Index

A

abs_filter() (in module celldetective.filters) alignment alpha_msd() (in module celldetective.signals) analyze_pair_signals() (in module celldetective.signals) analyze_pair_signals_at_position() (in module celldetective.signals) analyze_signals() (in module celldetective.signals) analyze_signals_at_position() (in module celldetective.signals) antibody apply_background_to_stack() (in module celldetective.preprocessing) apply_watershed() (in module celldetective.segmentation) area_dark_intensity() (in module celldetective.extra_properties)

area_dark_intensity_ninety() (in module celldetective.extra_properties) area_dark_intensity_ninetyfive() (in module celldetective.extra_properties) area_detected_in_intensity() (in module celldetective.extra_properties) augmenter() (in module celldetective.utils.image_augmenters) auto_correct_masks() (in module celldetective.utils.experiment) (in module celldetective.utils.mask_cleaning) auto_find_gpu() (in module celldetective.utils.resources) auto_load_number_of_frames() (in module celldetective.utils.experiment) (in module celldetective.utils.image_loaders) axes_check_and_normalize() (in module celldetective.utils.image_transforms) axes_dict() (in module celldetective.utils.image_transforms)

B

background correction

blob_detection() (in module celldetective.measure) blur() (in module celldetective.utils.image_augmenters)

C

cell population cell type celldetective.events module celldetective.extra_properties module celldetective.filters module celldetective.measure module celldetective.neighborhood module celldetective.preprocessing module celldetective.relative_measurements module celldetective.segmentation module celldetective.signals module celldetective.tracking module celldetective.utils module celldetective.utils.color_mappings module celldetective.utils.data_cleaning module celldetective.utils.data_loaders module celldetective.utils.dataset_helpers module celldetective.utils.downloaders module celldetective.utils.experiment module celldetective.utils.image_augmenters module celldetective.utils.image_cleaning module celldetective.utils.image_loaders module celldetective.utils.image_transforms module celldetective.utils.io module celldetective.utils.mask_cleaning module celldetective.utils.mask_transforms module celldetective.utils.masks module

celldetective.utils.maths module celldetective.utils.model_getters module celldetective.utils.model_loaders module celldetective.utils.normalization module celldetective.utils.parsing module celldetective.utils.resources module celldetective.utils.stats module celldetective.utils.types module censoring center_of_mass_to_abs_coordinates() (in module celldetective.measure) characteristic group Classifier Widget classify_cells_from_query() (in module celldetective.measure) classify_irreversible_events() (in module celldetective.measure) classify_tracks_from_query() (in module celldetective.measure) classify_transient_events() (in module celldetective.measure) classify_unique_states() (in module celldetective.measure) clean_trajectories() (in module celldetective.tracking) collapse_trajectories_by_status() (in module celldetective.utils.data_cleaning) collect_experiment_metadata() (in module celldetective.utils.experiment) color_from_class() (in module celldetective.utils.color_mappings) color_from_status() (in module celldetective.utils.color_mappings) columnwise_mean() (in module celldetective.signals) compute_attention_weight() (in module celldetective.neighborhood) compute_contact_neighborhood_at_position() (in module celldetective.neighborhood) compute_haralick_features() (in module celldetective.measure) compute_instantaneous_diffusion() (in module celldetective.tracking) compute_instantaneous_velocity() (in module celldetective.tracking) compute_neighborhood_at_position() (in module celldetective.neighborhood) compute_neighborhood_metrics() (in module celldetective.neighborhood) compute_survival() (in module celldetective.events) compute_weights() (in module celldetective.utils.dataset_helpers) concentration config_section_to_dict() (in module celldetective.utils.parsing) consume() (in module celldetective.utils.image_transforms) contact_neighborhood() (in module celldetective.neighborhood) contour measurements contour_of_instance_segmentation() (in module celldetective.utils.masks) control_tracking_table() (in module celldetective.utils.experiment) correct_background_model() (in module celldetective.preprocessing) correct_background_model_free() (in module celldetective.preprocessing) correct_channel_offset() (in module celldetective.preprocessing) correct_channel_offset_single_stack() (in module celldetective.preprocessing) create_patch_mask() (in module celldetective.utils.masks) cumulated presence

D

demangle_column_name() (in module celldetective.utils.parsing) derivative() (in module celldetective.utils.maths) differentiate_per_track() (in module celldetective.utils.maths) distance_cut_neighborhood() (in module celldetective.neighborhood)

dog_filter() (in module celldetective.filters) download_url_to_file() (in module celldetective.utils.downloaders) download_zenodo_file() (in module celldetective.utils.downloaders) drift_msd() (in module celldetective.signals) drop_tonal_features() (in module celldetective.measure)

E

estimate_background_per_condition() (in module celldetective.preprocessing) estimate_time() (in module celldetective.measure) estimate_unreliable_edge() (in module celldetective.utils.image_transforms) event Event Annotator event class event time expand_pair_table() (in module celldetective.relative_measurements) experiment project extract_blobs_in_image() (in module celldetective.measure) extract_cols_from_query() (in module celldetective.utils.parsing) extract_cols_from_table_list() (in module celldetective.utils.data_cleaning)

extract_experiment_channels() (in module celldetective.utils.experiment) extract_experiment_folder_output() (in module celldetective.utils.experiment) extract_experiment_from_position() (in module celldetective.utils.experiment) extract_experiment_from_well() (in module celldetective.utils.experiment) extract_identity_col() (in module celldetective.utils.data_cleaning) extract_neighborhood_in_pair_table() (in module celldetective.neighborhood) extract_neighborhood_settings() (in module celldetective.relative_measurements) extract_neighborhoods_from_pickles() (in module celldetective.relative_measurements) extract_objects_and_features() (in module celldetective.tracking) extract_position_name() (in module celldetective.utils.experiment) extract_well_from_position() (in module celldetective.utils.experiment) extract_well_name_and_number() (in module celldetective.utils.experiment) extrapolate_tracks() (in module celldetective.tracking)

F

field_correction() (in module celldetective.preprocessing) fill_label_holes() (in module celldetective.utils.mask_cleaning) filter_by_endpoints() (in module celldetective.tracking) filter_by_tracklength() (in module celldetective.tracking) filter_image() (in module celldetective.filters) filter_on_property() (in module celldetective.segmentation) find_contact_neighbors() (in module celldetective.neighborhood) first detection event

fit_and_apply_model_background_to_stack() (in module celldetective.preprocessing) fit_background_model() (in module celldetective.preprocessing) fit_paraboloid() (in module celldetective.preprocessing) fit_plane() (in module celldetective.preprocessing) fix_missing_labels() (in module celldetective.utils.experiment) (in module celldetective.utils.image_loaders) fraction_of_area_dark_intensity() (in module celldetective.extra_properties) fraction_of_area_detected_in_intensity() (in module celldetective.extra_properties)

G

gauss_filter() (in module celldetective.filters) get_config() (in module celldetective.utils.experiment) get_experiment_antibodies() (in module celldetective.utils.experiment) get_experiment_cell_types() (in module celldetective.utils.experiment) get_experiment_concentrations() (in module celldetective.utils.experiment) get_experiment_labels() (in module celldetective.utils.experiment) get_experiment_metadata() (in module celldetective.utils.experiment) get_experiment_pharmaceutical_agents() (in module celldetective.utils.experiment) get_experiment_populations() (in module celldetective.utils.experiment) get_experiment_wells() (in module celldetective.utils.experiment) get_pair_signal_models_list() (in module celldetective.utils.model_getters) get_position_movie_path() (in module celldetective.utils.experiment)

get_position_pickle() (in module celldetective.utils.data_loaders) get_position_table() (in module celldetective.utils.data_loaders) (in module celldetective.utils.experiment) get_positions_in_well() (in module celldetective.utils.experiment) get_segmentation_datasets_list() (in module celldetective.utils.model_getters) get_segmentation_models_list() (in module celldetective.utils.model_getters) get_signal_datasets_list() (in module celldetective.utils.model_getters) get_signal_models_list() (in module celldetective.utils.model_getters) get_spatial_calibration() (in module celldetective.utils.experiment) get_stack_normalization_values() (in module celldetective.utils.normalization) get_temporal_calibration() (in module celldetective.utils.experiment) get_tracking_configs_list() (in module celldetective.utils.model_getters) get_zenodo_files() (in module celldetective.utils.downloaders)

I

identify_markers_from_binary() (in module celldetective.segmentation) input spatial calibration instance segmentation instantaneous_diffusion() (in module celldetective.tracking) intensity_center_of_mass_displacement() (in module celldetective.extra_properties) intensity_center_of_mass_displacement_edge() (in module celldetective.extra_properties) intensity_median() (in module celldetective.extra_properties) intensity_nanmean() (in module celldetective.extra_properties) intensity_percentile_fifty() (in module celldetective.extra_properties) intensity_percentile_ninety() (in module celldetective.extra_properties) intensity_percentile_ninety_five() (in module celldetective.extra_properties) intensity_percentile_ninety_nine() (in module celldetective.extra_properties) intensity_percentile_seventy_five() (in module celldetective.extra_properties) intensity_percentile_twenty_five() (in module celldetective.extra_properties)

intensity_radial_gradient() (in module celldetective.extra_properties) intensity_std() (in module celldetective.extra_properties) Interaction Annotator interpolate_nan() (in module celldetective.utils.image_cleaning) interpolate_nan_multichannel() (in module celldetective.utils.image_cleaning) interpolate_nan_properties() (in module celldetective.tracking) interpolate_per_track() (in module celldetective.tracking) interpolate_time_gaps() (in module celldetective.tracking) interpret_track_classification() (in module celldetective.measure) interpret_tracking_configuration() (in module celldetective.utils.data_loaders) interpret_wells_and_positions() (in module celldetective.utils.experiment) invert_filter() (in module celldetective.filters) is_integer_array() (in module celldetective.utils.types) isotropic measurements

L

label laplace_filter() (in module celldetective.filters) linear_msd() (in module celldetective.signals) ln_filter() (in module celldetective.filters) load_experiment_tables() (in module celldetective.utils.data_loaders) load_frames() (in module celldetective.utils.image_loaders) load_image_dataset() (in module celldetective.utils.image_loaders) load_tracking_data() (in module celldetective.utils.data_loaders) (in module celldetective.utils.experiment) local_filter() (in module celldetective.filters) local_normalisation() (in module celldetective.measure)

locate_labels() (in module celldetective.utils.experiment) (in module celldetective.utils.image_loaders) locate_pair_signal_model() (in module celldetective.utils.model_loaders) locate_segmentation_dataset() (in module celldetective.utils.model_loaders) locate_segmentation_model() (in module celldetective.utils.model_loaders) locate_signal_dataset() (in module celldetective.utils.model_loaders) locate_signal_model() (in module celldetective.utils.model_loaders) locate_stack() (in module celldetective.utils.experiment) (in module celldetective.utils.image_loaders) locate_stack_and_labels() (in module celldetective.utils.experiment) (in module celldetective.utils.image_loaders) log_filter() (in module celldetective.filters)

M

magnitude_diffusion() (in module celldetective.tracking) magnitude_velocity() (in module celldetective.utils.maths) mask contact mask_contact_neighborhood() (in module celldetective.neighborhood) mask_edges() (in module celldetective.utils.image_transforms) maximum_filter() (in module celldetective.filters) mean_dark_intensity_eight_five_fillhole_false() (in module celldetective.extra_properties) mean_dark_intensity_eighty_five() (in module celldetective.extra_properties) mean_dark_intensity_ninety() (in module celldetective.extra_properties) mean_dark_intensity_ninety_fillhole_false() (in module celldetective.extra_properties) mean_dark_intensity_ninetyfive() (in module celldetective.extra_properties) mean_dark_intensity_ninetyfive_fillhole_false() (in module celldetective.extra_properties) mean_neighborhood_after_event() (in module celldetective.neighborhood) mean_neighborhood_before_event() (in module celldetective.neighborhood) mean_signal() (in module celldetective.signals) measure() (in module celldetective.measure) measure_at_position() (in module celldetective.measure) measure_features() (in module celldetective.measure) measure_isotropic_intensity() (in module celldetective.measure) measure_pair_signals_at_position() (in module celldetective.relative_measurements) measure_pairs() (in module celldetective.relative_measurements) measure_radial_distance_to_center() (in module celldetective.measure) median_filter() (in module celldetective.filters) merge_instance_segmentation() (in module celldetective.segmentation) merge_labels() (in module celldetective.neighborhood) minimum_filter() (in module celldetective.filters) module celldetective.events celldetective.extra_properties celldetective.filters celldetective.measure celldetective.neighborhood celldetective.preprocessing celldetective.relative_measurements celldetective.segmentation celldetective.signals celldetective.tracking celldetective.utils celldetective.utils.color_mappings celldetective.utils.data_cleaning celldetective.utils.data_loaders celldetective.utils.dataset_helpers celldetective.utils.downloaders celldetective.utils.experiment celldetective.utils.image_augmenters celldetective.utils.image_cleaning celldetective.utils.image_loaders celldetective.utils.image_transforms celldetective.utils.io celldetective.utils.mask_cleaning celldetective.utils.mask_transforms celldetective.utils.masks celldetective.utils.maths celldetective.utils.model_getters celldetective.utils.model_loaders celldetective.utils.normalization celldetective.utils.parsing celldetective.utils.resources celldetective.utils.stats celldetective.utils.types

morphological features move_image_axes() (in module celldetective.utils.image_transforms) multiotsu_filter() (in module celldetective.filters)

N

neighbor cell neighbor counts neighbor population neighborhood niblack_filter() (in module celldetective.filters)

noise() (in module celldetective.utils.image_augmenters) normalise_by_cell() (in module celldetective.measure) normalize() (in module celldetective.utils.normalization) normalize_mi_ma() (in module celldetective.utils.normalization) normalize_multichannel() (in module celldetective.utils.normalization) normalize_per_channel() (in module celldetective.utils.normalization)

O

orientation() (in module celldetective.utils.maths)

otsu_filter() (in module celldetective.filters)

P

paraboloid() (in module celldetective.preprocessing) parse_isotropic_radii() (in module celldetective.utils.parsing) percentile_filter() (in module celldetective.filters) percentile_five_dark_intensity_ninety() (in module celldetective.extra_properties) percentile_ninty_five_dark_intensity_ninety() (in module celldetective.extra_properties) percentile_one_dark_intensity_ninety() (in module celldetective.extra_properties) percentile_ten_dark_intensity_ninety() (in module celldetective.extra_properties)

percentile_zero_one_dark_intensity_ninety() (in module celldetective.extra_properties) pharmaceutical agents phenotype Phenotype Annotator plane() (in module celldetective.preprocessing) position preprocessing

R

random_fliprot() (in module celldetective.utils.image_augmenters) random_shift() (in module celldetective.utils.image_augmenters) reference cell reference population rel_measure_at_position() (in module celldetective.relative_measurements) relabel_segmentation() (in module celldetective.utils.experiment) (in module celldetective.utils.mask_cleaning)

relabel_segmentation_lazy() (in module celldetective.utils.experiment) remove_file_if_exists() (in module celldetective.utils.io) remove_redundant_features() (in module celldetective.utils.data_cleaning) remove_trajectory_measurements() (in module celldetective.utils.data_cleaning) rename_intensity_column() (in module celldetective.utils.data_cleaning)

S

safe_log() (in module celldetective.utils.maths) sauvola_filter() (in module celldetective.filters) save_tiff_imagej_compatible() (in module celldetective.utils.io) segment() (in module celldetective.segmentation) segment_at_position() (in module celldetective.segmentation) segment_frame_from_thresholds() (in module celldetective.segmentation) segment_from_threshold_at_position() (in module celldetective.segmentation) segment_from_thresholds() (in module celldetective.segmentation) set_live_status() (in module celldetective.neighborhood) sign() (in module celldetective.neighborhood)

signal single-cell measurement sliding_msd() (in module celldetective.signals) sliding_msd_drift() (in module celldetective.signals) split_by_ratio() (in module celldetective.utils.dataset_helpers) spreading event std_filter() (in module celldetective.filters) step_function() (in module celldetective.utils.maths) subtract_filter() (in module celldetective.filters) survival switch_to_events() (in module celldetective.events)

T

T_MSD() (in module celldetective.signals) Table Explorer test_2samp_generic() (in module celldetective.utils.stats) test_bool_array() (in module celldetective.utils.types) texture features threshold-based event detection threshold_image() (in module celldetective.utils.image_transforms) timeline_matching() (in module celldetective.relative_measurements)

tophat_filter() (in module celldetective.filters) track() (in module celldetective.tracking) track_at_position() (in module celldetective.tracking) tracks_to_btrack() (in module celldetective.utils.data_cleaning) (in module celldetective.utils.experiment) tracks_to_napari() (in module celldetective.utils.experiment) train_segmentation_model() (in module celldetective.segmentation) train_signal_model() (in module celldetective.signals) train_test_split() (in module celldetective.utils.dataset_helpers)

U

unpad() (in module celldetective.utils.image_transforms)

update_effector_table() (in module celldetective.relative_measurements)

V

variance_filter() (in module celldetective.filters) velocity() (in module celldetective.utils.maths)

velocity_per_track() (in module celldetective.utils.maths) view_tracks_in_napari() (in module celldetective.utils.experiment)

W

well	write_first_detection_class() (in module celldetective.measure) (in module celldetective.tracking)

Z

zoom_multiframes() (in module celldetective.utils.image_loaders)