czitools 0.17.0

Tools to simplify reading and CZI (Carl Zeiss Image) meta and pixel data

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