czi2ometiff

czi2ometiff is a Python tool for converting Zeiss CZI microscopy files into OME-TIFF, a widely used open standard for bioimaging data.
It provides a simple, reliable interface for extracting image data, channel names, and pixel sizes from CZI files and exporting them into high-quality OME-TIFF files.

Features

• Easy to use — convert a CZI file to OME-TIFF with a single function call.
• Automatic metadata extraction:
  • Channel names (from CZI metadata if available)
  • Pixel sizes in X, Y, and Z (converted to micrometers)
• Flexible output — works with multi-channel and multi-Z images.
• OME-TIFF pyramids — optional downsampled pyramid levels for fast viewing in tools like QuPath, OMERO, and napari.
• Built on numpy2ometiff — leverages robust OME-TIFF writing from the numpy2ometiff library.

Installation

Install directly via pip:

pip install czi2ometiff

Example Usage

from czi2ometiff import convert_czi_to_ometiff

# Input CZI file
input_file = "example_image.czi"

# Optional: specify output path
output_file = "example_image.ome.tiff"

# Convert to OME-TIFF
output_path = convert_czi_to_ometiff(
    input_path=input_file,
    output_path=output_file,   # Optional—defaults to input filename with .ome.tiff
    downsample_count=8          # Number of pyramid levels
)

print("Saved OME-TIFF:", output_path)

How It Works

czi2ometiff automatically:

1. Reads the CZI file using czifile
2. Extracts image data as a NumPy array
3. Detects channel names from CZI metadata
4. Extracts pixel sizes (stored in meters in CZI; converted to micrometers)
5. Reformats data into the (Z, C, Y, X) layout expected by OME-TIFF
6. Writes the final OME-TIFF using the numpy2ometiff.write_ome_tiff() function

All required metadata is set for compatibility with standard bioimaging software.

Contributing

Contributions are welcome!
If you'd like to add features, improve metadata parsing, or enhance compatibility with other CZI variants:

1. Fork the repository
2. Create a feature branch
3. Submit a pull request

For major changes, please open an issue first to discuss your ideas.

License

This project is licensed under the BSD 3-Clause License — see the LICENSE file for details.