Index

A

Acquisition (class in palmari.data_structure.acquisition) action_name (palmari.processing.steps.base.Detector property) (palmari.processing.steps.base.SubpixelLocalizer property) (palmari.processing.steps.base.Tracker property) (palmari.processing.steps.drift_corrector.BeadDriftCorrector property) (palmari.processing.steps.drift_corrector.CorrelationDriftCorrector property) (palmari.processing.steps.window_percentile.WindowPercentileFilter property) add_columns_to_loc() (palmari.data_structure.acquisition.Acquisition method)

add_index() (palmari.quot.track.Trajectory method) add_new_roi_to_index() (palmari.data_structure.experiment.Experiment method) add_traj_cols_to_locs() (palmari.data_structure.acquisition.Acquisition method) all_files (palmari.data_structure.experiment.Experiment property) amp_from_I() (in module palmari.quot.helper) angular_dist() (in module palmari.quot.plot) angular_dist_files() (in module palmari.quot.plot) assign_methods() (in module palmari.quot.helper) available_steps (palmari.processing.image_pipeline.ImagePipeline property)

B

b_splines() (in module palmari.image_tools.localization) BaseDetector (class in palmari.processing.steps.quot_localizer) basic_stats() (palmari.data_structure.acquisition.Acquisition method)

BeadDriftCorrector (class in palmari.processing.steps.drift_corrector) blink() (palmari.quot.track.Trajectory method) bond_angles() (in module palmari.quot.plot)

C

can_be_removed() (palmari.processing.image_pipeline.ImagePipeline method) centered_gauss() (in module palmari.quot.findSpots) centroid() (in module palmari.quot.subpixel) check_2d_gauss_fit() (in module palmari.quot.helper) check_export_folder_and_load_info() (palmari.data_structure.experiment.Experiment method) ChunkFilter (class in palmari.quot.chunkFilter) circshift() (in module palmari.quot.mask) close() (palmari.quot.read.ImageReader method) coarsen_histogram() (in module palmari.quot.plot) cols_dtype (palmari.processing.steps.base.Detector attribute) (palmari.processing.steps.base.SubpixelLocalizer attribute) (palmari.processing.steps.quot_localizer.MaxLikelihoodLocalizer attribute) (palmari.processing.steps.quot_localizer.RadialLocalizer attribute)

compute() (palmari.quot.track.ScipyMunkres method) compute_intensity() (palmari.data_structure.acquisition.Acquisition method) compute_tubeness() (palmari.data_structure.acquisition.Acquisition method) concat_tracks() (in module palmari.quot.helper) connected_components() (in module palmari.quot.helper) ConservativeTracker (class in palmari.processing.steps.trackpy_tracker) contains_class() (palmari.processing.image_pipeline.ImagePipeline method) correct_drift() (in module palmari.image_tools.correct_drift) (palmari.data_structure.acquisition.Acquisition method) CorrelationDriftCorrector (class in palmari.processing.steps.drift_corrector) custom_fields (palmari.data_structure.experiment.Experiment property)

D

default_with_name() (palmari.processing.image_pipeline.ImagePipeline class method) density_filtering() (in module palmari.image_tools.density_filtering) detect() (in module palmari.quot.findSpots) (palmari.processing.steps.base.Detector method) detect_frame() (palmari.processing.steps.base.Detector method) (palmari.processing.steps.quot_localizer.BaseDetector method)

Detector (class in palmari.processing.steps.base) diffusion_weight_matrix() (in module palmari.quot.track) DiffusionTracker (class in palmari.processing.steps.quot_tracker) dog() (in module palmari.quot.findSpots) dou() (in module palmari.quot.findSpots) drift_is_corrected (palmari.data_structure.acquisition.Acquisition property) dtype (palmari.quot.read.ImageReader property)

E

estimate_delta_t() (palmari.processing.steps.base.Tracker method) estimate_I0() (in module palmari.quot.helper) estimate_I0_multiple_points() (in module palmari.quot.helper) estimate_snr() (in module palmari.quot.helper)

euclidean_weight_matrix() (in module palmari.quot.track) EuclideanTracker (class in palmari.processing.steps.quot_tracker) exp_params_path() (palmari.processing.image_pipeline.ImagePipeline method) exp_run_df_path() (palmari.processing.image_pipeline.ImagePipeline method) Experiment (class in palmari.data_structure.experiment)

F

filter_frame() (palmari.quot.chunkFilter.ChunkFilter method) filter_on_spots_per_frame() (in module palmari.quot.trajUtils) fit_ls_int_gaussian() (in module palmari.quot.helper) fit_ls_point_gaussian() (in module palmari.quot.helper)

fit_poisson_int_gaussian() (in module palmari.quot.helper) from_dict() (palmari.processing.image_pipeline.ImagePipeline class method) from_single_tif() (palmari.data_structure.experiment.Experiment class method) from_yaml() (palmari.processing.image_pipeline.ImagePipeline class method)

G

gauss() (in module palmari.quot.findSpots) gauss_filt_min_max() (in module palmari.quot.findSpots) get_cell_mask() (in module palmari.image_tools.cell_mask) get_chunk_start() (palmari.quot.chunkFilter.ChunkFilter method) get_edges() (in module palmari.quot.helper) get_frame() (palmari.quot.read.ImageReader method) get_frame_range() (palmari.quot.read.ImageReader method) get_ID_of_acq() (palmari.data_structure.experiment.Experiment method) get_max_gap() (in module palmari.quot.trajUtils)

get_optimal_shift() (in module palmari.image_tools.correct_drift) get_ordered_mask_points() (in module palmari.quot.helper) get_property() (palmari.data_structure.acquisition.Acquisition method) get_slice() (palmari.quot.track.Trajectory method) get_spots_per_frame() (in module palmari.quot.trajUtils) get_subregion() (palmari.quot.read.ImageReader method) get_subregion_range() (palmari.quot.read.ImageReader method) get_traj() (palmari.data_structure.acquisition.Acquisition method) get_values_as_in_dict() (in module palmari.processing.utils)

H

has_alternatives_to() (palmari.processing.image_pipeline.ImagePipeline method) has_match() (in module palmari.quot.track) hess_det() (in module palmari.quot.findSpots)

hess_det_broad_var() (in module palmari.quot.findSpots) hess_det_var() (in module palmari.quot.findSpots) hex_cmap() (in module palmari.quot.plot) hollow_box_var() (in module palmari.quot.helper)

I

I0_is_crazy() (in module palmari.quot.helper) ID (palmari.data_structure.acquisition.Acquisition property) identity() (in module palmari.quot.chunkFilter) image (palmari.data_structure.acquisition.Acquisition property) ImagePipeline (class in palmari.processing.image_pipeline) ImageReader (class in palmari.quot.read) imlocdensities() (in module palmari.quot.plot) imlocdensity() (in module palmari.quot.plot) imread() (palmari.quot.read.ImageReader method) imsave() (palmari.quot.read.ImageReader method) imshow() (in module palmari.quot.plot) index_df (palmari.data_structure.experiment.Experiment property) index_of() (palmari.processing.image_pipeline.ImagePipeline method) indices() (in module palmari.quot.helper) indices_1d() (in module palmari.quot.helper) int_gauss_psf_1d() (in module palmari.quot.helper) int_gauss_psf_2d() (in module palmari.quot.helper)

int_gauss_psf_deriv_1d() (in module palmari.quot.helper) intensity (palmari.data_structure.acquisition.Acquisition property) intensity_is_computed (palmari.data_structure.acquisition.Acquisition property) intensity_path (palmari.data_structure.acquisition.Acquisition property) interpolate() (palmari.quot.mask.MaskInterpolator method) invert_hessian() (in module palmari.quot.helper) is_already_localized() (palmari.processing.image_pipeline.ImagePipeline method) is_already_tracked() (palmari.processing.image_pipeline.ImagePipeline method) is_detector (palmari.processing.steps.base.Detector property) (palmari.processing.steps.base.ProcessingStep property) is_duplicates() (in module palmari.quot.track) is_localized (palmari.data_structure.acquisition.Acquisition property) is_localizer (palmari.processing.steps.base.Detector property) (palmari.processing.steps.base.ProcessingStep property) (palmari.processing.steps.base.SubpixelLocalizer property) is_mandatory() (palmari.processing.image_pipeline.ImagePipeline method) is_processed (palmari.data_structure.acquisition.Acquisition property) is_tracked (palmari.data_structure.acquisition.Acquisition property)

J

jump_cdf_files() (in module palmari.quot.plot)

K

kill_ticks() (in module palmari.quot.plot)

L

label_spots() (in module palmari.quot.helper) last_pos() (palmari.quot.track.Trajectory method) llr() (in module palmari.quot.findSpots) llr_rect() (in module palmari.quot.findSpots) load_chunk() (palmari.quot.chunkFilter.ChunkFilter method) load_tracks_dir() (in module palmari.quot.helper) loc_processing() (palmari.processing.image_pipeline.ImagePipeline method) localize() (palmari.data_structure.acquisition.Acquisition method) (palmari.processing.steps.base.SubpixelLocalizer method) localize_file() (in module palmari.quot.core) localize_frame() (in module palmari.quot.subpixel) (palmari.processing.steps.base.SubpixelLocalizer method) (palmari.processing.steps.quot_localizer.MaxLikelihoodLocalizer method) (palmari.processing.steps.quot_localizer.RadialLocalizer method)

LocProcessor (class in palmari.processing.steps.base) locs (palmari.data_structure.acquisition.Acquisition property) locs_path (palmari.data_structure.acquisition.Acquisition property) locs_per_frame() (in module palmari.quot.plot) locs_per_frame_files() (in module palmari.quot.plot) log() (in module palmari.quot.findSpots) look_for_new_columns() (palmari.data_structure.experiment.Experiment method) look_for_updates() (palmari.data_structure.experiment.Experiment method) ls_int_gaussian() (in module palmari.quot.subpixel) ls_point_gaussian() (in module palmari.quot.subpixel) lsradialcenterfit() (in module palmari.image_tools.localization)

M

make_filters() (in module palmari.image_tools.localization) mark_as_localized() (palmari.processing.image_pipeline.ImagePipeline method) mark_as_tracked() (palmari.processing.image_pipeline.ImagePipeline method) MaskInterpolator (class in palmari.quot.mask) match_vertices() (in module palmari.quot.mask) max_int_proj() (in module palmari.quot.plot) (palmari.quot.read.ImageReader method) MaxLikelihoodLocalizer (class in palmari.processing.steps.quot_localizer) mean_intensity_center() (in module palmari.image_tools.intensity) measure_camera_gain() (in module palmari.quot.measureGain) min_max() (in module palmari.quot.findSpots) (palmari.quot.read.ImageReader method) mle_amp() (in module palmari.quot.findSpots) module palmari palmari.data_structure palmari.data_structure.acquisition palmari.data_structure.experiment palmari.image_tools palmari.image_tools.cell_mask palmari.image_tools.correct_drift palmari.image_tools.density_filtering palmari.image_tools.intensity palmari.image_tools.localization palmari.processing palmari.processing.image_pipeline palmari.processing.steps palmari.processing.steps.base palmari.processing.steps.drift_corrector palmari.processing.steps.quot_localizer palmari.processing.steps.quot_tracker palmari.processing.steps.trackpy_tracker palmari.processing.steps.window_percentile palmari.processing.utils palmari.quot palmari.quot.chunkFilter palmari.quot.core palmari.quot.findSpots palmari.quot.helper palmari.quot.mask palmari.quot.measureGain palmari.quot.plot palmari.quot.read palmari.quot.subpixel palmari.quot.track palmari.quot.trajUtils

movie_detection() (palmari.processing.steps.base.Detector method) movie_localization() (palmari.processing.image_pipeline.ImagePipeline method) (palmari.processing.steps.base.SubpixelLocalizer method) movie_preprocessing() (palmari.processing.image_pipeline.ImagePipeline method) MoviePreProcessor (class in palmari.processing.steps.base)

N

name (palmari.processing.steps.base.Detector property) (palmari.processing.steps.base.LocProcessor property) (palmari.processing.steps.base.MoviePreProcessor property) (palmari.processing.steps.base.ProcessingStep property) (palmari.processing.steps.base.SubpixelLocalizer property) (palmari.processing.steps.base.Tracker property) (palmari.processing.steps.drift_corrector.BeadDriftCorrector property) (palmari.processing.steps.drift_corrector.CorrelationDriftCorrector property) (palmari.processing.steps.quot_localizer.BaseDetector property) (palmari.processing.steps.quot_localizer.MaxLikelihoodLocalizer property) (palmari.processing.steps.quot_localizer.RadialLocalizer property) (palmari.processing.steps.quot_tracker.DiffusionTracker property) (palmari.processing.steps.quot_tracker.EuclideanTracker property) (palmari.processing.steps.trackpy_tracker.ConservativeTracker property) (palmari.processing.steps.window_percentile.WindowPercentileFilter property)

P

pad() (in module palmari.quot.helper) palmari module palmari.data_structure module palmari.data_structure.acquisition module palmari.data_structure.experiment module palmari.image_tools module palmari.image_tools.cell_mask module palmari.image_tools.correct_drift module palmari.image_tools.density_filtering module palmari.image_tools.intensity module palmari.image_tools.localization module palmari.processing module palmari.processing.image_pipeline module palmari.processing.steps module palmari.processing.steps.base module palmari.processing.steps.drift_corrector module palmari.processing.steps.quot_localizer module palmari.processing.steps.quot_tracker module palmari.processing.steps.trackpy_tracker module palmari.processing.steps.window_percentile module palmari.processing.utils module palmari.quot module palmari.quot.chunkFilter module palmari.quot.core module

palmari.quot.findSpots module palmari.quot.helper module palmari.quot.mask module palmari.quot.measureGain module palmari.quot.plot module palmari.quot.read module palmari.quot.subpixel module palmari.quot.track module palmari.quot.trajUtils module parameter_influence_on_stats() (palmari.data_structure.experiment.Experiment method) phaser() (in module palmari.image_tools.localization) plot_jump_cdfs() (in module palmari.quot.plot) plot_jump_pdfs() (in module palmari.quot.plot) plot_pixel_mean_variance() (in module palmari.quot.plot) plotRadialDisps() (in module palmari.quot.plot) plotRadialDispsBar() (in module palmari.quot.plot) plus_func() (in module palmari.image_tools.localization) point_gauss_psf_1d() (in module palmari.quot.helper) point_gauss_psf_2d() (in module palmari.quot.helper) poisson_int_gaussian() (in module palmari.quot.subpixel) polygon_files (palmari.data_structure.acquisition.Acquisition property) polygon_folder (palmari.data_structure.acquisition.Acquisition property) preprocess() (palmari.processing.steps.base.MoviePreProcessor method) (palmari.processing.steps.window_percentile.WindowPercentileFilter method) process() (palmari.processing.image_pipeline.ImagePipeline method) (palmari.processing.steps.base.Detector method) (palmari.processing.steps.base.LocProcessor method) (palmari.processing.steps.base.MoviePreProcessor method) (palmari.processing.steps.base.ProcessingStep method) (palmari.processing.steps.base.SubpixelLocalizer method) (palmari.processing.steps.base.Tracker method) (palmari.processing.steps.drift_corrector.BeadDriftCorrector method) (palmari.processing.steps.drift_corrector.CorrelationDriftCorrector method) ProcessingStep (class in palmari.processing.steps.base) psf_int_proj_denom() (in module palmari.quot.helper) psf_point_proj_denom() (in module palmari.quot.helper)

R

rad_disp_histogram_2d() (in module palmari.quot.plot) radial_disp_histograms() (in module palmari.quot.trajUtils) radial_disps() (in module palmari.quot.trajUtils) radial_symmetry() (in module palmari.quot.subpixel) radialCenter() (in module palmari.image_tools.localization) RadialLocalizer (class in palmari.processing.steps.quot_localizer) raw_locs (palmari.data_structure.acquisition.Acquisition property) raw_locs_path (palmari.data_structure.acquisition.Acquisition property) read_config() (in module palmari.quot.read) reconnect_conservative() (in module palmari.quot.track)

reconnect_diffusion() (in module palmari.quot.track) reconnect_euclidean() (in module palmari.quot.track) reconnect_hungarian() (in module palmari.quot.track) remove_old_roi_from_index() (palmari.data_structure.experiment.Experiment method) retrack_file() (in module palmari.quot.core) retrack_files() (in module palmari.quot.core) ring_mean() (in module palmari.quot.helper) ring_var() (in module palmari.quot.helper) rs() (in module palmari.quot.helper) runs_stats (palmari.data_structure.experiment.Experiment property)

S

save_config() (in module palmari.quot.read) save_index() (palmari.data_structure.experiment.Experiment method) scan_folder() (palmari.data_structure.experiment.Experiment method) ScipyMunkres (class in palmari.quot.track) set_chunk_size() (palmari.quot.chunkFilter.ChunkFilter method) set_method_kwargs() (palmari.quot.chunkFilter.ChunkFilter method) set_subregion() (palmari.quot.chunkFilter.ChunkFilter method) shape (palmari.quot.read.ImageReader property) shoelace() (in module palmari.quot.mask) simple_sub() (in module palmari.quot.chunkFilter) sliding_window_filter() (in module palmari.image_tools.localization) SMLM_filtering() (in module palmari.image_tools.localization) SMLM_localization() (in module palmari.image_tools.localization)

smooth_average() (in module palmari.image_tools.intensity) stable_divide_array() (in module palmari.quot.helper) stable_divide_float() (in module palmari.quot.helper) step_class_of() (palmari.processing.image_pipeline.ImagePipeline method) step_type_of() (palmari.processing.image_pipeline.ImagePipeline method) sub_gauss_filt_mean() (in module palmari.quot.chunkFilter) sub_gauss_filt_median() (in module palmari.quot.chunkFilter) sub_gauss_filt_min() (in module palmari.quot.chunkFilter) sub_mean() (in module palmari.quot.chunkFilter) sub_median() (in module palmari.quot.chunkFilter) sub_min() (in module palmari.quot.chunkFilter) SubpixelLocalizer (class in palmari.processing.steps.base) sum_proj() (palmari.quot.read.ImageReader method)

T

tag_localizations_per_cell() (in module palmari.image_tools.cell_mask) threshold_image() (in module palmari.quot.helper) time_f() (in module palmari.quot.helper) to_dict() (palmari.processing.image_pipeline.ImagePipeline method) (palmari.processing.steps.base.ProcessingStep method) to_yaml() (palmari.processing.image_pipeline.ImagePipeline method) track() (in module palmari.quot.track) (palmari.data_structure.acquisition.Acquisition method) (palmari.processing.steps.base.Tracker method) (palmari.processing.steps.quot_tracker.DiffusionTracker method) (palmari.processing.steps.quot_tracker.EuclideanTracker method) (palmari.processing.steps.trackpy_tracker.ConservativeTracker method) track_directory() (in module palmari.quot.core) track_file() (in module palmari.quot.core)

track_files() (in module palmari.quot.core) track_length() (in module palmari.quot.helper) (in module palmari.quot.plot) track_subset() (in module palmari.quot.track) tracked_mat_to_csv() (in module palmari.quot.helper) Tracker (class in palmari.processing.steps.base) tracking() (palmari.processing.image_pipeline.ImagePipeline method) traj_length() (in module palmari.quot.trajUtils) traj_loc_distance() (in module palmari.quot.track) trajectories_list() (palmari.data_structure.acquisition.Acquisition method) Trajectory (class in palmari.quot.track) tubeness (palmari.data_structure.acquisition.Acquisition property) tubeness_is_computed (palmari.data_structure.acquisition.Acquisition property) tubeness_path (palmari.data_structure.acquisition.Acquisition property)

U

update_param() (palmari.processing.steps.base.ProcessingStep method)

upsample_2d_path() (in module palmari.quot.mask)

V

view() (palmari.data_structure.acquisition.Acquisition method) view_points() (palmari.data_structure.acquisition.Acquisition method)

view_polygons() (palmari.data_structure.acquisition.Acquisition method) view_tracks() (palmari.data_structure.acquisition.Acquisition method)

W

widget_options (palmari.processing.steps.base.ProcessingStep attribute) (palmari.processing.steps.drift_corrector.BeadDriftCorrector attribute) (palmari.processing.steps.drift_corrector.CorrelationDriftCorrector attribute) (palmari.processing.steps.quot_localizer.BaseDetector attribute) (palmari.processing.steps.quot_localizer.MaxLikelihoodLocalizer attribute) (palmari.processing.steps.quot_localizer.RadialLocalizer attribute) (palmari.processing.steps.quot_tracker.DiffusionTracker attribute) (palmari.processing.steps.quot_tracker.EuclideanTracker attribute) (palmari.processing.steps.trackpy_tracker.ConservativeTracker attribute) (palmari.processing.steps.window_percentile.WindowPercentileFilter attribute) widget_type (palmari.processing.steps.drift_corrector.CorrelationDriftCorrector attribute)

widget_types (palmari.processing.steps.base.ProcessingStep attribute) (palmari.processing.steps.drift_corrector.BeadDriftCorrector attribute) (palmari.processing.steps.quot_localizer.BaseDetector attribute) (palmari.processing.steps.quot_localizer.MaxLikelihoodLocalizer attribute) (palmari.processing.steps.quot_tracker.DiffusionTracker attribute) (palmari.processing.steps.quot_tracker.EuclideanTracker attribute) (palmari.processing.steps.trackpy_tracker.ConservativeTracker attribute) (palmari.processing.steps.window_percentile.WindowPercentileFilter attribute) WindowPercentileFilter (class in palmari.processing.steps.window_percentile) wireframe_overlay() (in module palmari.quot.plot) wrapup() (in module palmari.quot.plot)