This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. It is available as a Python Package on PyPi.
For full documentation see sebi06.github.io/czitools.
pip install czitoolsfrom czitools.metadata_tools.czi_metadata import CziMetadata
from czitools.read_tools import read_tools
# read all metadata
mdata = CziMetadata("path/to/file.czi")
# read pixel data as a labelled STCZYX(A) array
array6d, mdata = read_tools.read_6darray("path/to/file.czi", use_dask=True, use_xarray=True)For installation options (PyPI, editable, conda) see the Installation docs. For detailed usage examples see the Usage docs.
CZI inside NDV
CZI inside Napari
| Topic | Link |
|---|---|
| Read CZI metadata |  |
| Read CZI pixel data | |
| Write OME-ZARR from CZI | |
| Save with ZSTD compression | |
| Show planetable as surface | |
| Segment with Voronoi-Otsu | |