Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X A abs_thresholds (meanap.params.Params attribute) adj_m_type (meanap.params.Params attribute) adjm_thr() (in module meanap.pipeline.probabilistic_threshold) align_peaks() (in module meanap.pipeline.spike_detection) auto_set_cartography_boundaries (meanap.params.Params attribute) auto_set_cartography_boundaries_per_lag (meanap.params.Params attribute) automatic_stim_detection (meanap.params.Params attribute) available_node_metrics (meanap.network_plot.MatData property) average_controllability() (in module meanap.pipeline.network_metrics) B bakkum_network_burst_isi_n_threshold (meanap.params.Params attribute) bandpass_filter() (in module meanap.pipeline.spike_detection) betweenness_wei() (in module meanap.pipeline.network_metrics) build_cell_type_matrix() (in module meanap.network_plot) burst_detect_isin() (in module meanap.pipeline.burst_detection) burst_detect_network() (in module meanap.pipeline.burst_detection) C cal_nmf() (in module meanap.pipeline.nmf) cartography_lag_val (meanap.params.Params attribute) cell_mask (meanap.catnap.loader.Suite2pData property) channel_layout (meanap.params.Params attribute) channels (meanap.pipeline.spike_detection.SpikeDetectionResult attribute) charpath() (in module meanap.pipeline.network_metrics) check_cancel() (in module meanap.pipeline.cancellation) circular_shift_spikes() (in module meanap.pipeline.probabilistic_threshold) classify_node_cartography() (in module meanap.pipeline.network_metrics) clustering_coef_wu() (in module meanap.pipeline.network_metrics) community_louvain() (in module meanap.pipeline.louvain) compute_network_metrics() (in module meanap.pipeline.step4) connector_hub_part_coef (meanap.params.Params attribute) consensus_coclassify() (in module meanap.pipeline.modularity) consensuscheck() (in module meanap.pipeline.modularity) convert_numpy() (in module meanap.pipeline.step2) cost_list (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) create_output_folders() (in module meanap.pipeline.output_folders) custom_grp_order (meanap.params.Params attribute) D d_samp_f (meanap.params.Params attribute) default_output_folder_name() (in module meanap.pipeline.runner) density_und() (in module meanap.pipeline.network_metrics) describe_data_file() (in module meanap.pipeline.report) describe_folder() (in module meanap.pipeline.report) describe_plot() (in module meanap.pipeline.report) detect_spikes (meanap.params.Params attribute) detect_spikes_recording() (in module meanap.pipeline.spike_detection) detect_spikes_threshold() (in module meanap.pipeline.spike_detection) detect_spikes_wavelet() (in module meanap.pipeline.spike_detection) distance_wei() (in module meanap.pipeline.network_metrics) div (meanap.pipeline.spreadsheet.RecordingInfo attribute) download_example_data() (in module meanap.pipeline.example_data) duration_s (meanap.catnap.loader.Suite2pData attribute) E edge_subsampling_method (meanap.params.Params attribute) eff_rank_cal_method (meanap.params.Params attribute) eff_rank_downsample_freq (meanap.params.Params attribute) effective_rank() (in module meanap.pipeline.network_metrics) efficiency_wei_global() (in module meanap.pipeline.network_metrics) efficiency_wei_local() (in module meanap.pipeline.network_metrics) event_areas (meanap.catnap.loader.Suite2pData attribute) exclude_edges_below_threshold (meanap.params.Params attribute) F F (meanap.catnap.loader.Suite2pData attribute) F_cells (meanap.catnap.loader.Suite2pData property) F_denoised (meanap.catnap.loader.Suite2pData attribute) F_denoised_cells (meanap.catnap.loader.Suite2pData property) fig_ext (meanap.params.Params attribute) filename (meanap.pipeline.spreadsheet.RecordingInfo attribute) filter_by_cell_types() (in module meanap.network_plot) filter_high_pass (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) filter_low_pass (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) find_node_deg_edge_weight() (in module meanap.pipeline.network_metrics) find_suite2p_recordings() (in module meanap.catnap.scanner) firing_rates_bursts() (in module meanap.pipeline.firing_rates) fs (meanap.catnap.loader.Suite2pData attribute) (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) (meanap.pipeline.spike_detection.SpikeDetectionResult attribute) full_svg (meanap.params.Params attribute) func_con_lag_val (meanap.params.Params attribute) G generate_report() (in module meanap.pipeline.report) get_active_indices() (meanap.network_plot.MatData method) get_adjM() (meanap.network_plot.MatData method) get_coords_from_layout() (in module meanap.pipeline.channel_layout) get_isin_threshold() (in module meanap.pipeline.burst_detection) get_metric() (meanap.network_plot.MatData method) get_netmet() (meanap.network_plot.MatData method) get_sttc() (in module meanap.pipeline.sttc) get_template_ref_period (meanap.params.Params attribute) grd (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) ground (meanap.pipeline.spreadsheet.RecordingInfo attribute) ground_spike_times_dict() (in module meanap.pipeline.spreadsheet) group (meanap.pipeline.spreadsheet.RecordingInfo attribute) H has_denoised (meanap.catnap.scanner.Suite2pRecording attribute) home_dir (meanap.params.Params attribute) hub_boundary_wm_d_deg (meanap.params.Params attribute) hub_classification() (in module meanap.pipeline.network_metrics) I include_channel_number_in_plots (meanap.params.Params attribute) include_nmf_components (meanap.params.Params attribute) include_not_box_plots (meanap.params.Params attribute) iscell (meanap.catnap.loader.Suite2pData attribute) K kde_height (meanap.params.Params attribute) kde_width_for_one_point (meanap.params.Params attribute) L lag_ms() (meanap.network_plot.MatData method) latmio_und_v2() (in module meanap.pipeline.null_models) line_plot_shade_metric (meanap.params.Params attribute) load_cell_type_file() (in module meanap.network_plot) load_raw_recording() (in module meanap.pipeline.io) load_spike_times_mat() (in module meanap.pipeline.io) load_spike_times_npz() (in module meanap.pipeline.io) load_suite2p() (in module meanap.catnap.loader) M MatData (class in meanap.network_plot) max_node_size (meanap.params.Params attribute) max_num_edges_to_plot (meanap.params.Params attribute) max_peak_thr_mult (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) max_peak_thr_multiplier (meanap.params.Params attribute) meanap.catnap module meanap.catnap.denoising module meanap.catnap.loader module meanap.catnap.scanner module meanap.network_plot module meanap.params module meanap.pipeline module meanap.pipeline.burst_detection module meanap.pipeline.cancellation module meanap.pipeline.channel_layout module meanap.pipeline.example_data module meanap.pipeline.firing_rates module meanap.pipeline.io module meanap.pipeline.louvain module meanap.pipeline.modularity module meanap.pipeline.network_metrics module meanap.pipeline.nmf module meanap.pipeline.null_models module meanap.pipeline.output_folders module meanap.pipeline.parula module meanap.pipeline.plotting module meanap.pipeline.plotting_step2 module meanap.pipeline.plotting_step4 module meanap.pipeline.probabilistic_threshold module meanap.pipeline.report module meanap.pipeline.runner module meanap.pipeline.spike_detection module meanap.pipeline.spreadsheet module meanap.pipeline.step2 module meanap.pipeline.step3 module meanap.pipeline.step4 module meanap.pipeline.sttc module min_activity_level (meanap.params.Params attribute) min_channel_network_burst (meanap.params.Params attribute) min_node_size (meanap.params.Params attribute) min_number_of_nodes_to_cal_net_met (meanap.params.Params attribute) min_peak_thr_mult (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) min_peak_thr_multiplier (meanap.params.Params attribute) min_spike_network_burst (meanap.params.Params attribute) mod_consensus_cluster_iterate() (in module meanap.pipeline.modularity) modal_controllability() (in module meanap.pipeline.network_metrics) module meanap.catnap meanap.catnap.denoising meanap.catnap.loader meanap.catnap.scanner meanap.network_plot meanap.params meanap.pipeline meanap.pipeline.burst_detection meanap.pipeline.cancellation meanap.pipeline.channel_layout meanap.pipeline.example_data meanap.pipeline.firing_rates meanap.pipeline.io meanap.pipeline.louvain meanap.pipeline.modularity meanap.pipeline.network_metrics meanap.pipeline.nmf meanap.pipeline.null_models meanap.pipeline.output_folders meanap.pipeline.parula meanap.pipeline.plotting meanap.pipeline.plotting_step2 meanap.pipeline.plotting_step4 meanap.pipeline.probabilistic_threshold meanap.pipeline.report meanap.pipeline.runner meanap.pipeline.spike_detection meanap.pipeline.spreadsheet meanap.pipeline.step2 meanap.pipeline.step3 meanap.pipeline.step4 meanap.pipeline.sttc module_degree_zscore() (in module meanap.pipeline.network_metrics) multi_template_method (meanap.params.Params attribute) multiple_templates (meanap.params.Params attribute) N n_cells (meanap.catnap.loader.Suite2pData property) n_frames (meanap.catnap.loader.Suite2pData attribute) n_scales (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) n_spikes (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) name (meanap.catnap.scanner.Suite2pRecording attribute) net_met_to_cal (meanap.params.Params attribute) network_burst_detection_method (meanap.params.Params attribute) network_plot_edge_threshold (meanap.params.Params attribute) network_plot_edge_threshold_method (meanap.params.Params attribute) network_plot_edge_threshold_percentile (meanap.params.Params attribute) nmf_downsample_freq (meanap.params.Params attribute) node_layout (meanap.params.Params attribute) node_scaling_method (meanap.params.Params attribute) node_scaling_power (meanap.params.Params attribute) non_hub_connector_part_coef (meanap.params.Params attribute) null_model_und_sign() (in module meanap.pipeline.null_models) num_2p_traces (meanap.params.Params attribute) O oasis_available() (in module meanap.catnap.denoising) optional_steps_to_run (meanap.params.Params attribute) output_data_folder (meanap.params.Params attribute) output_data_folder_name (meanap.params.Params attribute) output_spreadsheet_file_type (meanap.params.Params attribute) P Params (class in meanap.params) parse_ground_electrodes() (in module meanap.pipeline.spreadsheet) parse_spreadsheet_range() (in module meanap.pipeline.spreadsheet) participation_coef() (in module meanap.pipeline.network_metrics) participation_coef_norm() (in module meanap.pipeline.network_metrics) peak_end_frames (meanap.catnap.loader.Suite2pData attribute) peak_heights (meanap.catnap.loader.Suite2pData attribute) peak_start_frames (meanap.catnap.loader.Suite2pData attribute) peri_part_coef (meanap.params.Params attribute) PipelineCancelled plot_burst_detection_info() (in module meanap.pipeline.plotting_step2) plot_circular_cartography_network() (in module meanap.pipeline.plotting_step4) plot_circular_module_network() (in module meanap.pipeline.plotting_step4) plot_connectivity_stats() (in module meanap.pipeline.plotting_step4) plot_firing_rate_distribution() (in module meanap.pipeline.plotting_step2) plot_graph_metrics_by_node() (in module meanap.pipeline.plotting_step4) plot_heatmap() (in module meanap.pipeline.plotting_step2) plot_network() (in module meanap.network_plot) plot_neuronal_activity_checks() (in module meanap.pipeline.plotting_step2) plot_node_cartography() (in module meanap.pipeline.plotting_step4) plot_raster() (in module meanap.pipeline.plotting_step2) plot_spatial_network() (in module meanap.pipeline.plotting_step4) plot_spatial_network_combined() (in module meanap.pipeline.plotting_step4) plot_spike_detection_checks() (in module meanap.pipeline.plotting) plot_step2_group_comparisons() (in module meanap.pipeline.plotting_step2) plot_step4_group_comparisons() (in module meanap.pipeline.plotting_step4) pos_peak_thr_mult (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) pos_peak_thr_multiplier (meanap.params.Params attribute) potential_difference_unit (meanap.params.Params attribute) prior_analysis (meanap.params.Params attribute) prior_analysis_path (meanap.params.Params attribute) pro_hub_part_coef (meanap.params.Params attribute) prob_thresh_plot_checks (meanap.params.Params attribute) prob_thresh_plot_checks_n (meanap.params.Params attribute) prob_thresh_rep_num (meanap.params.Params attribute) prob_thresh_tail (meanap.params.Params attribute) process_suite2p_folder() (in module meanap.catnap.denoising) python_path (meanap.params.Params attribute) R randmio_und_signed() (in module meanap.pipeline.null_models) randmio_und_v2() (in module meanap.pipeline.null_models) randomise_spike_train() (in module meanap.pipeline.nmf) raster_colormap (meanap.params.Params attribute) raster_plot_upper_percentile (meanap.params.Params attribute) raw_data (meanap.params.Params attribute) read_recording_csv() (in module meanap.pipeline.spreadsheet) recompute_metrics (meanap.params.Params attribute) RecordingInfo (class in meanap.pipeline.spreadsheet) ref_period (meanap.params.Params attribute) ref_period_ms (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) remove_artifacts (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) remove_inactive_nodes (meanap.params.Params attribute) remove_nodes_with_no_peaks (meanap.params.Params attribute) rich_club_wu() (in module meanap.pipeline.network_metrics) run_pipeline() (in module meanap.pipeline.runner) run_spike_check_on_prev_spike_data (meanap.params.Params attribute) S save_spike_times_npz() (in module meanap.pipeline.io) show_one_fig (meanap.params.Params attribute) single_channel_burst_detection() (in module meanap.pipeline.burst_detection) single_channel_burst_detection_method (meanap.params.Params attribute) single_channel_burst_min_spike (meanap.params.Params attribute) single_channel_isi_threshold (meanap.params.Params attribute) small_worldness_rl_wu() (in module meanap.pipeline.network_metrics) spike_detected_data (meanap.params.Params attribute) spike_times (meanap.pipeline.spike_detection.SpikeDetectionResult attribute) spike_waveforms (meanap.pipeline.spike_detection.SpikeDetectionResult attribute) SpikeDetectionParams (class in meanap.pipeline.spike_detection) SpikeDetectionResult (class in meanap.pipeline.spike_detection) spikes_method (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) spks (meanap.catnap.loader.Suite2pData attribute) spks_cells (meanap.catnap.loader.Suite2pData property) spreadsheet_file_name (meanap.params.Params attribute) spreadsheet_range (meanap.params.Params attribute) start_analysis_step (meanap.params.Params attribute) stim_detection_method (meanap.params.Params attribute) stim_detection_val (meanap.params.Params attribute) stim_duration (meanap.params.Params attribute) stim_duration_for_plotting (meanap.params.Params attribute) stim_refractory_period (meanap.params.Params attribute) stimulation_mode (meanap.params.Params attribute) stop_analysis_step (meanap.params.Params attribute) strengths_und() (in module meanap.pipeline.network_metrics) sttc_pair() (in module meanap.pipeline.sttc) suite2p_dir (meanap.catnap.scanner.Suite2pRecording attribute) Suite2pData (class in meanap.catnap.loader) Suite2pRecording (class in meanap.catnap.scanner) T thresholds (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) (meanap.pipeline.spike_detection.SpikeDetectionResult attribute) time_points (meanap.catnap.loader.Suite2pData attribute) time_processes (meanap.params.Params attribute) trunc_length (meanap.params.Params attribute) trunc_rec (meanap.params.Params attribute) twop_activity (meanap.params.Params attribute) twop_denoising_threshold (meanap.params.Params attribute) twop_denoising_time_after_peak (meanap.params.Params attribute) twop_denoising_time_before_peak (meanap.params.Params attribute) twop_redo_denoising (meanap.params.Params attribute) U unit (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) use_min_max_all_recording_bounds (meanap.params.Params attribute) use_min_max_per_genotype_bounds (meanap.params.Params attribute) use_theoretical_bounds (meanap.params.Params attribute) V verbose_level (meanap.params.Params attribute) W weight_conversion_lengths() (in module meanap.pipeline.network_metrics) weight_conversion_normalize() (in module meanap.pipeline.network_metrics) wid_ms (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) wname_list (meanap.params.Params attribute) (meanap.pipeline.spike_detection.SpikeDetectionParams attribute) X xy_cells (meanap.catnap.loader.Suite2pData property) xy_loc (meanap.catnap.loader.Suite2pData attribute)