czitools#

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.

Quick Start#

pip install czitools

from 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

Colab Notebooks#

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