Index A | B | C | D | E | F | G | J | L | M | N | O | P | R | S | T | W | X | Y | Z A activity_sigma (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) AnalysisConfig (class in placecell.config) arena_bounds (placecell.config.DataPathsConfig attribute) arena_size_mm (placecell.config.DataPathsConfig attribute) B baseline (placecell.config.OasisConfig attribute) behavior (placecell.config.AnalysisConfig attribute) behavior_fps (placecell.config.BehaviorConfig attribute) behavior_graph (placecell.config.DataPathsConfig attribute) behavior_position (placecell.config.DataPathsConfig attribute) behavior_timestamp (placecell.config.DataPathsConfig attribute) behavior_video (placecell.config.DataPathsConfig attribute) BehaviorConfig (class in placecell.config) bin_width_mm (placecell.config.SpatialMap1DConfig attribute) bins (placecell.config.SpatialMap2DConfig attribute) block_shifts (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) bodypart (placecell.config.BehaviorConfig attribute) build_event_index_dataframe() (in module placecell.neural) build_event_place_dataframe() (in module placecell.behavior) C camera_height_mm (placecell.config.DataPathsConfig attribute) clip_to_arena() (in module placecell.behavior) compute_behavior_speed() (in module placecell.behavior) compute_coverage_curve() (in module placecell.analysis) compute_coverage_map() (in module placecell.analysis) compute_occupancy_map() (in module placecell.analysis) compute_overlap_time_range() (in module placecell.io) compute_place_field_mask() (in module placecell.analysis) compute_rate_map() (in module placecell.analysis) compute_raw_rate_map() (in module placecell.analysis) compute_shuffled_rate_percentile() (in module placecell.analysis) compute_spatial_information() (in module placecell.analysis) compute_stability_score() (in module placecell.analysis) compute_unit_analysis() (in module placecell.analysis) correct_perspective() (in module placecell.behavior) D DataPathsConfig (class in placecell.config) E event_threshold_sigma (placecell.config.SpatialMap2DConfig attribute) F filter_by_speed() (in module placecell.behavior) fps (placecell.config.NeuralConfig attribute) from_yaml() (placecell.config.DataPathsConfig class method) G g (placecell.config.OasisConfig attribute) gaussian_filter_normalized() (in module placecell.analysis) J jump_threshold_mm (placecell.config.BehaviorConfig attribute) L load_behavior_data() (in module placecell.io) load_calcium_traces() (in module placecell.neural) load_visualization_data() (in module placecell.io) M maze (placecell.config.BehaviorConfig attribute) MazeConfig (class in placecell.config) min_occupancy (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) min_shift_seconds (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) model_config (placecell.config.AnalysisConfig attribute) (placecell.config.BehaviorConfig attribute) (placecell.config.DataPathsConfig attribute) (placecell.config.MazeConfig attribute) (placecell.config.NeuralConfig attribute) (placecell.config.OasisConfig attribute) (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) module placecell.analysis placecell.behavior placecell.config placecell.io placecell.neural placecell.visualization N n_shuffles (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) n_split_blocks (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) neural (placecell.config.AnalysisConfig attribute) neural_path (placecell.config.DataPathsConfig attribute) neural_timestamp (placecell.config.DataPathsConfig attribute) NeuralConfig (class in placecell.config) O oasis (placecell.config.DataPathsConfig attribute) (placecell.config.NeuralConfig attribute) OasisConfig (class in placecell.config) occupancy_sigma (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) P p_value_threshold (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) penalty (placecell.config.OasisConfig attribute) 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 module placecell.behavior module placecell.config module placecell.io module placecell.neural module placecell.visualization module 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_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_summary_scatter() (in module placecell.visualization) R random_seed (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) recompute_speed() (in module placecell.behavior) remove_position_jumps() (in module placecell.behavior) run_deconvolution() (in module placecell.neural) S s_min (placecell.config.OasisConfig attribute) si_weight_mode (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) spatial_map_1d (placecell.config.BehaviorConfig attribute) spatial_map_2d (placecell.config.BehaviorConfig attribute) SpatialMap1DConfig (class in placecell.config) SpatialMap2DConfig (class in placecell.config) speed_threshold (placecell.config.BehaviorConfig attribute) speed_window_frames (placecell.config.BehaviorConfig attribute) split_by_direction (placecell.config.MazeConfig attribute) T trace_name (placecell.config.NeuralConfig attribute) trace_time_window (placecell.config.SpatialMap1DConfig attribute) (placecell.config.SpatialMap2DConfig attribute) tracking_height_mm (placecell.config.DataPathsConfig attribute) tube_order (placecell.config.MazeConfig attribute) tube_position_column (placecell.config.MazeConfig attribute) type (placecell.config.BehaviorConfig attribute) W with_data_overrides() (placecell.config.AnalysisConfig method) X x_col (placecell.config.BehaviorConfig attribute) Y y_col (placecell.config.BehaviorConfig attribute) Z zone_column (placecell.config.MazeConfig attribute)