pycziutils

Python utilities to read (tiled) CZI files and parse metadata through python-bioformats

• Free software: BSD license
• Documentation: https://pycziutils.readthedocs.io.

Important notice

This repository has been archived as aicsimageio https://github.com/AllenCellModeling/aicsimageio can now read tiled CZI images. No further update is expected.

Installation

$ pip install pycziutils

Features

A tiny utility module to parse Zeiss CZI files in Python through python-bioformats. Parse tiled images, organize planes into pandas.DataFrame, and parse some hard-to-get metadata.

Example

import pycziutils


@pycziutils.with_javabridge
def main():
    czi_file_path="path/to/czi/file.czi"
    tiled_czi_ome_xml=pycziutils.get_tiled_omexml_metadata(czi_file_path)
    tiled_properties_dataframe=pycziutils.parse_planes(tiled_czi_ome_xml)

    print(tiled_properties_dataframe.columns)
    #Index(['index', 'X', 'Y', 'Z', 'T', 'C', 'C_index', 'T_index', 'Z_index', 'image',
    #       'plane', 'image_acquisition_T', 'absolute_T'],
    #        dtype='object')

    print(tiled_properties_dataframe.iloc[0])
    #index                                                 0
    #X                                             -1165.624
    #Y                                               122.694
    #Z                                                 0.001
    #T                                                 1.027
    #C                                                 Phase
    #C_index                                               0
    #T_index                                               0
    #Z_index                                               0
    #image                                                 0
    #plane                                                 0
    #image_acquisition_T    2021-04-12 02:12:21.340000+00:00
    #absolute_T             2021-04-12 02:12:22.367000+00:00
    #Name: 0, dtype: object

    #returns bioformats reader for tiled images
    reader=pycziutils.get_tiled_reader(czi_file_path)
    for i, row in tiled_properties_dataframe.iterrows():
        image = reader.read(
            series=row["image"],
            t=row["T_index"],
            z=row["Z_index"],
            c=row["C_index"],
        )

if __name__=="__main__":
    main()

Credits

This package uses python-bioformats to connect CZI files to Python.

This package was created with Cookiecutter and the wboxx1/cookiecutter-pypackage-poetry project template.

This package uses pysen for linting and formatting.