Index

_

__init__() (hitips.Analysis.ImageAnalyzer method) (hitips.AnalysisGUI.analyzer method) (hitips.BatchAnalyzer.BatchAnalysis method) (hitips.Display.imagedisplayer method) (hitips.GridLayout.gridgenerator method) (hitips.GUI_parameters.Gui_Params method) (hitips.InputOutput.inputoutput_control method) (hitips.IO_ResourceGUI.InOut_resource method) (hitips.MetaData_Reader.ImageReader method)

A

ADJUST_IMAGE_CONTRAST() (hitips.Display.imagedisplayer method) Anaconda Distribution

analyzer (class in hitips.AnalysisGUI) apply_lut_color() (hitips.Display.imagedisplayer method)

B

BATCH_ANALYZER() (hitips.BatchAnalyzer.BatchAnalysis method)

BatchAnalysis (class in hitips.BatchAnalyzer)

C

Calculate_Spot_Distances() (hitips.BatchAnalyzer.BatchAnalysis method) cell_level_file_name() (hitips.BatchAnalyzer.BatchAnalysis method) cellpose_segmenter() (hitips.Analysis.ImageAnalyzer method)

check_and_append_args() (hitips.BatchAnalyzer.BatchAnalysis method) ControlPanel (class in hitips.HiTIPS) controlUi() (hitips.HiTIPS.ControlPanel method) COORDINATES_TO_CIRCLE() (hitips.Analysis.ImageAnalyzer method)

D

deepcell_segmenter() (hitips.Analysis.ImageAnalyzer method) deepcell_tracking() (hitips.Cell_Spot_Tracker.Tracking method) disable_field_signals() (hitips.GridLayout.gridgenerator method) disable_time_signals() (hitips.GridLayout.gridgenerator method)

disable_well_signals() (hitips.GridLayout.gridgenerator method) disable_z_signals() (hitips.GridLayout.gridgenerator method) display_initializer() (hitips.Display.imagedisplayer method) DISTANCE_calculator() (hitips.BatchAnalyzer.BatchAnalysis method)

E

EXIT_CODE_REBOOT (hitips.HiTIPS.ControlPanel attribute)

F

file_save() (hitips.GUI_parameters.Gui_Params method)

FIRST_THRESH_LABEL_UPDATE() (hitips.AnalysisGUI.analyzer method) first_time (hitips.GridLayout.gridgenerator attribute)

G

gather_analysis_params() (hitips.GUI_parameters.Gui_Params method) gather_spot_df_list() (hitips.BatchAnalyzer.BatchAnalysis method) GET_IMAGE_NAME() (hitips.Display.imagedisplayer method) get_package_versions() (hitips.BatchAnalyzer.BatchAnalysis method) get_spot_patch() (hitips.Cell_Spot_Tracker.Tracking method)

gmask_fit() (hitips.Analysis.ImageAnalyzer method) grid_data (hitips.Display.imagedisplayer attribute) GRID_INITIALIZER() (hitips.GridLayout.gridgenerator method) gridgenerator (class in hitips.GridLayout) Gui_Params (class in hitips.GUI_parameters) gui_params (hitips.Analysis.ImageAnalyzer attribute)

H

hitips.Analysis module hitips.AnalysisGUI module hitips.BatchAnalyzer module hitips.Cell_Spot_Tracker module hitips.Display module hitips.GridLayout module

hitips.GUI_parameters module hitips.HiTIPS module hitips.InputOutput module hitips.IO_ResourceGUI module hitips.logging_decorator module hitips.MetaData_Reader module

I

IMAGE_FOR_SPOT_DETECTION() (hitips.BatchAnalyzer.BatchAnalysis method) (hitips.Display.imagedisplayer method) IMAGE_TO_BE_MASKED() (hitips.Display.imagedisplayer method) ImageAnalyzer (class in hitips.Analysis) imagedisplayer (class in hitips.Display) ImageReader (class in hitips.MetaData_Reader)

IMG_FOR_NUC_MASK() (hitips.BatchAnalyzer.BatchAnalysis method) imgchannels (hitips.Display.imagedisplayer attribute) INITIALIZE_SEGMENTATION_PARAMETERS() (hitips.AnalysisGUI.analyzer method) INITIALIZE_SPOT_ANALYSIS_PARAMS() (hitips.GUI_parameters.Gui_Params method) InOut_resource (class in hitips.IO_ResourceGUI) inputoutput_control (class in hitips.InputOutput) itemActivated_event() (hitips.GridLayout.gridgenerator method)

L

LOAD_BIOFORMAT_DATA() (hitips.MetaData_Reader.ImageReader method) LOAD_CONFIGURATION() (hitips.GUI_parameters.Gui_Params method)

local_background() (hitips.Analysis.ImageAnalyzer method) log_errors() (in module hitips.logging_decorator)

M

main() (in module hitips.HiTIPS) MAX_HIST_SLIDER_UPDATE() (hitips.Display.imagedisplayer method) max_z_project() (hitips.Analysis.ImageAnalyzer method) merge_small_clusters() (hitips.Cell_Spot_Tracker.Tracking method) MERGEIAMGES() (hitips.Display.imagedisplayer method) Meta_Data_df (hitips.HiTIPS.ControlPanel attribute) METADATA_DATAFRAME (hitips.Display.imagedisplayer attribute) MICROMANAGER_READER() (hitips.MetaData_Reader.ImageReader method) MIN_HIST_SLIDER_UPDATE() (hitips.Display.imagedisplayer method) Miniconda Miniforge module hitips.Analysis hitips.AnalysisGUI hitips.BatchAnalyzer hitips.Cell_Spot_Tracker hitips.Display hitips.GridLayout hitips.GUI_parameters hitips.HiTIPS hitips.InputOutput hitips.IO_ResourceGUI hitips.logging_decorator hitips.MetaData_Reader

mutual_information() (hitips.Cell_Spot_Tracker.Tracking method)

N

neuceli_segmenter() (hitips.Analysis.ImageAnalyzer method) normalize_stack() (hitips.BatchAnalyzer.BatchAnalysis method)

NUCLEI_AREA_LABEL_UPDATE() (hitips.AnalysisGUI.analyzer method) Num_CPU_cores (hitips.IO_ResourceGUI.InOut_resource attribute) Num_GPU_inuse (hitips.IO_ResourceGUI.InOut_resource attribute)

O

ON_ADJUST_INTENSITY() (hitips.Display.imagedisplayer method) ON_APPLYBUTTON() (hitips.BatchAnalyzer.BatchAnalysis method) on_click_FOV_list() (hitips.GridLayout.gridgenerator method) on_click_list() (hitips.GridLayout.gridgenerator method) ON_CLICK_LOADBUTTON() (hitips.InputOutput.inputoutput_control method) (hitips.MetaData_Reader.ImageReader method) ON_CLICK_LOADIMGBUTTON() (hitips.MetaData_Reader.ImageReader method) on_click_table() (hitips.GridLayout.gridgenerator method)

on_click_table_save_wells() (hitips.GridLayout.gridgenerator method) on_click_Time_list() (hitips.GridLayout.gridgenerator method) on_click_Z_list() (hitips.GridLayout.gridgenerator method) ON_CPU_INQUIRY_BUTTON() (hitips.IO_ResourceGUI.InOut_resource method) ON_GPU_num_change() (hitips.IO_ResourceGUI.InOut_resource method) ON_RESET_BUTTON() (hitips.HiTIPS.ControlPanel method) on_run_analysis() (hitips.HiTIPS.ControlPanel method) OUTPUT_FOLDER_LOADBTN() (hitips.GUI_parameters.Gui_Params method) (hitips.IO_ResourceGUI.InOut_resource method)

P

phase_correlation() (hitips.Cell_Spot_Tracker.Tracking method)

PROCESS_ALL_SPOT_CHANNELS() (hitips.BatchAnalyzer.BatchAnalysis method) process_channel() (hitips.BatchAnalyzer.BatchAnalysis method)

R

RADIAL_DIST_CALC() (hitips.BatchAnalyzer.BatchAnalysis method) RAW_IMAGE_LOADER() (hitips.BatchAnalyzer.BatchAnalysis method) READ_FROM_METADATA() (hitips.InputOutput.inputoutput_control method) (hitips.MetaData_Reader.ImageReader method) READ_IMAGE() (hitips.Display.imagedisplayer method) registration_features() (hitips.Cell_Spot_Tracker.Tracking method)

remove_readonly() (hitips.BatchAnalyzer.BatchAnalysis method) retranslateUi() (hitips.HiTIPS.ControlPanel method) rotate_point() (hitips.Cell_Spot_Tracker.Tracking method) rotation_register_img_prep() (hitips.Cell_Spot_Tracker.Tracking method) RUN_BTRACK() (hitips.Cell_Spot_Tracker.Tracking method) run_clustering() (hitips.Cell_Spot_Tracker.Tracking method) run_registration_rotation() (hitips.Cell_Spot_Tracker.Tracking method)

S

SAVE_CONFIGURATION() (hitips.BatchAnalyzer.BatchAnalysis method) (hitips.GUI_parameters.Gui_Params method) SAVE_NUCLEI_INFORMATION() (hitips.BatchAnalyzer.BatchAnalysis method) SAVE_SPOT_INFO() (hitips.BatchAnalyzer.BatchAnalysis method) SECOND_THRESH_LABEL_UPDATE() (hitips.AnalysisGUI.analyzer method) segmenter_function() (hitips.Analysis.ImageAnalyzer method) select_data_subset() (hitips.HiTIPS.ControlPanel method) set_analysisgui() (hitips.IO_ResourceGUI.InOut_resource method) set_gui_params() (hitips.AnalysisGUI.analyzer method) set_image_analyzer() (hitips.AnalysisGUI.analyzer method)

set_imdisplay() (hitips.AnalysisGUI.analyzer method) set_ImDisplay() (hitips.GUI_parameters.Gui_Params method) set_MetaData_Reader() (hitips.IO_ResourceGUI.InOut_resource method) setup_connections() (hitips.GridLayout.gridgenerator method) SHOWIMAGE() (hitips.Display.imagedisplayer method) spot_level_file_name() (hitips.BatchAnalyzer.BatchAnalysis method) SPOT_THRESH_LABEL_UPDATE() (hitips.AnalysisGUI.analyzer method) SpotDetector() (hitips.Analysis.ImageAnalyzer method) spots_information() (hitips.Analysis.ImageAnalyzer method) SPOTS_TO_BOUNDARY() (hitips.Analysis.ImageAnalyzer method)

T

Tracking (class in hitips.Cell_Spot_Tracker)

U

update_cell_index_in_all_spot_channels() (hitips.BatchAnalyzer.BatchAnalysis method) update_cell_index_in_channel() (hitips.BatchAnalyzer.BatchAnalysis method) update_params_dict() (hitips.Analysis.ImageAnalyzer method) (hitips.BatchAnalyzer.BatchAnalysis method)

UPDATE_SPOT_ANALYSIS_GUI_PARAMS() (hitips.GUI_parameters.Gui_Params method) UPDATE_SPOT_ANALYSIS_PARAMS() (hitips.GUI_parameters.Gui_Params method) update_values() (hitips.GUI_parameters.Gui_Params method)

W

watershed_scikit() (hitips.Analysis.ImageAnalyzer method)

X

XYZ_SPOT_COORDINATES() (hitips.BatchAnalyzer.BatchAnalysis method)

Z

Z_STACK_NUC_LABLER() (hitips.BatchAnalyzer.BatchAnalysis method)

Z_STACK_NUC_SEGMENTER() (hitips.BatchAnalyzer.BatchAnalysis method) zero_pad_patch() (hitips.Cell_Spot_Tracker.Tracking method)