Welcome to pyRASP’s documentation!

Contents:

• Introduction
  • Limitations
  • Getting Started with pyRASP
• src
  • AnalysisFunctions module
    • Analysis_Functions
      • Analysis_Functions.Gauss2DFitting()
      • Analysis_Functions.calculate_rdf_with_thresholds()
      • Analysis_Functions.colocalise_spots_with_threshold()
      • Analysis_Functions.colocalise_with_threshold()
      • Analysis_Functions.count_spots()
      • Analysis_Functions.create_labelled_cellmasks()
      • Analysis_Functions.filter_cellmask_intensity()
      • Analysis_Functions.filter_lo_intensity()
      • Analysis_Functions.generate_indices()
      • Analysis_Functions.number_of_puncta_per_segmented_cell_with_threshold()
      • Analysis_Functions.reject_outliers()
      • Analysis_Functions.threshold_cell_areas_2d()
      • Analysis_Functions.threshold_cell_areas_3d()
  • HelperFunctions module
    • Helper_Functions
      • Helper_Functions.clean_database()
      • Helper_Functions.file_search()
      • Helper_Functions.gen_CSRmats()
      • Helper_Functions.make_datarray_cell()
      • Helper_Functions.make_datarray_largeobjects()
      • Helper_Functions.make_datarray_spot()
  • IOFunctions module
    • IO_Functions
      • IO_Functions.load_json()
      • IO_Functions.make_directory()
      • IO_Functions.read_tiff()
      • IO_Functions.read_tiff_tophotons()
      • IO_Functions.save_SMD_analysis()
      • IO_Functions.save_abovebelowthresholdcoloc()
      • IO_Functions.save_analysis()
      • IO_Functions.save_analysis_params()
      • IO_Functions.save_as_json()
      • IO_Functions.write_tiff()
  • Image_Analysis_Functions module
    • ImageAnalysis_Functions
      • ImageAnalysis_Functions.calculate_gradient_field()
      • ImageAnalysis_Functions.calculate_radiality()
      • ImageAnalysis_Functions.calculate_region_properties()
      • ImageAnalysis_Functions.compute_image_props()
      • ImageAnalysis_Functions.compute_spot_and_cell_props()
      • ImageAnalysis_Functions.create_filled_region()
      • ImageAnalysis_Functions.create_gaussian_kernel()
      • ImageAnalysis_Functions.create_kernel()
      • ImageAnalysis_Functions.default_SMD_routine()
      • ImageAnalysis_Functions.default_spotanalysis_routine()
      • ImageAnalysis_Functions.detect_large_features()
      • ImageAnalysis_Functions.detect_large_features_3D()
      • ImageAnalysis_Functions.estimate_intensity()
      • ImageAnalysis_Functions.infocus_indices()
      • ImageAnalysis_Functions.infocus_indices_old()
      • ImageAnalysis_Functions.intensity_pixel_indices()
      • ImageAnalysis_Functions.ricker_wavelet()
      • ImageAnalysis_Functions.small_feature_kernel()
  • MultiD_RD_functions module
    • multid_rdf()
    • paralell_hist_loop()
  • PlottingFunctions module
    • Plotter
      • Plotter.cell_punctum_analysis_plot()
      • Plotter.histogram_plot()
      • Plotter.image_plot()
      • Plotter.image_scatter_plot()
      • Plotter.line_plot()
      • Plotter.one_column_plot()
      • Plotter.scatter_plot()
      • Plotter.two_column_plot()
  • RASPRoutines module
    • RASP_Routines
      • RASP_Routines.SMD_analysis()
      • RASP_Routines.analyse_images()
      • RASP_Routines.calculate_spot_mask_rdf_with_threshold()
      • RASP_Routines.calculate_spot_rdf_with_threshold()
      • RASP_Routines.calculate_two_puncta_channels_rdf_with_thresholds()
      • RASP_Routines.calibrate_area()
      • RASP_Routines.calibrate_radiality()
      • RASP_Routines.count_puncta_in_individual_cells_threshold()
      • RASP_Routines.count_puncta_in_individual_cells_threshold_3D()
      • RASP_Routines.get_infocus_planes()
      • RASP_Routines.lo_colocalise_wrapper()
      • RASP_Routines.single_image_analysis()
      • RASP_Routines.spot_colocalisation_wrapper()

Indices and tables

• Index

• Module Index

• Search Page