cerebellar_models package

Module contents

Implementation of the BSB framework for cerebellar cortex reconstructions and simulations.

Subpackages

• cerebellar_models.connectome package
  • Module contents
  • Submodules
    • cerebellar_models.connectome.presyn_dist_strat module
      • PresynDistStrat
      • get_close_chunks()
    • cerebellar_models.connectome.to_glomerulus module
      • ConnectomeGlomerulus
      • ConnectomeMossyGlomerulus
      • ConnectomeUBCGlomerulus
      • norm_exp_dist()
    • cerebellar_models.connectome.glomerulus_granule module
      • ConnectomeGlomerulusGranule
      • TooFewGlomeruliClusters
    • cerebellar_models.connectome.glomerulus_golgi module
      • ConnectomeGlomerulusGolgi
    • cerebellar_models.connectome.golgi_glomerulus module
      • ConnectomeGolgiGlomerulus
    • cerebellar_models.connectome.glomerulus_ubc module
      • ConnectomeGlomerulusUBC
    • cerebellar_models.connectome.io_molecular module
      • ConnectomeIO_MLI
    • cerebellar_models.connectome.io_purkinje module
      • DuplicateSynapses
• cerebellar_models.placement package
  • Module contents
  • Submodules
    • cerebellar_models.placement.microzones module
      • LabelCells
      • LabelMicrozones
• cerebellum.analysis package
  • Module contents
    • BSBReport
      • BSBReport.add_plot()
      • BSBReport.cell_names
      • BSBReport.labelled_abbreviations
      • BSBReport.labelled_cell_names
    • BasicSimulationReport
      • BasicSimulationReport.preprocessing()
    • CellPlacement3D
      • CellPlacement3D.ignored_ct
      • CellPlacement3D.init_plot()
      • CellPlacement3D.plot()
      • CellPlacement3D.set_axes_equal()
    • ConnectivityTable
      • ConnectivityTable.dict_abv
      • ConnectivityTable.extract_strat_name()
      • ConnectivityTable.get_convergences()
      • ConnectivityTable.get_divergences()
      • ConnectivityTable.get_nb_synapse_per_pair()
      • ConnectivityTable.get_synapse_counts()
      • ConnectivityTable.plot()
      • ConnectivityTable.update()
    • FiringRatesPlot
      • FiringRatesPlot.kernel
      • FiringRatesPlot.plot()
      • FiringRatesPlot.update()
    • FrequencyPlot
      • FrequencyPlot.plot()
      • FrequencyPlot.update()
    • ISIPlot
      • ISIPlot.nb_bins
      • ISIPlot.plot()
    • Legend
      • Legend.plot()
      • Legend.remove_ct()
    • PlacementTable
      • PlacementTable.dict_abv
      • PlacementTable.extract_ct_name()
      • PlacementTable.get_counts()
      • PlacementTable.get_densities()
      • PlacementTable.get_volumes()
      • PlacementTable.plot()
      • PlacementTable.update()
    • Plot
      • Plot.axes
      • Plot.clear()
      • Plot.dict_colors
      • Plot.fig_size
      • Plot.figure
      • Plot.get_ax()
      • Plot.get_axes()
      • Plot.init_plot()
      • Plot.is_initialized
      • Plot.is_plotted
      • Plot.is_updated
      • Plot.nb_cols
      • Plot.nb_rows
      • Plot.plot()
      • Plot.save_figure()
      • Plot.set_axis_off()
      • Plot.set_color()
      • Plot.show()
      • Plot.update()
    • PlotTypeInfo
      • PlotTypeInfo.abbreviation
      • PlotTypeInfo.color
      • PlotTypeInfo.name
    • RasterPSTHPlot
      • RasterPSTHPlot.clear()
      • RasterPSTHPlot.init_plot()
      • RasterPSTHPlot.nb_bins
      • RasterPSTHPlot.plot()
    • Report
      • Report.abbreviations
      • Report.add_plot()
      • Report.cell_types_info
      • Report.colors
      • Report.plots
      • Report.preprocessing()
      • Report.print_report()
      • Report.save_plot()
      • Report.set_color()
      • Report.set_plot_colors()
      • Report.show()
      • Report.show_plot()
    • RunStructureReport
      • RunStructureReport.get_node_name()
      • RunStructureReport.output_filename
      • RunStructureReport.postprocess()
    • ScaffoldPlot
      • ScaffoldPlot.get_labelled_ct_name()
      • ScaffoldPlot.get_unique_labels()
      • ScaffoldPlot.labelled_dict_colors
      • ScaffoldPlot.set_scaffold()
    • SimResultsTable
      • SimResultsTable.dict_abv
      • SimResultsTable.get_firing_rates()
      • SimResultsTable.get_isis_values()
      • SimResultsTable.plot()
      • SimResultsTable.update()
    • SortedPSTH
      • SortedPSTH.nb_bins
      • SortedPSTH.plot()
      • SortedPSTH.sample_size
    • Spike2Columns
      • Spike2Columns.init_plot()
    • SpikeCorrelationPlot
      • SpikeCorrelationPlot.bin_size
      • SpikeCorrelationPlot.dict_abv
      • SpikeCorrelationPlot.plot()
      • SpikeCorrelationPlot.update()
    • SpikePlot
      • SpikePlot.dt
      • SpikePlot.filt_spikes
      • SpikePlot.nb_neurons
      • SpikePlot.populations
      • SpikePlot.spiking_results
      • SpikePlot.time_from
      • SpikePlot.time_to
    • SpikeSimulationReport
      • SpikeSimulationReport.add_plot()
      • SpikeSimulationReport.dt
      • SpikeSimulationReport.filt_spikes
      • SpikeSimulationReport.nb_neurons
      • SpikeSimulationReport.populations
      • SpikeSimulationReport.time_from
      • SpikeSimulationReport.time_to
    • SpikingResults
      • SpikingResults.dt
      • SpikingResults.filt_spikes
      • SpikingResults.folder_nio
      • SpikingResults.ignored_ct
      • SpikingResults.load_spikes()
      • SpikingResults.nb_neurons
      • SpikingResults.populations
      • SpikingResults.scaffold
      • SpikingResults.simulation_name
      • SpikingResults.time_from
      • SpikingResults.time_to
    • StructureReport
      • StructureReport.preprocessing()
    • TablePlot
      • TablePlot.columns
      • TablePlot.plot_table()
      • TablePlot.reset_table()
      • TablePlot.rows
      • TablePlot.table_values
    • extract_isis()
    • get_correlation_coefficients()
    • get_firing_rates()
    • get_frequencies()
  • Submodules
    • cerebellar_models.analysis.plots module
      • Legend
      • Plot
      • ScaffoldPlot
    • cerebellar_models.analysis.report module
      • BSBReport
      • LIST_CT_INFO
      • PlotTypeInfo
      • Report
    • cerebellar_models.analysis.structure_analysis module
      • AdjacencyMatrix
      • CellPlacement3D
      • ConnectivityTable
      • PlacementTable
      • RunStructureReport
      • StructureReport
      • TablePlot
    • cerebellar_models.analysis.spike_plots module
      • BasicSimulationReport
      • FiringRatesPlot
      • FrequencyPlot
      • ISIPlot
      • RasterPSTHPlot
      • SimResultsTable
      • SortedPSTH
      • Spike2Columns
      • SpikeCorrelationPlot
      • SpikePlot
      • SpikeSimulationReport
    • cerebellar_models.analysis.spiking_results module
      • SpikingResults
      • extract_isis()
      • get_correlation_coefficients()
      • get_firing_rates()
      • get_frequencies()
      • get_spike_matrix()