Index

_

_perform_reanalysis_xy() (AcquisitionPipeline method)

_perform_reanalysis_z() (AcquisitionPipeline method)

A

acquire_overview() (AcquisitionPipeline method)

AcquisitionGrid (built-in class) AcquisitionPipeline (built-in class)

C

calculate_points_for_overview() (AcquisitionGrid method) capture_objects() (AcquisitionPipeline method) Cellpose_algorithm (class in data_processing.image_analysis.cellpose), [1] choose_the_closest_point() (in module utils) Circles (class in data_processing.image_analysis.circles), [1]

convert_points() (data_processing.image_analysis.pixel_stage_converter.PixelStageConverter method), [1] convert_xy() (data_processing.image_analysis.pixel_stage_converter.PixelStageConverter method), [1] convert_z() (data_processing.image_analysis.pixel_stage_converter.PixelStageConverter method), [1] convert_z_auto() (data_processing.image_analysis.pixel_stage_converter.PixelStageConverter method), [1] CziFileReader (class in IO.read_czi_file)

D

data_processing module data_processing.image_analysis module data_processing.image_analysis.analysis_registry module data_processing.image_analysis.base_image_analyzer module, [1] data_processing.image_analysis.cellpose module, [1] data_processing.image_analysis.circles module, [1]

data_processing.image_analysis.hexagonal_mesh module, [1] data_processing.image_analysis.pixel_stage_converter module, [1] data_processing.image_analysis.z_scan_max_intensity module, [1] data_processing.processor module data_processing.processor.zeiss_FCS_processor module, [1] data_processing.processor.zeiss_image_processor module, [1]

E

execute_current_experiment() (ZeissApiProcessor method) execute_python module

extract_metadata() (IO.read_czi_file.CziFileReader method)

F

filter_by_size() (data_processing.image_analysis.circles.Circles method), [1] filter_cellpose_masks() (data_processing.image_analysis.cellpose.Cellpose_algorithm static method), [1]

filter_edges_by_distance() (data_processing.image_analysis.hexagonal_mesh.HexagonalMesh method), [1] find_highest_intensity_file() (data_processing.processor.zeiss_FCS_processor.ZeissFCSProcessor method), [1] find_midpoints_and_centroids() (data_processing.image_analysis.hexagonal_mesh.HexagonalMesh method), [1]

G

generate_grid_from_args() (AcquisitionGrid method) get_analysis_type() (data_processing.processor.zeiss_image_processor.ZeissImageProcessor method), [1] get_available_analysis() (in module data_processing.image_analysis.analysis_registry) get_contour_centers_and_radii() (data_processing.image_analysis.circles.Circles static method), [1] get_delaunay_edges() (data_processing.image_analysis.hexagonal_mesh.HexagonalMesh method), [1] get_image_analysis_type() (in module data_processing.image_analysis.analysis_registry) get_image_to_analyze() (IO.read_czi_file.CziFileReader method) get_latest_fcs_and_raws() (path_manager_main_macro.PathManager method) get_max_intensity() (data_processing.image_analysis.z_scan_max_intensity.Max_intensity_Z_Scan method), [1]

get_measurement_points() (data_processing.image_analysis.base_image_analyzer.ImageAnalysisTemplate method), [1] (data_processing.image_analysis.cellpose.Cellpose_algorithm method), [1] (data_processing.image_analysis.circles.Circles method), [1] (data_processing.image_analysis.hexagonal_mesh.HexagonalMesh method), [1] (data_processing.image_analysis.z_scan_max_intensity.Max_intensity_Z_Scan method), [1] (data_processing.processor.zeiss_FCS_processor.ZeissFCSProcessor method), [1] (data_processing.processor.zeiss_image_processor.ZeissImageProcessor method), [1] get_mesh_nodes() (data_processing.image_analysis.hexagonal_mesh.HexagonalMesh method), [1] get_stage_focus_position() (ZeissApiProcessor method)

H

HexagonalMesh (class in data_processing.image_analysis.hexagonal_mesh), [1]

I

image_segmentation() (data_processing.image_analysis.cellpose.Cellpose_algorithm method), [1] ImageAnalysisTemplate (class in data_processing.image_analysis.base_image_analyzer), [1] IO.read_czi_file module

IO.read_raw_corr_file module IO.write_json_file module

L

load_experiment() (ZeissApiProcessor method)

log() (in module execute_python) (in module path_manager_main_macro)

M

Max_intensity_Z_Scan (class in data_processing.image_analysis.z_scan_max_intensity), [1] mean_intensity_from_photon_data() (data_processing.processor.zeiss_FCS_processor.ZeissFCSProcessor method), [1] module data_processing data_processing.image_analysis data_processing.image_analysis.analysis_registry data_processing.image_analysis.base_image_analyzer, [1] data_processing.image_analysis.cellpose, [1] data_processing.image_analysis.circles, [1] data_processing.image_analysis.hexagonal_mesh, [1] data_processing.image_analysis.pixel_stage_converter, [1] data_processing.image_analysis.z_scan_max_intensity, [1] data_processing.processor data_processing.processor.zeiss_FCS_processor, [1] data_processing.processor.zeiss_image_processor, [1] execute_python IO.read_czi_file IO.read_raw_corr_file IO.write_json_file path_manager_main_macro utils

move() (ZeissApiProcessor method)

O

overview_image_path() (path_manager_main_macro.PathManager method)

P

parse_args_to_dict() (in module utils) path_manager_main_macro module

PathManager (class in path_manager_main_macro) PixelStageConverter (class in data_processing.image_analysis.pixel_stage_converter), [1] PythonAnalysisRunner (class in execute_python)

R

read_confo_cor3() (in module IO.read_raw_corr_file) read_czi_file() (IO.read_czi_file.CziFileReader method) register_class() (in module data_processing.image_analysis.analysis_registry)

result_dir() (path_manager_main_macro.PathManager method) result_path() (path_manager_main_macro.PathManager method) run() (execute_python.PythonAnalysisRunner method)

S

save_experiment_result() (ZeissApiProcessor method) save_measurement_points() (data_processing.processor.zeiss_FCS_processor.ZeissFCSProcessor method), [1] (data_processing.processor.zeiss_image_processor.ZeissImageProcessor method), [1]

save_overview_points() (AcquisitionGrid method)

T

temp_file_path() (path_manager_main_macro.PathManager method)

U

utils module

V

visualize_points() (in module utils)

Z

z_no_transform() (in module data_processing.image_analysis.pixel_stage_converter), [1] z_normal() (in module data_processing.image_analysis.pixel_stage_converter), [1]

ZeissApiProcessor (built-in class) ZeissFCSProcessor (class in data_processing.processor.zeiss_FCS_processor), [1] ZeissImageProcessor (class in data_processing.processor.zeiss_image_processor), [1]