hitips

• hitips package
  • Submodules
  • hitips.Analysis module
    • ImageAnalyzer
      • ImageAnalyzer.gui_params
      • ImageAnalyzer.__init__()
      • ImageAnalyzer.update_params_dict()
      • ImageAnalyzer.neuceli_segmenter()
      • ImageAnalyzer.deepcell_segmenter()
      • ImageAnalyzer.cellpose_segmenter()
      • ImageAnalyzer.segmenter_function()
      • ImageAnalyzer.watershed_scikit()
      • ImageAnalyzer.max_z_project()
      • ImageAnalyzer.SpotDetector()
      • ImageAnalyzer.spots_information()
      • ImageAnalyzer.gmask_fit()
      • ImageAnalyzer.local_background()
      • ImageAnalyzer.COORDINATES_TO_CIRCLE()
      • ImageAnalyzer.SPOTS_TO_BOUNDARY()
  • hitips.AnalysisGUI module
    • analyzer
      • analyzer.__init__()
      • analyzer.set_image_analyzer()
      • analyzer.set_imdisplay()
      • analyzer.FIRST_THRESH_LABEL_UPDATE()
      • analyzer.SECOND_THRESH_LABEL_UPDATE()
      • analyzer.NUCLEI_AREA_LABEL_UPDATE()
      • analyzer.SPOT_THRESH_LABEL_UPDATE()
      • analyzer.set_gui_params()
      • analyzer.INITIALIZE_SEGMENTATION_PARAMETERS()
  • hitips.BatchAnalyzer module
    • BatchAnalysis
      • BatchAnalysis.__init__()
      • BatchAnalysis.update_params_dict()
      • BatchAnalysis.check_and_append_args()
      • BatchAnalysis.ON_APPLYBUTTON()
      • BatchAnalysis.remove_readonly()
      • BatchAnalysis.get_package_versions()
      • BatchAnalysis.SAVE_NUCLEI_INFORMATION()
      • BatchAnalysis.SAVE_SPOT_INFO()
      • BatchAnalysis.process_channel()
      • BatchAnalysis.gather_spot_df_list()
      • BatchAnalysis.PROCESS_ALL_SPOT_CHANNELS()
      • BatchAnalysis.update_cell_index_in_channel()
      • BatchAnalysis.update_cell_index_in_all_spot_channels()
      • BatchAnalysis.normalize_stack()
      • BatchAnalysis.cell_level_file_name()
      • BatchAnalysis.spot_level_file_name()
      • BatchAnalysis.BATCH_ANALYZER()
      • BatchAnalysis.Calculate_Spot_Distances()
      • BatchAnalysis.DISTANCE_calculator()
      • BatchAnalysis.IMG_FOR_NUC_MASK()
      • BatchAnalysis.RAW_IMAGE_LOADER()
      • BatchAnalysis.Z_STACK_NUC_SEGMENTER()
      • BatchAnalysis.Z_STACK_NUC_LABLER()
      • BatchAnalysis.IMAGE_FOR_SPOT_DETECTION()
      • BatchAnalysis.XYZ_SPOT_COORDINATES()
      • BatchAnalysis.RADIAL_DIST_CALC()
      • BatchAnalysis.SAVE_CONFIGURATION()
  • hitips.Cell_Spot_Tracker module
    • Tracking
      • Tracking.RUN_BTRACK()
      • Tracking.deepcell_tracking()
      • Tracking.mutual_information()
      • Tracking.zero_pad_patch()
      • Tracking.registration_features()
      • Tracking.rotation_register_img_prep()
      • Tracking.run_registration_rotation()
      • Tracking.phase_correlation()
      • Tracking.rotate_point()
      • Tracking.get_spot_patch()
      • Tracking.merge_small_clusters()
      • Tracking.run_clustering()
  • hitips.Display module
    • imagedisplayer
      • imagedisplayer.METADATA_DATAFRAME
      • imagedisplayer.imgchannels
      • imagedisplayer.grid_data
      • imagedisplayer.__init__()
      • imagedisplayer.display_initializer()
      • imagedisplayer.MAX_HIST_SLIDER_UPDATE()
      • imagedisplayer.MIN_HIST_SLIDER_UPDATE()
      • imagedisplayer.GET_IMAGE_NAME()
      • imagedisplayer.READ_IMAGE()
      • imagedisplayer.ADJUST_IMAGE_CONTRAST()
      • imagedisplayer.MERGEIAMGES()
      • imagedisplayer.apply_lut_color()
      • imagedisplayer.SHOWIMAGE()
      • imagedisplayer.IMAGE_TO_BE_MASKED()
      • imagedisplayer.IMAGE_FOR_SPOT_DETECTION()
      • imagedisplayer.ON_ADJUST_INTENSITY()
  • hitips.GUI_parameters module
    • Gui_Params
      • Gui_Params.__init__()
      • Gui_Params.gather_analysis_params()
      • Gui_Params.update_values()
      • Gui_Params.set_ImDisplay()
      • Gui_Params.INITIALIZE_SPOT_ANALYSIS_PARAMS()
      • Gui_Params.UPDATE_SPOT_ANALYSIS_PARAMS()
      • Gui_Params.UPDATE_SPOT_ANALYSIS_GUI_PARAMS()
      • Gui_Params.SAVE_CONFIGURATION()
      • Gui_Params.file_save()
      • Gui_Params.LOAD_CONFIGURATION()
      • Gui_Params.OUTPUT_FOLDER_LOADBTN()
  • hitips.GridLayout module
    • gridgenerator
      • gridgenerator.first_time
      • gridgenerator.__init__()
      • gridgenerator.disable_well_signals()
      • gridgenerator.disable_field_signals()
      • gridgenerator.disable_z_signals()
      • gridgenerator.disable_time_signals()
      • gridgenerator.setup_connections()
      • gridgenerator.on_click_table_save_wells()
      • gridgenerator.on_click_FOV_list()
      • gridgenerator.on_click_Z_list()
      • gridgenerator.on_click_Time_list()
      • gridgenerator.GRID_INITIALIZER()
      • gridgenerator.on_click_table()
      • gridgenerator.on_click_list()
      • gridgenerator.itemActivated_event()
  • hitips.HiTIPS module
    • ControlPanel
      • ControlPanel.EXIT_CODE_REBOOT
      • ControlPanel.Meta_Data_df
      • ControlPanel.controlUi()
      • ControlPanel.on_run_analysis()
      • ControlPanel.select_data_subset()
      • ControlPanel.retranslateUi()
      • ControlPanel.ON_RESET_BUTTON()
    • main()
  • hitips.IO_ResourceGUI module
    • InOut_resource
      • InOut_resource.Num_CPU_cores
      • InOut_resource.Num_GPU_inuse
      • InOut_resource.__init__()
      • InOut_resource.OUTPUT_FOLDER_LOADBTN()
      • InOut_resource.ON_CPU_INQUIRY_BUTTON()
      • InOut_resource.ON_GPU_num_change()
      • InOut_resource.set_analysisgui()
      • InOut_resource.set_MetaData_Reader()
  • hitips.InputOutput module
    • inputoutput_control
      • inputoutput_control.__init__()
      • inputoutput_control.ON_CLICK_LOADBUTTON()
      • inputoutput_control.READ_FROM_METADATA()
  • hitips.MetaData_Reader module
    • ImageReader
      • ImageReader.__init__()
      • ImageReader.ON_CLICK_LOADBUTTON()
      • ImageReader.ON_CLICK_LOADIMGBUTTON()
      • ImageReader.READ_FROM_METADATA()
      • ImageReader.MICROMANAGER_READER()
      • ImageReader.LOAD_BIOFORMAT_DATA()
  • hitips.logging_decorator module
    • log_errors()