Installation#
Work in Progress
This documentation is still incomplete and actively being updated. Some sections may be missing or subject to change.
Requirements#
| Requirement | Details |
|---|---|
| Python | 3.12, 3.13 |
| Operating System | Windows, Linux, macOS |
Install from PyPI#
Install the core package:
pip install czitools
Install with all optional dependencies (visualization, OME-ZARR, NDV, etc.):
pip install "czitools[all]"
Local / Editable Install#
Useful for development or when working directly from a cloned repository.
Core only:
pip install -e .
Full functionality:
pip install -e ".[all]"
Dependencies#
Core dependencies#
These are installed automatically with pip install czitools:
| Package | Purpose |
|---|---|
pylibCZIrw>=5 | Reading and writing CZI files |
czifile | Subblock-level CZI access |
numpy | Array operations |
xarray[complete] | Labelled multi-dimensional arrays |
pandas | Planetable data manipulation |
python-box[all] | Attribute-style metadata access |
pydantic | Data validation |
loguru / colorlog | Logging |
progressbar2 | Progress reporting |
python-dateutil | Date parsing |
Optional dependencies ([all])#
| Package | Purpose |
|---|---|
seaborn / plotly | Plotting and visualization |
qtpy / pyqtgraph | Qt-based visualization |
colormap | Colormap utilities |
ngff-zarr | OME-ZARR export support |
bioio / bioio-czi / bioio-ome-zarr | BioIO readers |
ndv[pyqt,vispy] | NDV viewer integration |
Conda / Pixi Environment#
A ready-to-use conda environment file is provided:
conda env create -f env_czitools.yml
conda activate czitools
Verify Installation#
import czitools
print(czitools.__version__)