Metadata-Version: 2.1
Name: czitools
Version: 0.0.17
Summary: Tools to simplify reading CZI (Carl Zeiss Image) meta and pixel data in Python and other things
Home-page: https://github.com/sebi06/czitools
Author: Sebastian Rhode
Author-email: sebrhode@gmail.com
License: GNU General Public License v3 (GPLv3)
Project-URL: Bug Tracker, https://github.com/sebi06/czitools/issues
Project-URL: Documentation, https://github.com/sebi06/czitools/#README.md
Project-URL: Source Code, https://github.com/sebi06/czitools/
Project-URL: User Support, https://github.com/sebi06/czitools//issues
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: Unix
Classifier: Operating System :: Microsoft :: Windows
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE

# czitools

[![PyPI](https://img.shields.io/pypi/v/czitools.svg?color=green)](https://pypi.org/project/czitools)
[![PyPI - Downloads](https://img.shields.io/pypi/dm/czitools)](https://pypistats.org/packages/czitools)
[![License](https://img.shields.io/pypi/l/czitools.svg?color=green)](https://github.com/sebi06/czitools/raw/master/LICENSE)
[![Python Version](https://img.shields.io/pypi/pyversions/czitools.svg?color=green)](https://python.org)
[![Development Status](https://img.shields.io/pypi/status/czitools.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)

This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari (needs to be installed). It is also available as a [Python Package on PyPi](https://pypi.org/project/czitools/)

## Reading the metadata

Please check [use_pylibczirw_metadata_class.py](examples/scripts/use_pylibczirw_metadata_class.py) for some examples.

```python
# get the metadata at once as one big class
mdata_sel = czimd.CziMetadata(filepath)

# get only specific metadata
czi_dimensions = czimd.CziDimensions(filepath)
print("SizeS: ", czi_dimensions.SizeS)
print("SizeT: ", czi_dimensions.SizeT)
print("SizeZ: ", czi_dimensions.SizeZ)
print("SizeC: ", czi_dimensions.SizeC)
print("SizeY: ", czi_dimensions.SizeY)
print("SizeX: ", czi_dimensions.SizeX)

# and get more info about various aspects of the CZI
czi_scaling = czimd.CziScaling(filepath)
czi_channels = czimd.CziChannelInfo(filepath)
czi_bbox = czimd.CziBoundingBox(filepath)
czi_info = czimd.CziInfo(filepath)
czi_objectives = czimd.CziObjectives(filepath)
czi_detectors = czimd.CziDetector(filepath)
czi_microscope = czimd.CziMicroscope(filepath)
czi_sample = czimd.CziSampleInfo(filepath)
```

## Reading CZI pixeldata

While the [pylibCZIrw](https://pypi.org/project/pylibCZIrw/) is focussing on reading individual planes it is also helpful to read CZI pixel data as a STZCYX(A) stack. Please check [use_pylibczirw_md_read.py](https://github.com/sebi06/czitools/raw/main/demo/scripts/use_pylibczirw_md_read.py) for some examples.

```python
# return a array with dimension order STZCYX(A)
array6d, mdata, dim_string6d = pylibczirw_tools.read_6darray(filepath,
                                                             output_order="STZCYX",
                                                             output_dask=False,
                                                             remove_Adim=True
                                                             )

# show array inside napari viewer
viewer = napari.Viewer()
layers = napari_tools.show(viewer, array6d, mdata,
                           dim_string=dim_string6d,
                           blending="additive",
                           contrast='napari_auto',
                           gamma=0.85,
                           add_mdtable=True,
                           name_sliders=True)

napari.run()
```

![5D CZI inside Napari](https://github.com/sebi06/czitools/raw/main/images/czi_napari1.png)
