrait mode with nucleus name in title
        • 2.4. Create the plot for customization
    • Plot Average Instantaneous Rate
  • plot_mean_rate_all_neurons_across_time_in_ax()
  • plot_mean_rate_isi()
  • plot_mean_rate_isi_in_ax()
  • plot_mean_rate_spikecounts_in_ax()
  • plot_pool_avg_inst_rates()
  • plot_pool_avg_inst_rates_in_ax()
  • plot_true_avg_inst_rate()
  • plot_true_avg_inst_rate_in_ax()
• Distribution Plotting of CBGTC spike times
  • Distribution Plotting
    • 1. Pre-requisites
      • 1.1. Import Modules
      • 1.2. Load file and get spike times
    • 2. Cases
      • 2.1. Standard plot
      • 2.2. Create the plot for customization
  • plot_isi_distrib()
  • plot_latencydist()
  • plot_latencydist_in_ax()
  • plot_ratedist()
  • plot_ratedist_in_ax()
  • plot_spike_counts_distrib()
  • plot_spike_counts_distrib_in_ax()
  • plot_spike_density_distrib()
  • plot_spike_density_distrib_line_in_ax()
  • plot_spike_density_distrib_stacked_in_ax()
• Visualize Variation Statistics of CBGTC spike times
  • Plot Variation Statistics
    • 1. Pre-requisites
      • 1.1. Import Modules
      • 1.2. Load file and get spike times
    • 2. Cases
      • 2.1. Standard plot
      • 2.2. Create the plot for customization
  • plotCV()
  • plotCV2()
  • plotCV2_in_ax()
  • plotCV_in_ax()
  • plotLV()
  • plotLV_in_ax()
• Peri-Stimulus Time Histogram (PSTH) of CBGTC spike times
  • VizPSTH
    • VizPSTH.plot_avg()
    • VizPSTH.plot_avg_in_ax()
    • VizPSTH.plot_pool()
    • VizPSTH.plot_pool_in_ax()
• Population Spike Rate Histogram (PSRH) of CBGTC spike times
  • PSRH
    • PSRH.analytics()
    • PSRH.plot()
    • PSRH.plot_ratevar()
• Population Activity of CBGTC spike times
  • VizPopAct
    • VizPopAct.plot_heatmap()
    • VizPopAct.plot_heatmap_in_ax()
    • VizPopAct.plot_pcatraj()
    • VizPopAct.plot_pcatraj_in_ax()
    • VizPopAct.plot_popcount_dist_in_ax()
    • VizPopAct.plot_popcount_vs_time_in_ax()
• Power Spectral Density Plots of CBGTC spike times
  • VizPSD
    • VizPSD.plot()
    • VizPSD.plot_PSD_of_rate()
    • VizPSD.plot_PSD_of_rate_in_ax()
    • VizPSD.plot_aggstat()
    • VizPSD.plot_aggstat_in_ax()
    • VizPSD.plot_cluster()
    • VizPSD.plot_cluster_in_ax()
    • VizPSD.plot_heatmap()
    • VizPSD.plot_heatmap_in_ax()
    • VizPSD.plot_in_ax()
    • VizPSD.plot_spiketrain_in_ax()
    • VizPSD.plot_with_spiketrains()
• Tabular Spiking Statistics of CBGTC spike times
  • SpikingStats
    • SpikingStats.compute_stats()
    • SpikingStats.plot()
• Scalogram for CBGTC spike times
  • Scalogram
    • Scalogram.accurate_coi_scalogram()
    • Scalogram.matlab_jet_cmap()
    • Scalogram.plot_avg()
    • Scalogram.plot_avg_coi()
    • Scalogram.plot_avg_coi1()
    • Scalogram.plot_avg_coi2()
    • Scalogram.plot_single()
    • Scalogram.plot_sum()

Composite Visualizers

Available composite visualizer functions:

• Spiking Statistics of CBGTC spike times
  • get_observables()
  • plot_observables()
• Current Distributions of CBGTC spike times
  • get_observables()
  • plotH_current_distrib()
  • plot_current_distrib()
  • plot_current_distrib2()