ZeissAutomation

Contents:

  • Overview
    • Key Features
    • Typical Workflow
    • Architecture
    • Adaptive Measurements
  • ZeissAPI
    • Overview
    • Main Macro: main_macro.czmac
      • ZeissApiProcessor
        • ZeissApiProcessor
      • AcquisitionPipeline
        • AcquisitionPipeline
    • Adaptive Experiments
    • Overview Grid Generation: find_overview_positions.czmac
      • AcquisitionGrid
        • AcquisitionGrid
    • Python Analysis Bridge
      • execute_python
        • log()
        • PythonAnalysisRunner
      • path_manager_main_macro
        • log()
        • PathManager
  • config
    • Files
      • path_config.json
      • preprocessing_config.json
  • utils
    • visualize_points()
    • parse_args_to_dict()
    • choose_the_closest_point()
  • IO
    • Submodules
    • IO.read_czi_file module
      • CziFileReader
        • CziFileReader.read_czi_file()
        • CziFileReader.extract_metadata()
        • CziFileReader.get_image_to_analyze()
    • IO.read_raw_corr_file module
      • read_confo_cor3()
    • IO.write_json_file module
  • data_processing
    • main_processor
      • Usage
      • Notes
    • processor
      • ZeissFCSProcessor
        • ZeissFCSProcessor.mean_intensity_from_photon_data()
        • ZeissFCSProcessor.find_highest_intensity_file()
        • ZeissFCSProcessor.get_measurement_points()
        • ZeissFCSProcessor.save_measurement_points()
      • ZeissImageProcessor
        • ZeissImageProcessor.get_analysis_type()
        • ZeissImageProcessor.get_measurement_points()
        • ZeissImageProcessor.save_measurement_points()
    • image_analysis
      • ImageAnalysisTemplate
        • ImageAnalysisTemplate.get_measurement_points()
      • Cellpose_algorithm
        • Cellpose_algorithm.filter_cellpose_masks()
        • Cellpose_algorithm.image_segmentation()
        • Cellpose_algorithm.get_measurement_points()
      • Circles
        • Circles.get_contour_centers_and_radii()
        • Circles.filter_by_size()
        • Circles.get_measurement_points()
      • HexagonalMesh
        • HexagonalMesh.get_mesh_nodes()
        • HexagonalMesh.get_delaunay_edges()
        • HexagonalMesh.filter_edges_by_distance()
        • HexagonalMesh.find_midpoints_and_centroids()
        • HexagonalMesh.get_measurement_points()
      • z_no_transform()
      • z_normal()
      • PixelStageConverter
        • PixelStageConverter.convert_xy()
        • PixelStageConverter.convert_z_auto()
        • PixelStageConverter.convert_z()
        • PixelStageConverter.convert_points()
      • Max_intensity_Z_Scan
        • Max_intensity_Z_Scan.get_max_intensity()
        • Max_intensity_Z_Scan.get_measurement_points()
ZeissAutomation
  • Overview: module code

All modules for which code is available

  • IO.read_czi_file
  • IO.read_raw_corr_file
  • data_processing.image_analysis.analysis_registry
  • data_processing.image_analysis.base_image_analyzer
  • data_processing.image_analysis.cellpose
  • data_processing.image_analysis.circles
  • data_processing.image_analysis.hexagonal_mesh
  • data_processing.image_analysis.pixel_stage_converter
  • data_processing.image_analysis.z_scan_max_intensity
  • data_processing.processor.zeiss_FCS_processor
  • data_processing.processor.zeiss_image_processor
  • execute_python
  • path_manager_main_macro
  • utils

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