IO

Input output module for reading the .czi and .raw files.

Submodules

IO.read_czi_file module

class IO.read_czi_file.CziFileReader(path, analysis_channel)[source]

Bases: object

Class for reading a CZI file and extracting image data and metadata for analysis.

read_czi_file(path)[source]: Open CZI file, extract metadata and image data for the chosen channel. :return: tuple (image_data as ndarray, metadata as dict)

extract_metadata(metadata_str)[source]: Parse CZI metadata string into structured dictionary. :return: dict with scaling, channels, stage position, z_scan, and tiles info

get_image_to_analyze(czidoc, analysis_channel)[source]: Extract image data for the chosen channel as ndarray, handling Z-stack and scenes. :return: ndarray of image data (Z, H, W) or (H, W) depending on file

IO.read_raw_corr_file module

IO.read_raw_corr_file.read_confo_cor3(filepath)[source]: Reads Zeiss ConfoCor3 .raw photon arrival time files. Returns dict compatible with photonData struct.

IO.write_json_file module