Skip to main content

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

Project description

https://github.com/yfukai/pycziutils/actions/workflows/python-test.yml/badge.svg https://img.shields.io/pypi/v/pycziutils.svg Documentation Status

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

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pycziutils-0.3.2.tar.gz (8.8 kB view hashes)

Uploaded source

Built Distribution

pycziutils-0.3.2-py3-none-any.whl (8.6 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page