Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | Z _ _active_mask() (bactoscoop.image.Image method) _apply_curation_labels() (bactoscoop.imagecollection.ImageCollection method) _atomic_write() (bactoscoop.imagecollection.ImageCollection method) _collect_touching_label_pairs() (in module bactoscoop.utilities) _get_mesh_dataframe_lookup() (bactoscoop.imagecollection.ImageCollection method) _iter_processing_targets() (bactoscoop.imagecollection.ImageCollection method) _max_feret_diameter_px() (in module bactoscoop.utilities) _normalize_channel_list() (bactoscoop.imagecollection.ImageCollection method) _record_cell_error() (bactoscoop.imagecollection.ImageCollection method) _record_processing_error() (bactoscoop.imagecollection.ImageCollection method) _record_stage_success() (bactoscoop.imagecollection.ImageCollection method) _require_image_folder_path() (bactoscoop.imagecollection.ImageCollection method) _require_loaded_images() (bactoscoop.imagecollection.ImageCollection method) _resolve_log_level() (in module bactoscoop.logging_utils) _to_parquet() (bactoscoop.imagecollection.ImageCollection method) _to_pickle() (bactoscoop.imagecollection.ImageCollection method) _tutorial_channel_cmap() (in module bactoscoop.plot) _tutorial_channel_color() (in module bactoscoop.plot) _tutorial_contrast() (in module bactoscoop.plot) _tutorial_crop() (in module bactoscoop.plot) _validate_max_daughter_cell_mesh_rows() (in module bactoscoop.utilities) _validate_phase_image_state() (bactoscoop.imagecollection.ImageCollection method) _write_pickle_file() (bactoscoop.imagecollection.ImageCollection method) A add_cell() (bactoscoop.image.Image method) add_channels() (bactoscoop.imagecollection.ImageCollection method) add_info_feature_df() (bactoscoop.image.Image method) add_meshdata_to_dataframe() (bactoscoop.imagecollection.ImageCollection method) add_poles() (in module bactoscoop.utilities) align() (in module bactoscoop.utilities) align_contour_start() (in module bactoscoop.utilities) align_objects() (in module bactoscoop.utilities) angle_between_vector() (in module bactoscoop.utilities) apply_neighbor_prefilter() (bactoscoop.image.Image method) assign_values() (in module bactoscoop.utilities) B bactoscoop.curation module bactoscoop.features module bactoscoop.image module bactoscoop.imagecollection module bactoscoop.logging_utils module bactoscoop.omni module bactoscoop.plot module bactoscoop.signalcorrelation module bactoscoop.utilities module batch_calculate_features() (bactoscoop.imagecollection.ImageCollection method) batch_calculate_signal_correlation_features() (bactoscoop.imagecollection.ImageCollection method) batch_detect_objects() (bactoscoop.imagecollection.ImageCollection method) batch_load_mesh() (bactoscoop.imagecollection.ImageCollection method) batch_mask2mesh() (bactoscoop.imagecollection.ImageCollection method) batch_process_mesh() (bactoscoop.imagecollection.ImageCollection method) batch_shift_correction() (bactoscoop.imagecollection.ImageCollection method) bending_energy() (in module bactoscoop.utilities) C calculate() (bactoscoop.signalcorrelation.SignalCorrelation method) calculate_contour_haralick_features() (in module bactoscoop.utilities) calculate_features() (bactoscoop.image.Image method) calculate_haralick_features() (in module bactoscoop.utilities) calculate_object_haralick_features() (in module bactoscoop.utilities) Cell (class in bactoscoop.image) change_contour_array_length() (in module bactoscoop.utilities) channel_interp2d() (bactoscoop.image.Image method) closing_mask() (in module bactoscoop.utilities) colocalization() (bactoscoop.features.Features method) compiled_curation() (bactoscoop.curation.Curation method) compiled_process() (bactoscoop.omni.Omnipose method) configure_bactoscoop_logging() (in module bactoscoop.logging_utils) constr_degree() (in module bactoscoop.utilities) constr_degree_single_cell_min() (in module bactoscoop.utilities) construct_bg_function() (in module bactoscoop.utilities) contour2mesh() (in module bactoscoop.utilities) contour_selection() (bactoscoop.features.Features method) cosine_similarity() (bactoscoop.signalcorrelation.SignalCorrelation method) covariance() (bactoscoop.signalcorrelation.SignalCorrelation method) create_cell_object() (bactoscoop.image.Image method) create_co_occurrence_matrix() (in module bactoscoop.utilities) create_image_object() (bactoscoop.imagecollection.ImageCollection method) create_image_objects() (bactoscoop.imagecollection.ImageCollection method) crop() (in module bactoscoop.utilities) crop_image() (in module bactoscoop.utilities) crop_signal_with_optional_shift() (in module bactoscoop.utilities) curate_dataset() (bactoscoop.imagecollection.ImageCollection method) Curation (class in bactoscoop.curation) D dataframe_from_dict() (bactoscoop.image.Image method) dataframe_to_parquet() (bactoscoop.imagecollection.ImageCollection method) dataframe_to_pkl() (bactoscoop.imagecollection.ImageCollection method) direct_intersect_distance() (in module bactoscoop.utilities) discard_bad_meshes() (bactoscoop.features.Features method) discard_large_meshes() (bactoscoop.features.Features method) distance() (in module bactoscoop.utilities) distance_correlation() (bactoscoop.signalcorrelation.SignalCorrelation method) distance_matrix() (in module bactoscoop.utilities) divide_contour_by_midline() (in module bactoscoop.utilities) draw_mask() (in module bactoscoop.utilities) E entropy_difference() (bactoscoop.signalcorrelation.SignalCorrelation method) erode_contour() (in module bactoscoop.utilities) expand_contour() (in module bactoscoop.utilities) export_curated_masks() (bactoscoop.imagecollection.ImageCollection method) extend_skeleton() (in module bactoscoop.utilities) extract_skeleton() (in module bactoscoop.utilities) F Features (class in bactoscoop.features) features_to_dataframe() (bactoscoop.image.Image method) fft_energy_ratio() (bactoscoop.signalcorrelation.SignalCorrelation method) fft_peak_ratio() (bactoscoop.signalcorrelation.SignalCorrelation method) fill_nan_values() (in module bactoscoop.utilities) filter_labels_by_neighbor_count() (in module bactoscoop.utilities) find_centroid_in_largest_mask() (in module bactoscoop.utilities) find_poles() (in module bactoscoop.utilities) find_signal_peaks() (in module bactoscoop.utilities) G gaussian_smoothing() (in module bactoscoop.utilities) get_additional_regionprops_features() (in module bactoscoop.utilities) get_approx_nucleoid_volume() (in module bactoscoop.utilities) get_area() (in module bactoscoop.utilities) get_area_asymmetry() (in module bactoscoop.utilities) get_avg_distance_from_center() (in module bactoscoop.utilities) get_avg_width() (in module bactoscoop.utilities) get_avg_width_no_px() (in module bactoscoop.utilities) get_bactoscoop_logger() (in module bactoscoop.logging_utils) get_bg_channel() (bactoscoop.image.Image method) get_cell_convexity() (in module bactoscoop.utilities) get_cell_mask() (in module bactoscoop.utilities) get_cell_pairs() (in module bactoscoop.utilities) get_cell_perimeter_measurements() (in module bactoscoop.utilities) get_cell_width_variability() (in module bactoscoop.utilities) get_cellular_mesh() (in module bactoscoop.utilities) get_centroid() (in module bactoscoop.utilities) get_channel_interp2d() (bactoscoop.image.Image method) get_complemented_contour_intensity() (in module bactoscoop.utilities) get_contour_intensity() (in module bactoscoop.utilities) get_control() (bactoscoop.curation.Curation method) get_cropped_cell_data() (in module bactoscoop.utilities) get_cropped_object_data() (in module bactoscoop.utilities) get_cumulative_step_length_midline() (in module bactoscoop.utilities) get_curvature_characteristics() (in module bactoscoop.utilities) get_glcm_feature_means() (in module bactoscoop.utilities) get_homogeneity() (in module bactoscoop.utilities) get_image_for_frame() (in module bactoscoop.utilities) get_interobject_distance() (in module bactoscoop.utilities) get_inverted_image() (bactoscoop.image.Image method) get_inverted_interp2d() (bactoscoop.image.Image method) get_kurtosis() (in module bactoscoop.utilities) get_label_neighbor_counts() (in module bactoscoop.utilities) get_label_proportions() (bactoscoop.curation.Curation method) get_length() (in module bactoscoop.utilities) get_major_axis_line_coordinates() (in module bactoscoop.utilities) get_mesh_area() (in module bactoscoop.utilities) get_mesh_coordinates() (in module bactoscoop.utilities) get_mesh_dataframe() (bactoscoop.imagecollection.ImageCollection method) get_method() (bactoscoop.signalcorrelation.SignalCorrelation method) get_minima() (in module bactoscoop.utilities) get_nucleoid_volume() (in module bactoscoop.utilities) get_nucleoid_width_variability() (in module bactoscoop.utilities) get_obj_avg_width() (in module bactoscoop.utilities) get_obj_mesh_coords() (in module bactoscoop.utilities) get_object_area() (in module bactoscoop.utilities) get_object_aspect_ratio() (in module bactoscoop.utilities) get_object_avg_width() (in module bactoscoop.utilities) get_object_centroid() (in module bactoscoop.utilities) get_object_contours() (in module bactoscoop.utilities) get_object_convexity() (in module bactoscoop.utilities) get_object_curvature_characteristics() (in module bactoscoop.utilities) get_object_intensities() (in module bactoscoop.utilities) get_object_masks() (in module bactoscoop.utilities) get_object_mesh() (in module bactoscoop.utilities) get_object_midpoint() (in module bactoscoop.utilities) get_object_params() (in module bactoscoop.utilities) get_object_perimeter_measurements() (in module bactoscoop.utilities) get_object_rect_length() (in module bactoscoop.utilities) get_object_sinuosity() (in module bactoscoop.utilities) get_object_step_length() (in module bactoscoop.utilities) get_object_surface_area() (in module bactoscoop.utilities) get_object_surface_area_over_volume() (in module bactoscoop.utilities) get_object_width_variability() (in module bactoscoop.utilities) get_objects_kurtosis() (in module bactoscoop.utilities) get_objects_mean() (in module bactoscoop.utilities) get_objects_skewness() (in module bactoscoop.utilities) get_objects_std() (in module bactoscoop.utilities) get_ordered_list() (in module bactoscoop.utilities) get_phase_mask() (in module bactoscoop.utilities) get_pole_coordinates() (in module bactoscoop.utilities) get_pole_object_distances() (in module bactoscoop.utilities) get_profile_mesh() (in module bactoscoop.utilities) get_shortest_pole_object_distances() (in module bactoscoop.utilities) get_signal_mask() (in module bactoscoop.utilities) get_skew() (in module bactoscoop.utilities) get_step_length() (in module bactoscoop.utilities) get_step_length_no_px() (in module bactoscoop.utilities) get_subcellular_objects() (in module bactoscoop.utilities) get_surface_area() (in module bactoscoop.utilities) get_surface_area_over_volume() (in module bactoscoop.utilities) get_total_phaco_intensity() (in module bactoscoop.utilities) get_uncropped_cell_data() (in module bactoscoop.utilities) get_variance() (in module bactoscoop.utilities) get_volume() (in module bactoscoop.utilities) get_weighted_intprofile() (in module bactoscoop.utilities) get_width() (in module bactoscoop.utilities) H histogram_intersection() (bactoscoop.signalcorrelation.SignalCorrelation method) I identify_minima() (in module bactoscoop.utilities) Image (class in bactoscoop.image) image_field_key() (in module bactoscoop.utilities) ImageCollection (class in bactoscoop.imagecollection) interp2d() (in module bactoscoop.utilities) intersect_matrix() (in module bactoscoop.utilities) is_valid_signal() (bactoscoop.signalcorrelation.SignalCorrelation method) J join_cells() (bactoscoop.image.Image method) join_split_pipeline() (bactoscoop.image.Image method) K keep_significant_masks() (in module bactoscoop.utilities) kendall_tau() (bactoscoop.signalcorrelation.SignalCorrelation method) kurtosis_ratio() (bactoscoop.signalcorrelation.SignalCorrelation method) L li_icq() (bactoscoop.signalcorrelation.SignalCorrelation method) line_contour_intersection() (in module bactoscoop.utilities) line_intersect() (in module bactoscoop.utilities) line_length() (in module bactoscoop.utilities) linear_interpolation() (in module bactoscoop.utilities) list_field_ids() (in module bactoscoop.plot) load_channel_images() (bactoscoop.imagecollection.ImageCollection method) load_masks() (bactoscoop.imagecollection.ImageCollection method) load_model() (bactoscoop.curation.Curation method) load_models() (bactoscoop.omni.Omnipose method) load_phase_images() (bactoscoop.imagecollection.ImageCollection method) M make_predictions() (bactoscoop.curation.Curation method) manders_overlap_coefficient() (bactoscoop.signalcorrelation.SignalCorrelation method) mask2mesh() (bactoscoop.image.Image method) maybe_reverse_orientation() (in module bactoscoop.utilities) mean_background() (in module bactoscoop.utilities) measure_along_objects_midline_interp2d() (in module bactoscoop.utilities) measure_contour_variability() (in module bactoscoop.utilities) measure_intensity_interp2d() (in module bactoscoop.utilities) measure_smoothened_intensity() (in module bactoscoop.utilities) measure_width() (in module bactoscoop.utilities) median_background() (in module bactoscoop.utilities) membrane() (bactoscoop.features.Features method) merge_dataframes() (bactoscoop.imagecollection.ImageCollection method) mesh2contour() (in module bactoscoop.utilities) mesh2midline() (in module bactoscoop.utilities) meshdata_to_parquet() (bactoscoop.imagecollection.ImageCollection method) midline_midpoint() (in module bactoscoop.utilities) module bactoscoop.curation bactoscoop.features bactoscoop.image bactoscoop.imagecollection bactoscoop.logging_utils bactoscoop.omni bactoscoop.plot bactoscoop.signalcorrelation bactoscoop.utilities morphological() (bactoscoop.features.Features method) N normalize_per_cell() (in module bactoscoop.utilities) normalized_cross_correlation() (bactoscoop.signalcorrelation.SignalCorrelation method) normalized_intensity_by_image() (in module bactoscoop.utilities) O object_bending_energy() (in module bactoscoop.utilities) object_detection() (bactoscoop.image.Image method) objects() (bactoscoop.features.Features method) Omnipose (class in bactoscoop.omni) orthogonal_intersection_point() (in module bactoscoop.utilities) P pearson_correlation_coefficient() (bactoscoop.signalcorrelation.SignalCorrelation method) pick_detected_cell() (in module bactoscoop.plot) pick_representative_cell() (in module bactoscoop.plot) plot_aligned_contours() (in module bactoscoop.plot) plot_C2_alignment() (in module bactoscoop.plot) plot_cell_contour_gallery() (in module bactoscoop.plot) plot_cell_gallery() (in module bactoscoop.plot) plot_contour() (in module bactoscoop.plot) plot_curation_review() (in module bactoscoop.plot) plot_demograph_rotated() (in module bactoscoop.plot) plot_feature_histogram() (in module bactoscoop.plot) plot_feature_overview() (in module bactoscoop.plot) plot_feature_scatter() (in module bactoscoop.plot) plot_field_channels() (in module bactoscoop.plot) plot_mask() (in module bactoscoop.plot) plot_mesh_overlay() (in module bactoscoop.plot) plot_mesh_scientific() (in module bactoscoop.plot) plot_morphology_summary() (in module bactoscoop.plot) plot_multichannel_overview() (in module bactoscoop.plot) plot_normalized_axial_intensity() (in module bactoscoop.plot) plot_object_area_vs_cell_area() (in module bactoscoop.plot) plot_object_contours() (in module bactoscoop.plot) plot_object_mesh() (in module bactoscoop.plot) plot_pairwise_metric_heatmap() (in module bactoscoop.plot) plot_random_axial() (in module bactoscoop.plot) plot_random_contours() (in module bactoscoop.plot) plot_random_objects() (in module bactoscoop.plot) plot_segmentation_review() (in module bactoscoop.plot) plot_signal_gallery() (in module bactoscoop.plot) plot_signal_profile() (in module bactoscoop.plot) plot_signal_summary() (in module bactoscoop.plot) plot_svm_controls() (in module bactoscoop.plot) plot_width() (in module bactoscoop.plot) poly_func() (in module bactoscoop.utilities) prepare_dataframe() (bactoscoop.curation.Curation method) prepare_feature_pair() (bactoscoop.signalcorrelation.SignalCorrelation method) process() (bactoscoop.omni.Omnipose method) processing_summary() (bactoscoop.imagecollection.ImageCollection method) profiling() (bactoscoop.features.Features method) projection_on_midline() (in module bactoscoop.utilities) R radial_intensities() (in module bactoscoop.utilities) ratio() (bactoscoop.signalcorrelation.SignalCorrelation method) ratio_mesh_over_total_area() (in module bactoscoop.utilities) read_channels() (in module bactoscoop.utilities) read_tiff_folder() (in module bactoscoop.utilities) rescale_image_255() (in module bactoscoop.utilities) S save_masks() (bactoscoop.omni.Omnipose method) segment_images() (bactoscoop.imagecollection.ImageCollection method) select_example_cell() (in module bactoscoop.plot) separate_meshdata() (in module bactoscoop.utilities) separate_singleframe_meshdata() (in module bactoscoop.utilities) set_bg_zero() (in module bactoscoop.utilities) shift_contour() (in module bactoscoop.utilities) shift_correction() (bactoscoop.image.Image method) shift_image() (in module bactoscoop.utilities) SignalCorrelation (class in bactoscoop.signalcorrelation) sinuosity() (in module bactoscoop.utilities) skeleton_endpoints() (in module bactoscoop.utilities) skewness_product() (bactoscoop.signalcorrelation.SignalCorrelation method) smallest_path() (in module bactoscoop.utilities) snapshot_cell_contours() (in module bactoscoop.plot) spearman_rank_correlation() (bactoscoop.signalcorrelation.SignalCorrelation method) spline_approximation() (in module bactoscoop.utilities) split_array() (in module bactoscoop.utilities) split_cells() (bactoscoop.image.Image method) split_mesh2mesh() (in module bactoscoop.utilities) split_point() (in module bactoscoop.utilities) straighten_by_orthogonal_lines() (in module bactoscoop.utilities) svm() (bactoscoop.features.Features method) T tqdm_if_verbose() (in module bactoscoop.logging_utils) U unit_perpendicular_vector() (in module bactoscoop.utilities) V validate_inputs() (bactoscoop.signalcorrelation.SignalCorrelation method) Z zero_crossings_difference() (bactoscoop.signalcorrelation.SignalCorrelation method)