Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | W | X | Y | Z _ __call__() (sdt.flatfield.Corrector method) (sdt.funcs.ECDF method) (sdt.funcs.StepFunction method) (sdt.multicolor.Registrator method) (sdt.optimize.AffineModel method) (sdt.optimize.AffineModelResult method) (sdt.optimize.ExpSumModel method) (sdt.optimize.ExpSumModelResult method) (sdt.roi.MaskROI method) (sdt.roi.PathROI method) (sdt.roi.ROI method) A a (sdt.loc.z_fit.Parameters.Tuple attribute) acceptor_channel (sdt.fret.SmFRETTracker attribute) adaptive_thresh() (in module sdt.image) AffineModel (class in sdt.optimize) AffineModelResult (class in sdt.optimize) algorithm (sdt.nbui.Locator attribute) (sdt.nbui.Thresholder attribute) align_panellabels() (in module sdt.plot) AnomalousDiffusion (class in sdt.motion) AnomalousDiffusion.Result (class in sdt.motion) apply_filters() (sdt.fret.SmFRETAnalyzer method) apply_track_filters() (in module sdt.fret) area (sdt.roi.MaskROI property) (sdt.roi.PathROI attribute) auto_scale() (sdt.nbui.ImageDisplay method) avg_img (sdt.flatfield.Corrector attribute) ax (sdt.nbui.ImageDisplay attribute) B batch() (in module sdt.loc.cg) (in module sdt.loc.daostorm_3d) batch_func (sdt.nbui.Locator property) batch_roi() (in module sdt.loc.cg) (in module sdt.loc.daostorm_3d) batch_roi_func (sdt.nbui.Locator property) BayesOffline (class in sdt.changepoint) BayesOnline (class in sdt.changepoint) best_values (sdt.optimize.AffineModelResult attribute) (sdt.optimize.ExpSumModelResult attribute) bg (sdt.flatfield.Corrector attribute) bleach_step() (sdt.fret.SmFRETAnalyzer method) bleach_thresh (sdt.fret.SmFRETAnalyzer attribute) bottom_right (sdt.roi.ROI attribute) bounding_box (sdt.roi.PathROI attribute) bounding_box_int (sdt.roi.PathROI attribute) brightness_options (sdt.fret.SmFRETTracker attribute) brownian_track() (in module sdt.sim) BrownianMotion (class in sdt.motion) buffer (sdt.roi.PathROI attribute) C calc_detection_eff() (sdt.fret.SmFRETAnalyzer method) calc_detection_excitation_effs() (sdt.fret.SmFRETAnalyzer method) calc_direct_excitation() (sdt.fret.SmFRETAnalyzer method) calc_excitation_eff() (sdt.fret.SmFRETAnalyzer method) calc_fret_values() (sdt.fret.SmFRETAnalyzer method) calc_leakage() (sdt.fret.SmFRETAnalyzer method) calc_pair_distance() (in module sdt.multicolor) calibrate() (sdt.loc.z_fit.Parameters class method) categories (sdt.nbui.ROISelector attribute) center() (in module sdt.image) cg() (in module sdt.image) cg_bg() (in module sdt.image) channel_names (sdt.multicolor.Registrator attribute) (sdt.nbui.ChannelSplitter attribute) ChannelSplitter (class in sdt.nbui) chdir() (in module sdt.io) CircleMask (class in sdt.image) close() (sdt.io.ImageSequence method) closed (sdt.io.ImageSequence property) cmap (sdt.nbui.ImageDisplay attribute) coloc_dist (sdt.fret.SmFRETTracker attribute) colors (sdt.nbui.ChannelSplitter attribute) columns (in module sdt.config) (sdt.fret.SmFRETAnalyzer attribute) (sdt.fret.SmFRETTracker attribute) (sdt.multicolor.Registrator attribute) ConstHazard (class in sdt.changepoint) ConstPrior (class in sdt.changepoint) corr_img (sdt.flatfield.Corrector attribute) Corrector (class in sdt.flatfield) cost() (sdt.changepoint.CostL1 method) (sdt.changepoint.CostL2 method) CostL1 (class in sdt.changepoint) CostL2 (class in sdt.changepoint) cp_detector (sdt.fret.SmFRETAnalyzer attribute) cur_dir (sdt.nbui.FileDialog attribute) D dataframe_mask() (sdt.roi.MaskROI method) (sdt.roi.PathROI method) (sdt.roi.ROI method) density_scatter() (in module sdt.plot) detection_eff (sdt.fret.SmFRETAnalyzer attribute) determine_parameters() (sdt.multicolor.Registrator method) DiamondMask (class in sdt.image) direct_excitation (sdt.fret.SmFRETAnalyzer attribute) Distribution (class in sdt.brightness) draw_track() (in module sdt.fret) dump() (in module sdt.io.yaml) dump_all() (in module sdt.io.yaml) Dumper (class in sdt.io.yaml) E ECDF (class in sdt.funcs) EllipseROI (class in sdt.roi) eval() (sdt.optimize.AffineModel static method) (sdt.optimize.AffineModelResult method) (sdt.optimize.ExpSumModel static method) (sdt.optimize.ExpSumModelResult method) eval_seq() (sdt.multicolor.FrameSelector method) excitation_eff (sdt.fret.SmFRETAnalyzer attribute) excitation_seq (sdt.fret.SmFRETTracker property) (sdt.multicolor.FrameSelector attribute) exp (sdt.optimize.ExpSumModelResult attribute) exp_factor_der() (sdt.loc.z_fit.Parameters method) exp_factor_from_z() (sdt.loc.z_fit.Parameters method) exp_sum() (in module sdt.funcs) exp_sum_lmfit() (in module sdt.funcs) exposure_time_corr() (sdt.motion.AnomalousDiffusion static method) ExpSumModel (class in sdt.optimize) ExpSumModelResult (class in sdt.optimize) F feat1 (sdt.multicolor.Registrator attribute) feat2 (sdt.multicolor.Registrator attribute) FileDialog (class in sdt.nbui) fill_gamut() (in module sdt.image) find_changepoints() (sdt.changepoint.BayesOffline method) (sdt.changepoint.BayesOnline method) (sdt.changepoint.Pelt method) find_closest_pairs() (in module sdt.multicolor) find_codiffusion() (in module sdt.multicolor) find_colocalizations() (in module sdt.multicolor) find_immobilizations() (in module sdt.motion) find_immobilizations_int() (in module sdt.motion) find_other_frames() (sdt.multicolor.FrameSelector method) find_pairs() (sdt.multicolor.Registrator method) fit (sdt.motion.AnomalousDiffusion.Result attribute) fit() (sdt.loc.z_fit.Fitter method) (sdt.motion.Msd method) (sdt.motion.MsdDist method) (sdt.optimize.AffineModel method) (sdt.optimize.ExpSumModel method) (sdt.optimize.ProbExpSumModel method) (sdt.optimize.RANSAC method) fit_amplitude (sdt.flatfield.Corrector attribute) fit_err (sdt.motion.AnomalousDiffusion.Result attribute) fit_parameters() (sdt.multicolor.Registrator method) fit_result (sdt.flatfield.Corrector attribute) Fitter (class in sdt.loc.z_fit) flag_excitation_type() (sdt.fret.SmFRETTracker method) flatfield_correction() (sdt.fret.SmFRETAnalyzer method) flatten_multiindex() (in module sdt.helper) frame_selector (sdt.fret.SmFRETTracker attribute) FrameSelector (class in sdt.multicolor) fret_correction() (sdt.fret.SmFRETAnalyzer method) from_class() (sdt.helper.Slicerator class method) from_func() (sdt.helper.Slicerator class method) from_raw_image() (in module sdt.brightness) from_yaml() (sdt.fret.SmFRETTracker class method) (sdt.multicolor.Registrator class method) (sdt.roi.MaskROI class method) (sdt.roi.PathROI class method) (sdt.roi.ROI class method) FullCovObsLikelihood (class in sdt.changepoint) func (sdt.nbui.Thresholder property) G gauss_psf() (in module sdt.sim) gauss_psf_full() (in module sdt.sim) gauss_psf_numba() (in module sdt.sim) Gaussian1DModel (class in sdt.optimize) Gaussian2DModel (class in sdt.optimize) gaussian_1d() (in module sdt.funcs) gaussian_2d() (in module sdt.funcs) gaussian_filter() (in module sdt.image) gaussian_mixture_split() (in module sdt.fret) GaussianObsLikelihood (class in sdt.changepoint) GeometricPrior (class in sdt.changepoint) get_data() (sdt.io.ImageSequence method) get_factors() (sdt.flatfield.Corrector method) get_files() (in module sdt.io) get_meta_data() (sdt.io.ImageSequence method) get_metadata() (sdt.io.ImageSequence method) get_msd() (sdt.motion.Msd method) (sdt.motion.MsdDist method) get_probabilities() (sdt.changepoint.BayesOnline method) get_raw_features() (in module sdt.loc) get_results() (sdt.motion.AnomalousDiffusion method) get_settings() (sdt.nbui.Locator method) graph (sdt.brightness.Distribution attribute) guess_gaussian_parameters() (in module sdt.optimize) H has_near_neighbor() (in module sdt.spatial) hazard() (sdt.changepoint.ConstHazard method) I IfmObsLikelihood (class in sdt.changepoint) image_display (sdt.nbui.Locator attribute) image_mask (sdt.roi.PathROI attribute) image_mask() (sdt.fret.SmFRETAnalyzer method) ImageDisplay (class in sdt.nbui) images (sdt.nbui.ImageSelector attribute) (sdt.nbui.Locator attribute) (sdt.nbui.ROISelector attribute) ImageSelector (class in sdt.nbui) ImageSequence (class in sdt.io) independent_vars (sdt.optimize.RANSAC attribute) index (sdt.nbui.ImageSelector attribute) initial_guess (sdt.optimize.RANSAC attribute) initialize() (sdt.helper.Singleton method) (sdt.helper.ThreadSafeSingleton method) input (sdt.nbui.ChannelSplitter attribute) (sdt.nbui.ImageDisplay attribute) (sdt.nbui.Locator attribute) instance (sdt.helper.Singleton property) (sdt.helper.ThreadSafeSingleton property) interpolate (sdt.fret.SmFRETTracker attribute) interpolate_coords() (in module sdt.spatial) is_initialized (sdt.helper.Singleton property) (sdt.helper.ThreadSafeSingleton property) is_slice (sdt.io.ImageSequence property) L label_mobile() (in module sdt.motion) leakage (sdt.fret.SmFRETAnalyzer attribute) likelihood() (sdt.changepoint.FullCovObsLikelihood method) (sdt.changepoint.GaussianObsLikelihood method) (sdt.changepoint.IfmObsLikelihood method) link_options (sdt.fret.SmFRETTracker attribute) load() (in module sdt.io) (in module sdt.io.yaml) (sdt.flatfield.Corrector class method) (sdt.loc.z_fit.Parameters class method) (sdt.multicolor.Registrator class method) load_all() (in module sdt.io.yaml) load_csv() (in module sdt.io) load_imagej() (in module sdt.roi) load_imagej_zip() (in module sdt.roi) load_msdplot() (in module sdt.io) load_pkmatrix() (in module sdt.io) load_pks() (in module sdt.io) load_pt2d() (in module sdt.io) load_trc() (in module sdt.io) Loader (class in sdt.io.yaml) locate() (in module sdt.loc.cg) (in module sdt.loc.daostorm_3d) locate_func (sdt.nbui.Locator property) locate_roi() (in module sdt.loc.cg) (in module sdt.loc.daostorm_3d) locate_roi_func (sdt.nbui.Locator property) Locator (class in sdt.nbui) M mant (sdt.optimize.ExpSumModelResult attribute) mask (sdt.roi.MaskROI attribute) mask_origin (sdt.roi.MaskROI attribute) MaskROI (class in sdt.roi) mass_changepoints() (sdt.fret.SmFRETAnalyzer method) max_error (sdt.optimize.RANSAC attribute) max_outliers (sdt.optimize.RANSAC attribute) mean() (sdt.brightness.Distribution method) merge_channels() (in module sdt.multicolor) min_length (sdt.fret.SmFRETTracker attribute) min_size (sdt.changepoint.CostL1 attribute) (sdt.changepoint.CostL2 attribute) mode() (sdt.brightness.Distribution method) model (sdt.optimize.AffineModelResult attribute) (sdt.optimize.ExpSumModelResult attribute) (sdt.optimize.RANSAC attribute) module sdt sdt.brightness sdt.changepoint sdt.config sdt.flatfield sdt.fret sdt.funcs sdt.helper sdt.image sdt.io sdt.loc, [1] sdt.loc.cg sdt.loc.daostorm_3d sdt.loc.z_fit sdt.motion sdt.multicolor sdt.nbui sdt.optimize sdt.plot sdt.roi sdt.sim sdt.spatial most_probable() (sdt.brightness.Distribution method) Msd (class in sdt.motion) msd (sdt.motion.Msd.Result attribute) (sdt.motion.MsdDist.Result attribute) Msd.Result (class in sdt.motion) msd_err (sdt.motion.Msd.Result attribute) (sdt.motion.MsdDist.Result attribute) MsdDist (class in sdt.motion) MsdDist.Result (class in sdt.motion) multi (sdt.nbui.ROISelector attribute) N n_exp (sdt.optimize.ExpSumModel attribute) n_fit (sdt.optimize.RANSAC attribute) n_iter (sdt.optimize.RANSAC attribute) NegBinomialPrior (class in sdt.changepoint) neighbor_radius (sdt.fret.SmFRETTracker attribute) norm (sdt.optimize.RANSAC attribute) num_data (sdt.brightness.Distribution attribute) numeric_exc_type() (in module sdt.fret) O observations (sdt.funcs.ECDF property) ode_coeff (sdt.optimize.ExpSumModelResult attribute) offset (sdt.optimize.ExpSumModelResult attribute) open() (sdt.io.ImageSequence method) options (sdt.nbui.Locator attribute) (sdt.nbui.Thresholder attribute) otsu_thresh() (in module sdt.image) output (sdt.nbui.ImageSelector attribute) P pairs (sdt.multicolor.Registrator attribute) PanelLabel (class in sdt.plot) Parameters (class in sdt.loc.z_fit) Parameters.Tuple (class in sdt.loc.z_fit) parameters1 (sdt.multicolor.Registrator attribute) parameters2 (sdt.multicolor.Registrator attribute) path (sdt.roi.PathROI attribute) PathROI (class in sdt.roi) pdf() (sdt.changepoint.StudentT method) Pelt (class in sdt.changepoint) percentile_thresh() (in module sdt.image) Pipeline (class in sdt.helper) pipeline() (in module sdt.helper) pixel_size (sdt.roi.MaskROI attribute) plot() (sdt.brightness.Distribution method) (sdt.motion.AnomalousDiffusion method) plot_changepoints() (in module sdt.changepoint) plot_codiffusion() (in module sdt.multicolor) poly_order (sdt.optimize.ExpSumModel attribute) polygon_area() (in module sdt.spatial) polygon_center() (in module sdt.spatial) prior() (sdt.changepoint.ConstPrior method) (sdt.changepoint.GeometricPrior method) ProbExpSumModel (class in sdt.optimize) Q query() (sdt.fret.SmFRETAnalyzer method) query_particles() (sdt.fret.SmFRETAnalyzer method) R raise_in_thread() (in module sdt.helper) random_state (sdt.optimize.RANSAC attribute) RANSAC (class in sdt.optimize) rc (in module sdt.config) reader_args (sdt.io.ImageSequence attribute) RectangleROI (class in sdt.roi) RectMask (class in sdt.image) register_yaml_class() (in module sdt.io.yaml) Registrator (class in sdt.multicolor) registrator (sdt.fret.SmFRETTracker attribute) renumber_frames() (sdt.multicolor.FrameSelector method) reset() (sdt.changepoint.BayesOnline method) (sdt.changepoint.StudentT method) reset_filters() (sdt.fret.SmFRETAnalyzer method) reset_origin() (sdt.roi.MaskROI method) (sdt.roi.PathROI method) (sdt.roi.ROI method) restore_frame_numbers() (sdt.multicolor.FrameSelector method) ROI (class in sdt.roi) rois (sdt.nbui.ChannelSplitter attribute) (sdt.nbui.ROISelector attribute) ROISelector (class in sdt.nbui) S safe_dump() (in module sdt.io.yaml) safe_dump_all() (in module sdt.io.yaml) safe_load() (in module sdt.io.yaml) safe_load_all() (in module sdt.io.yaml) SafeDumper (class in sdt.io.yaml) SafeLoader (class in sdt.io.yaml) same_size (sdt.nbui.ChannelSplitter attribute) save() (in module sdt.io) (sdt.flatfield.Corrector method) (sdt.loc.z_fit.Parameters method) (sdt.multicolor.Registrator method) save_as_tiff() (in module sdt.io) save_pt2d() (in module sdt.io) save_trc() (in module sdt.io) sdt module sdt.brightness module sdt.changepoint module sdt.config module sdt.flatfield module sdt.fret module sdt.funcs module sdt.helper module sdt.image module sdt.io module sdt.loc module, [1] sdt.loc.cg module sdt.loc.daostorm_3d module sdt.loc.z_fit module sdt.motion module sdt.multicolor module sdt.nbui module sdt.optimize module sdt.plot module sdt.roi module sdt.sim module sdt.spatial module segment_stats() (in module sdt.changepoint) select() (sdt.multicolor.FrameSelector method) selected (sdt.nbui.FileDialog attribute) set_columns() (in module sdt.config) set_data() (sdt.changepoint.ConstPrior method) (sdt.changepoint.CostL1 method) (sdt.changepoint.CostL2 method) (sdt.changepoint.FullCovObsLikelihood method) (sdt.changepoint.GaussianObsLikelihood method) (sdt.changepoint.GeometricPrior method) (sdt.changepoint.IfmObsLikelihood method) set_rois() (sdt.nbui.ROISelector method) set_settings() (sdt.nbui.Locator method) show_file_buttons (sdt.nbui.ImageSelector property) sigma_from_z() (sdt.loc.z_fit.Parameters method) simulate_brownian() (in module sdt.sim) simulate_gauss() (in module sdt.sim) Singleton (class in sdt.helper) Slicerator (class in sdt.helper) smallest_enclosing_circle() (in module sdt.spatial) smfret_hist() (in module sdt.fret) smfret_scatter() (in module sdt.fret) SmFRETAnalyzer (class in sdt.fret) SmFRETTracker (class in sdt.fret) split_dataframe() (in module sdt.helper) std() (sdt.brightness.Distribution method) StepFunction (class in sdt.funcs) StudentT (class in sdt.changepoint) T test() (sdt.multicolor.Registrator method) theoretical() (sdt.motion.AnomalousDiffusion static method) (sdt.motion.BrownianMotion static method) ThreadSafeSingleton (class in sdt.helper) Thresholder (class in sdt.nbui) to_yaml() (sdt.fret.SmFRETTracker class method) (sdt.multicolor.Registrator class method) (sdt.roi.MaskROI class method) (sdt.roi.PathROI class method) (sdt.roi.ROI class method) top_left (sdt.roi.ROI attribute) track() (sdt.fret.SmFRETTracker method) tracks (sdt.fret.SmFRETAnalyzer attribute) transform (sdt.optimize.AffineModelResult attribute) transform() (sdt.roi.PathROI method) U update() (sdt.changepoint.BayesOnline method) update_theta() (sdt.changepoint.StudentT method) uri (sdt.io.ImageSequence attribute) use_defaults() (in module sdt.config) W wavelet() (in module sdt.image) wavelet_bg() (in module sdt.image) weight (sdt.motion.MsdDist.Result attribute) weight_err (sdt.motion.MsdDist.Result attribute) X x (sdt.funcs.StepFunction property) (sdt.loc.z_fit.Parameters property) Y y (sdt.funcs.StepFunction property) (sdt.loc.z_fit.Parameters property) Z z_range (sdt.loc.z_fit.Parameters attribute)