Index Symbols | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z Symbols --arms placecell-define-zones command line option --config placecell-analysis command line option --data placecell-analysis command line option placecell-define-zones command line option placecell-detect-zones command line option --force-redetect placecell-analysis command line option --interpolate placecell-detect-zones command line option --output placecell-analysis command line option placecell-detect-zones command line option --playback-speed placecell-detect-zones command line option --rooms placecell-define-zones command line option --show placecell-analysis command line option --subset-frames placecell-analysis command line option --subset-units placecell-analysis command line option --workers placecell-analysis command line option --yes placecell-analysis command line option -c placecell-analysis command line option -d placecell-analysis command line option placecell-define-zones command line option placecell-detect-zones command line option -o placecell-analysis command line option placecell-detect-zones command line option -w placecell-analysis command line option -y placecell-analysis command line option A AnalysisConfig (class in placecell.config) analyze_units() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) (placecell.dataset.maze.MazeDataset method) (placecell.dataset.MazeDataset method) apply_time_window() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) arena_bounds (placecell.config.ArenaDataConfig attribute) arena_size_mm (placecell.config.ArenaDataConfig attribute) ArenaDataConfig (class in placecell.config) ArenaDataset (class in placecell.dataset) (class in placecell.dataset.arena) arm_decay_power (placecell.config.ZoneDetectionConfig attribute) arm_max_distance (placecell.config.ZoneDetectionConfig attribute) arm_order (placecell.config.MazeDataConfig attribute) arm_position_column (placecell.config.MazeDataConfig attribute) assign_traversal_direction() (in module placecell.maze_helper) B BaseDataConfig (class in placecell.config) baseline (placecell.config.OasisConfig attribute) BasePlaceCellDataset (class in placecell.dataset) (class in placecell.dataset.base) BaseSpatialMapConfig (class in placecell.config) behavior (placecell.config.AnalysisConfig attribute) behavior_fps (placecell.config.BaseDataConfig attribute) behavior_graph (placecell.config.MazeDataConfig attribute) behavior_position (placecell.config.BaseDataConfig attribute) behavior_timestamp (placecell.config.BaseDataConfig attribute) behavior_video (placecell.config.BaseDataConfig attribute) behavior_video_frame (placecell.dataset.base.BasePlaceCellDataset attribute) BehaviorConfig (class in placecell.config) bin_width_mm (placecell.config.SpatialMap1DConfig attribute) bins (placecell.config.SpatialMap2DConfig attribute) block_shift (placecell.config.BaseSpatialMapConfig attribute) bodypart (placecell.config.BaseDataConfig attribute) C camera_height_mm (placecell.config.ArenaDataConfig attribute) canonical (placecell.dataset.base.BasePlaceCellDataset attribute) clip_to_arena() (in module placecell.behavior) compute_arm_lengths() (in module placecell.maze_helper) compute_coverage_curve() (in module placecell.analysis.spatial_2d) compute_coverage_map() (in module placecell.analysis.spatial_2d) compute_occupancy() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) (placecell.dataset.maze.MazeDataset method) (placecell.dataset.MazeDataset method) compute_occupancy_map() (in module placecell.analysis.spatial_2d) compute_occupancy_map_1d() (in module placecell.analysis.spatial_1d) compute_overlap_time_range() (in module placecell.loaders) compute_place_field_mask() (in module placecell.analysis.spatial_2d) compute_rate_map() (in module placecell.analysis.spatial_2d) compute_rate_map_1d() (in module placecell.analysis.spatial_1d) compute_raw_rate_map() (in module placecell.analysis.spatial_2d) compute_raw_rate_map_1d() (in module placecell.analysis.spatial_1d) compute_shuffled_rate_percentile() (in module placecell.analysis.spatial_2d) compute_spatial_information() (in module placecell.analysis.spatial_2d) compute_spatial_information_1d() (in module placecell.analysis.spatial_1d) compute_speed_1d() (in module placecell.maze_helper) compute_stability_score() (in module placecell.analysis.spatial_2d) compute_stability_score_1d() (in module placecell.analysis.spatial_1d) compute_unit_analysis() (in module placecell.analysis.spatial_2d) compute_unit_analysis_1d() (in module placecell.analysis.spatial_1d) config_override (placecell.config.BaseDataConfig attribute) correct_perspective() (in module placecell.behavior) coverage() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) D deconvolve() (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) E event_count_rate (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) event_index (placecell.dataset.base.BasePlaceCellDataset attribute) event_place (placecell.dataset.base.BasePlaceCellDataset attribute) event_threshold_sigma (placecell.config.SpatialMap2DConfig attribute) F filter_complete_traversals() (in module placecell.maze_helper) footprints (placecell.dataset.base.BasePlaceCellDataset attribute) fps (placecell.config.NeuralConfig attribute) from_yaml() (placecell.config.AnalysisConfig class method) (placecell.config.BaseDataConfig class method) (placecell.dataset.base.BasePlaceCellDataset class method) (placecell.dataset.BasePlaceCellDataset class method) G g (placecell.config.OasisConfig attribute) gaussian_filter_normalized() (in module placecell.analysis.spatial_2d) gaussian_filter_normalized_1d() (in module placecell.analysis.spatial_1d) good_unit_ids (placecell.dataset.base.BasePlaceCellDataset attribute) H hampel_n_sigmas (placecell.config.BehaviorConfig attribute) (placecell.config.ZoneDetectionConfig attribute) hampel_window_frames (placecell.config.BehaviorConfig attribute) (placecell.config.ZoneDetectionConfig attribute) I interpolate (placecell.config.ZoneDetectionConfig attribute) L load() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) (placecell.dataset.maze.MazeDataset method) (placecell.dataset.MazeDataset method) load_behavior_data() (in module placecell.loaders) load_bundle() (placecell.dataset.base.BasePlaceCellDataset class method) (placecell.dataset.BasePlaceCellDataset class method) (placecell.dataset.maze.MazeDataset class method) (placecell.dataset.MazeDataset class method) load_calcium_traces() (in module placecell.neural) load_graph_polylines() (in module placecell.maze_helper) load_visualization_data() (in module placecell.loaders) M match_events() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) (placecell.dataset.maze.MazeDataset method) (placecell.dataset.MazeDataset method) max_proj (placecell.dataset.base.BasePlaceCellDataset attribute) MazeDataConfig (class in placecell.config) MazeDataset (class in placecell.dataset) (class in placecell.dataset.maze) min_confidence (placecell.config.ZoneDetectionConfig attribute) min_confidence_forbidden (placecell.config.ZoneDetectionConfig attribute) min_occupancy (placecell.config.BaseSpatialMapConfig attribute) min_seconds_forbidden (placecell.config.ZoneDetectionConfig attribute) min_seconds_same (placecell.config.ZoneDetectionConfig attribute) min_shift_seconds (placecell.config.BaseSpatialMapConfig attribute) mm_per_pixel (placecell.config.MazeDataConfig attribute) mm_per_px (placecell.dataset.arena.ArenaDataset property) (placecell.dataset.ArenaDataset property) mm_per_px_xy (placecell.dataset.arena.ArenaDataset property) (placecell.dataset.ArenaDataset property) model_config (placecell.config.AnalysisConfig attribute) (placecell.config.ArenaDataConfig attribute) (placecell.config.BaseDataConfig attribute) (placecell.config.BaseSpatialMapConfig attribute) (placecell.config.BehaviorConfig attribute) (placecell.config.MazeDataConfig attribute) (placecell.config.NeuralConfig attribute) (placecell.config.OasisConfig attribute) (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) (placecell.config.ZoneDetectionConfig attribute) module placecell.analysis.spatial_1d placecell.analysis.spatial_2d placecell.behavior placecell.config placecell.dataset placecell.dataset.arena placecell.dataset.base placecell.dataset.maze placecell.loaders placecell.maze_helper placecell.neural placecell.visualization N n_shuffles (placecell.config.BaseSpatialMapConfig attribute) n_split_blocks (placecell.config.BaseSpatialMapConfig attribute) neural (placecell.config.AnalysisConfig attribute) neural_fps (placecell.dataset.base.BasePlaceCellDataset property) (placecell.dataset.BasePlaceCellDataset property) neural_path (placecell.config.BaseDataConfig attribute) neural_timestamp (placecell.config.BaseDataConfig attribute) NeuralConfig (class in placecell.config) O oasis (placecell.config.NeuralConfig attribute) OasisConfig (class in placecell.config) occupancy_time (placecell.dataset.base.BasePlaceCellDataset attribute) overall_rate (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) overlay_frame_index (placecell.config.BaseDataConfig attribute) P p_val (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) p_value_threshold (placecell.config.BaseSpatialMapConfig attribute) (placecell.dataset.arena.ArenaDataset property) (placecell.dataset.ArenaDataset property) (placecell.dataset.base.BasePlaceCellDataset property) (placecell.dataset.BasePlaceCellDataset property) (placecell.dataset.maze.MazeDataset property) (placecell.dataset.MazeDataset property) penalty (placecell.config.OasisConfig attribute) place_cells() (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) place_field_min_bins (placecell.config.SpatialMap2DConfig attribute) place_field_seed_percentile (placecell.config.SpatialMap2DConfig attribute) place_field_threshold (placecell.config.SpatialMap2DConfig attribute) placecell-analysis command line option --config --data --force-redetect --output --show --subset-frames --subset-units --workers --yes -c -d -o -w -y placecell-define-zones command line option --arms --data --rooms -d placecell-detect-zones command line option --data --interpolate --output --playback-speed -d -o placecell.analysis.spatial_1d module placecell.analysis.spatial_2d module placecell.behavior module placecell.config module placecell.dataset module placecell.dataset.arena module placecell.dataset.base module placecell.dataset.maze module placecell.loaders module placecell.maze_helper module placecell.neural module placecell.visualization module playback_speed (placecell.config.ZoneDetectionConfig attribute) plot_arena_calibration() (in module placecell.visualization) plot_behavior_preview() (in module placecell.visualization) plot_coverage() (in module placecell.visualization) plot_diagnostics() (in module placecell.visualization) plot_footprints() (in module placecell.visualization) plot_footprints_filled() (in module placecell.visualization) plot_graph_overlay() (in module placecell.visualization) plot_occupancy_preview() (in module placecell.visualization) plot_occupancy_preview_1d() (in module placecell.visualization) plot_position_and_traces_1d() (in module placecell.visualization) plot_position_and_traces_2d() (in module placecell.visualization) plot_preprocess_steps() (in module placecell.visualization) plot_rate_map_1d() (in module placecell.visualization) plot_session_summary() (in module placecell.visualization) plot_shuffle_test_1d() (in module placecell.visualization) plot_speed_histogram() (in module placecell.visualization) plot_summary_scatter() (in module placecell.visualization) plot_timestamp_diagnostics() (in module placecell.visualization) preprocess_behavior() (placecell.dataset.arena.ArenaDataset method) (placecell.dataset.ArenaDataset method) (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) (placecell.dataset.maze.MazeDataset method) (placecell.dataset.MazeDataset method) R random_seed (placecell.config.BaseSpatialMapConfig attribute) rate_map (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) rate_map_first (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) rate_map_raw (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) rate_map_second (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) remove_position_jumps() (in module placecell.behavior) require_complete_traversal (placecell.config.SpatialMap1DConfig attribute) room_decay_power (placecell.config.ZoneDetectionConfig attribute) run_deconvolution() (in module placecell.neural) S S_list (placecell.dataset.base.BasePlaceCellDataset attribute) s_min (placecell.config.OasisConfig attribute) save_bundle() (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) (placecell.dataset.maze.MazeDataset method) (placecell.dataset.MazeDataset method) serialize_arm_position() (in module placecell.maze_helper) shuffled_rate_p95 (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) shuffled_sis (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) shuffled_stability (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) si (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) si_weight_mode (placecell.config.BaseSpatialMapConfig attribute) soft_boundary (placecell.config.ZoneDetectionConfig attribute) spatial (placecell.dataset.arena.ArenaDataset property) (placecell.dataset.ArenaDataset property) spatial_1d (placecell.dataset.maze.MazeDataset property) (placecell.dataset.MazeDataset property) spatial_map_1d (placecell.config.BehaviorConfig attribute) spatial_map_2d (placecell.config.BehaviorConfig attribute) spatial_sigma (placecell.config.BaseSpatialMapConfig attribute) SpatialMap1DConfig (class in placecell.config) SpatialMap2DConfig (class in placecell.config) speed_threshold (placecell.config.BehaviorConfig attribute) speed_window_seconds (placecell.config.BehaviorConfig attribute) split_by_direction (placecell.config.SpatialMap1DConfig attribute) stability_corr (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) stability_p_val (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) stability_z (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) subset() (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) summary() (placecell.dataset.base.BasePlaceCellDataset method) (placecell.dataset.BasePlaceCellDataset method) T to_yaml() (placecell.config.AnalysisConfig method) trace_data (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) trace_name (placecell.config.NeuralConfig attribute) trace_times (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) traces (placecell.dataset.base.BasePlaceCellDataset attribute) tracking_height_mm (placecell.config.ArenaDataConfig attribute) trajectory (placecell.dataset.base.BasePlaceCellDataset attribute) trajectory_filtered (placecell.dataset.base.BasePlaceCellDataset attribute) trajectory_raw (placecell.dataset.base.BasePlaceCellDataset attribute) type (placecell.config.ArenaDataConfig attribute) (placecell.config.BehaviorConfig attribute) (placecell.config.MazeDataConfig attribute) U unique_bundle_path() (in module placecell.dataset) (in module placecell.dataset.base) unit_data (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) unit_results (placecell.dataset.base.BasePlaceCellDataset attribute) UnitResult (class in placecell.dataset) (class in placecell.dataset.base) V valid_mask (placecell.dataset.base.BasePlaceCellDataset attribute) vis_data_above (placecell.dataset.base.UnitResult attribute) (placecell.dataset.UnitResult attribute) W with_data_overrides() (placecell.config.AnalysisConfig method) X x_col (placecell.config.BaseDataConfig attribute) x_edges (placecell.dataset.base.BasePlaceCellDataset attribute) Y y_col (placecell.config.BaseDataConfig attribute) y_edges (placecell.dataset.base.BasePlaceCellDataset attribute) Z zone_column (placecell.config.MazeDataConfig attribute) zone_connections (placecell.config.MazeDataConfig attribute) zone_detection (placecell.config.MazeDataConfig attribute) zone_tracking (placecell.config.MazeDataConfig attribute) ZoneDetectionConfig (class in placecell.config)