data_processing.processor package

Submodules

data_processing.processor.zeiss_FCS_processor module

class data_processing.processor.zeiss_FCS_processor.ZeissFCSProcessor(folder_path)

Bases: object

Processes Zeiss ConfoCor3 .raw files and identifies the file with the highest mean photon intensity. At this moment requires ‘FCS_points.json’ in the result file for reading the corresponding stage positions.

mean_intensity_from_photon_data(photon_data)

Calculate mean photon intensity (photons per second) from photon arrival time data.

Parameters:

photon_data – Dictionary containing photon timing data

Returns:

Mean photon intensity [photons/s]

find_highest_intensity_file()

Process all .raw files, compute their mean intensity, and return the file with the highest intensity.

Returns:

(best_file_path, max_intensity)

get_measurement_points()

Connects chosen file with the position from FCS_points.json

save_measurement_points(saving_path)

Saves measurement_points dict to a JSON file.

data_processing.processor.zeiss_image_processor module

class data_processing.processor.zeiss_image_processor.ZeissImageProcessor(czi_file_path, analysis_channel=1, chosen_analysis='FluorescentGUV', **analysis_details)

Bases: object

Processes Zeiss .czi files, by reading them, calling for the segmentation algorithm from image_analysis and saving the results as JSON files.

get_analysis_type(chosen_analysis, **kwargs)

Method for initialization of the segmentation algorithm :param chosen_analysis: name of the class in image_analysis folder for segmentation :param kwargs: additional arguments for the analyzing script like: :return: initialized object of the segmentation class

get_measurement_points()

Initializes the image segmentation in the chosen algorhitm. :return: list of dictionaries with positions and properties of segmented objects

save_measurement_points(filename)

Function responsible for saving the positions and properties of the found objects in the stage coordinates in the JSON file. :param filename: saving path of the JSON file :return: None

Module contents