Welcome to pyS3M’s documentation!
Contents:
- Introduction
- Installation
- Running the GUI
- Getting Started
- Contributing
- API Reference
- Core Analysis
SuperRes_FunctionsAnalysisPipelineAnalysisPipeline.calibrate()AnalysisPipeline.dcfAnalysisPipeline.filter_and_cluster()AnalysisPipeline.fit()AnalysisPipeline.load_calibration()AnalysisPipeline.load_localisations()AnalysisPipeline.load_localisations_per_fov()AnalysisPipeline.make_smoothing_function()AnalysisPipeline.nile_redAnalysisPipeline.smAnalysisPipeline.srAnalysisPipeline.undrift()
FittingConfigextract_SMsEllipticalFittingProcessorFittingConstantsFittingParametersFittingProcessorFittingResultProcessorFittingStrategyFittingValidationErrorImage_Analysis_FunctionsJustColourFittingProcessorNoColourFittingProcessorPosthenColourFittingProcessorRawColourFittingProcessorStandardDataFittingProcessorStandardFittingProcessorStandardIGFittingProcessorStandardIterFittingProcessor
- Drift Correction
AIMDriftCorrectorAutoDriftCorrectorDriftCorrectionErrorDriftCorrectionFactoryDriftCorrectorDriftMethodDriftParametersDriftParameters.auto_detect_fiducialsDriftParameters.displayDriftParameters.fiducial_box_size_nmDriftParameters.fiducial_histogram_binsDriftParameters.fiducial_min_frames_fractionDriftParameters.fiducial_threshold_percentileDriftParameters.intersect_dDriftParameters.pixel_size_nmDriftParameters.progress_callbackDriftParameters.roi_rDriftParameters.segmentationDriftParameters.validate()
DriftResultDrift_Correction_FunctionsDrift_Correction_Functions.apply_drift_correction()Drift_Correction_Functions.apply_validated_fiducial_drift_correction()Drift_Correction_Functions.available_methods()Drift_Correction_Functions.bin_localisations_spatially()Drift_Correction_Functions.convert_nm_to_pixels()Drift_Correction_Functions.convert_pixels_to_nm()Drift_Correction_Functions.create_spatial_grid()Drift_Correction_Functions.detect_fiducials()Drift_Correction_Functions.detect_high_density_regions_from_image()Drift_Correction_Functions.identify_real_fiducials_with_clustering()Drift_Correction_Functions.identify_real_fiducials_with_clustering_delegated()Drift_Correction_Functions.method_info()Drift_Correction_Functions.run_aim_2d()Drift_Correction_Functions.run_aim_3d()Drift_Correction_Functions.select_puncta_from_regions()Drift_Correction_Functions.undrift()Drift_Correction_Functions.undrift_with_fiducial_detection()
FiducialDetectionResultFiducialDriftCorrectorundrift_aim()undrift_auto()DriftPlotterDriftPlotter.create_separate_plots()DriftPlotter.plot_clustering_overlay()DriftPlotter.plot_clustering_results()DriftPlotter.plot_clustering_summary_only()DriftPlotter.plot_fiducial_detection_results()DriftPlotter.plot_fiducial_detection_steps()DriftPlotter.plot_individual_clustering_details()DriftPlotter.plot_puncta_selection_results()DriftPlotter.plot_region_data_with_datashader()
FiducialDetector
- Clustering & Coordinate Processing
BatchMixinClusteringBaseMixinClusteringConfigClusteringConfig.D_priorClusteringConfig.alphaClusteringConfig.clustering_methodClusteringConfig.dtClusteringConfig.epsilon_multiplierClusteringConfig.max_dark_timeClusteringConfig.max_distanceClusteringConfig.max_framesClusteringConfig.min_cluster_sizeClusteringConfig.min_framesClusteringConfig.remove_staticClusteringConfig.sigma_locClusteringConfig.spectral_columnsClusteringConfig.spectral_tolClusteringConfig.start_frameClusteringConfig.static_epsClusteringConfig.static_min_samplesClusteringConfig.verboseClusteringConfig.w_spatialClusteringConfig.w_spectral
DBSCANMixinHDBSCANMixinLinkedMixinCoordinateProcessorCoordinateProcessor.apply_drift_correction()CoordinateProcessor.bin_localisations_spatially()CoordinateProcessor.convert_nm_to_pixels()CoordinateProcessor.convert_pixels_to_nm()CoordinateProcessor.create_spatial_grid()CoordinateProcessor.extract_metadata()CoordinateProcessor.interpolate_coordinates()CoordinateProcessor.interpolate_missing_frames()CoordinateProcessor.validate_localisations()
SegmentationHandler- LinkingFunctions
joint_spectral_spatial_cluster()link_localisations()
- Spot Detection & PSF Fitting
KernelCacheSpotDetection_FunctionsSpotDetection_Functions.cacfar()SpotDetection_Functions.cacfar_background_mean_estimate()SpotDetection_Functions.cacfar_background_std_estimate()SpotDetection_Functions.cacfar_segmentation()SpotDetection_Functions.detect_puncta_in_image()SpotDetection_Functions.detect_puncta_in_images()SpotDetection_Functions.detect_puncta_in_stack_parallel()SpotDetection_Functions.filter_image()SpotDetection_Functions.gauss2d()SpotDetection_Functions.get_detection_points()SpotDetection_Functions.get_local_max_points()SpotDetection_Functions.get_mf()SpotDetection_Functions.get_single_spot()SpotDetection_Functions.get_square_annulus()SpotDetection_Functions.intensity_pixel_indices()SpotDetection_Functions.is_local_max()SpotDetection_Functions.isf_threshold()SpotDetection_Functions.mask2points()SpotDetection_Functions.neigborhood()SpotDetection_Functions.points2mask()SpotDetection_Functions.real_puncta_indices()SpotDetection_Functions.remove_nonlocal_maxima()SpotDetection_Functions.spots_and_quality_from_futures()SpotDetection_Functions.spots_from_futures()
PSF_FunctionsPSF_Functions.diffraction_limit()PSF_Functions.gen_photoelectrons()PSF_Functions.gen_photoelectrons_vectorized_frames()PSF_Functions.gen_photons_hitting_detector()PSF_Functions.gen_spatial_PSF()PSF_Functions.gen_spatial_PSF_fast()PSF_Functions.generate_noisy_image_matrix()PSF_Functions.photoelectrons_to_image()PSF_Functions.sigma_PSF()
WLS_chi_elliptical_nobounds()WLS_chi_justcolour_nobounds()WLS_chi_nobounds()WLS_chi_nocolour_nobounds()WLS_justcolour_model_nobounds()WLS_model_elliptical_nobounds()WLS_model_nobounds()WLS_nocolour_model_nobounds()WLS_rawcolour_chi_nobounds()WLS_rawcolour_model_nobounds()compute_A_median()gaussian_unscaled_model()gaussian_unscaled_model_elliptical()initial_guess()initial_guess_elliptical()- localise
gradient_at()identify_in_image()local_maxima()net_gradient()render()render_gaussian()render_gaussian_RGB()render_gaussian_colour()render_hist()render_smooth()- postprocess
get_block_locs_at()get_index_blocks()get_link_groups()index_blocks_shape()picked_locs()remove_fiducials()segment_locs_by_rendered_image()undrift_from_picked()- picasso/lib
append_to_rec()check_if_in_polygon()check_if_in_rectangle()get_pick_polygon_corners()get_pick_rectangle_corners()is_loc_at()locs_at()locs_in_polygon()locs_in_rectangle()remove_from_rec()Mask_Functions
- Calibration & Camera
Calibration_FunctionsDatabaseQueryHandlerDyeSpectrumProcessorFilterSpectrumProcessorSpectralConstantsSpectralDataTypeSpectral_FuncsSpectral_Funcs.calculate_colourratio_from_photon_wavelengths()Spectral_Funcs.chi2_spectrum()Spectral_Funcs.fwhm_sigma_conversion()Spectral_Funcs.gaussian_model()Spectral_Funcs.generate_bootstrap_colour_ratios()Spectral_Funcs.get_absolute_pixel_QYs()Spectral_Funcs.get_dye_or_filter_data()Spectral_Funcs.get_pixel_fractions_dye_and_filters()Spectral_Funcs.get_pixel_fractions_rawspectra()Spectral_Funcs.get_spectral_data()Spectral_Funcs.getobjectiveefficiency()Spectral_Funcs.getpixelefficiency()Spectral_Funcs.moment_calculations()Spectral_Funcs.sample_photons_from_spectrum()Spectral_Funcs.skew_gaussian_model()Spectral_Funcs.spectral_fit_dye()Spectral_Funcs.wavelength_to_energy()
SpectrumProcessorsCMOS_FunctionsCAMERASCameraConfigget_camera_config()- FRCFunctions
bin_localisations()fire()frc()frc_to_resolution()ChannelUnmixingMixinMixtureAnalysisMixinNileRed_FunctionsNileRed_Functions.apply_optical_filters()NileRed_Functions.calculate_psf_width_from_spectrum()NileRed_Functions.calculate_rgb_from_spectrum()NileRed_Functions.fit_nile_red_wavelength()NileRed_Functions.fit_wavelengths_from_h5()NileRed_Functions.fit_wavelengths_pixelated()NileRed_Functions.generate_nile_red_spectrum()NileRed_Functions.nile_red_forward_model()NileRed_Functions.residuals_nile_red()NileRed_Functions.setup_optical_system()NileRed_Functions.simulate_wavelength_precision()NileRed_Functions.spectral_centre_of_mass()NileRed_Functions.wavelength_center_for_centre_of_mass()NileRed_Functions.wavelength_center_for_peak()
- Simulation
BindingKineticsBindingKinetics.calculate_propensities()BindingKinetics.can_bind()BindingKinetics.choose_event()BindingKinetics.execute_binding()BindingKinetics.execute_unbinding()BindingKinetics.find_potential_binding_pairs()BindingKinetics.get_binding_rate()BindingKinetics.get_unbinding_rate()BindingKinetics.process_events()
CameraAdapterCameraParametersCameraParameters.gainCameraParameters.masksCameraParameters.mosaic_unitCameraParameters.offsetCameraParameters.pixel_QYsCameraParameters.pixel_orderCameraParameters.pixel_order_indicesCameraParameters.readnoiseCameraParameters.rqeCameraParameters.validate_and_create()CameraParameters.variance
DiffusionSimulator2DFittingResultProcessorFittingStrategyLangevinDiffusion2DMoleculeMultiC_Sim_FuncsMultiC_Sim_Funcs_CompatibilityMultiC_Sim_Funcs_RefactoredSimulationConfigSimulationConfig.NASimulationConfig.background_colourSimulationConfig.background_photonsSimulationConfig.cpu_fractionSimulationConfig.defocus_z_umSimulationConfig.demosaic_strategySimulationConfig.distance_from_coverslip_umSimulationConfig.frame_exposure_msSimulationConfig.motion_velocity_nm_per_sSimulationConfig.n_bootstrapSimulationConfig.n_unit_cellsSimulationConfig.pixel_sizeSimulationConfig.save_raw_resultsSimulationConfig.save_summary_csvsSimulationConfig.saverawimagesSimulationConfig.sbrSimulationConfig.subtractx0y0SimulationConfig.use_lutSimulationConfig.use_stochastic_photonsSimulationConfig.verbose
SimulationValidationErrorcompute_msd_from_trajectory()estimate_D_from_msd()
- Step Detection & FRET
- Plotting
AnalysisPlotterBasePlotterBasePlotter.add_colorbar()BasePlotter.add_scalebar()BasePlotter.colour_image_plot()BasePlotter.create_figure()BasePlotter.create_image_plot()BasePlotter.histogram_plot()BasePlotter.image_plot()BasePlotter.line_plot()BasePlotter.line_plot_with_error()BasePlotter.one_column_plot()BasePlotter.save_or_show()BasePlotter.scatter_plot()BasePlotter.setup_axis()BasePlotter.two_column_plot()
DatashaderMixinImagePlotMixinPlottingConfigPlottingConfig.DEFAULT_COLORBAR_PADPlottingConfig.DEFAULT_COLORBAR_WIDTHPlottingConfig.DEFAULT_COLORMAPPlottingConfig.DEFAULT_DPIPlottingConfig.DEFAULT_FIGSIZEPlottingConfig.DEFAULT_GRID_ALPHAPlottingConfig.DEFAULT_GRID_COLORPlottingConfig.DEFAULT_MARKER_SIZEPlottingConfig.DEFAULT_SAVE_DPIPlottingConfig.DEFAULT_SCALEBAR_COLORPlottingConfig.DEFAULT_SCALEBAR_FONTSIZEPlottingConfig.DEFAULT_SCATTER_COLORPlottingConfig.DEFAULT_VMAX_PERCENTILEPlottingConfig.DEFAULT_VMIN_PERCENTILEPlottingConfig.axis_labelsizePlottingConfig.dark_backgroundPlottingConfig.font_sizePlottingConfig.legend_fontsizePlottingConfig.line_widthPlottingConfig.poster_modePlottingConfig.tick_labelsizePlottingConfig.tick_length
PublicationConstantsPublicationConstants.DEFAULT_PANEL_HEIGHT_RATIOPublicationConstants.DEFAULT_TWO_COLUMN_ROW_HEIGHTPublicationConstants.MAX_HEIGHTPublicationConstants.ONE_COLUMN_WIDTHPublicationConstants.POSTER_AXIS_LABELSIZEPublicationConstants.POSTER_FONT_SIZEPublicationConstants.POSTER_LEGEND_FONTSIZEPublicationConstants.POSTER_LINE_WIDTHPublicationConstants.POSTER_TICK_LABELSIZEPublicationConstants.POSTER_TICK_LENGTHPublicationConstants.STANDARD_AXIS_LABELSIZEPublicationConstants.STANDARD_FONT_SIZEPublicationConstants.STANDARD_LEGEND_FONTSIZEPublicationConstants.STANDARD_LINE_WIDTHPublicationConstants.STANDARD_TICK_LABELSIZEPublicationConstants.STANDARD_TICK_LENGTHPublicationConstants.TWO_COLUMN_WIDTH
PublicationPlotterTernaryPlotMixinplot_bayer_pattern()
- Utilities
IO_FunctionsIO_Functions.apply_smoothing()IO_Functions.convert_to_photoelectrons()IO_Functions.generate_weights()IO_Functions.get_n_frames()IO_Functions.get_num_pages_in_TIF()IO_Functions.metadata_nframes_reader_imageJ()IO_Functions.metadata_reader_Thorlabs()IO_Functions.metadata_reader_imageJ()IO_Functions.read_h5_database()IO_Functions.read_hyperstack()IO_Functions.read_json()IO_Functions.read_json_streaming_first_framekey()IO_Functions.read_tiff()IO_Functions.read_tiff_tophotoelectrons()IO_Functions.save_simulation_results()IO_Functions.sort_h5_by_frame()IO_Functions.write_h5_database()IO_Functions.write_tiff()
Helper_FunctionsImportManagerImportStatusModuleInfoget_module()is_available()PyBayerSMLMFormatterconfigure_matplotlib_logging()setup_logger()ProgressBarConfigProgressBarManageranalysis_progress_bar()clean_progress_bar()fitting_progress_bar()set_progress_enabled()AnalysisConfigCalibrationConstantsDefaultParametersDriftConstantsFilteringConstantsFilteringCriteriaProcessingConstantsResultColumns
- GUI
- Core Analysis
- Licence