Processing czi files

[huangtinglin]

Hi Thanks for this great tool which helps me a lot.

I am working on the dataset Surgen (https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1285) and try to process the WSIs using this tool. However, it seems that the current library doesn't support CZI files, as OpenSlide is unable to open them.

Do you have any suggestions or workarounds for processing these files? Any guidance would be greatly appreciated.

[guillaumejaume]

Try using:

from pylibCZIrw import czi as pyczi
import numpy as np
from PIL import Image
import os

Image.MAX_IMAGE_PIXELS = None

def process_czi_file(czi_file: str, output_dir: str, pixel_size: float, bigtiff: bool = False) -> None:
    """Process a CZI file and save it as JPEG and pyramidal TIFF in the specified output directory.

    Args:
        czi_file (str): Path to the CZI file.
        output_dir (str): Directory where the output files will be saved.
        pixel_size (float): Pixel size (in um/px) that will be embedded in the TIFF.
        bigtiff (bool, optional): Save as BigTiff if the image exceeds 4.1 GB. Defaults to False.
    """
    print(f'Start reading CZI: {czi_file}')
    with pyczi.open_czi(czi_file) as czidoc:
        img = czidoc.read(zoom=0.25)
    print(f'Done reading CZI, image shape: {img.shape}')
    
    # Create output directories if they don't exist
    jpeg_dir = os.path.join(output_dir, 'jpeg')
    tiff_dir = os.path.join(output_dir, 'tiff')
    os.makedirs(jpeg_dir, exist_ok=True)
    os.makedirs(tiff_dir, exist_ok=True)
    
    # Extract filename without extension
    base_filename = os.path.splitext(os.path.basename(czi_file))[0]
    
    # Save as JPEG
    print(f'Start saving as JPEG')
    jpeg_path = os.path.join(jpeg_dir, f'{base_filename}.jpeg')
    pil_image = Image.fromarray(img)
    pil_image.save(jpeg_path, 'JPEG')
    print(f'Done saving as JPEG')

    # Re-open the JPEG and save as TIFF
    print(f'Start saving as TIFF')
    img = Image.open(jpeg_path)
    img = np.array(img)
    tiff_path = os.path.join(tiff_dir, f'{base_filename}.tiff')
    tiff_save(img, tiff_path, pixel_size, bigtiff)
    print(f'Done saving as TIFF')

def tiff_save(img: np.ndarray, save_path: str, pixel_size: float, bigtiff=False) -> None:
    """Save an image stored in a numpy array to the generic TIFF format.

    Args:
        img (np.ndarray): Image stored in a numpy array, shape must be H x W x C.
        save_path (str): Full path to TIFF (including filename).
        pixel_size (float): Pixel size (in um/px) that will be embedded in the TIFF.
        bigtiff (bool, optional): Save as BigTiff if the resulting image exceeds 4.1 GB. Defaults to False.
    """
    try:
        import pyvips
    except ImportError:
        print("Couldn't import pyvips, verify that libvips is installed on your system")
        return

    print(f'Saving to pyramidal TIFF: {save_path} (this may take some time)')
    pyvips_img = pyvips.Image.new_from_array(img)
    pyvips_img.tiffsave(
        save_path,
        bigtiff=bigtiff,
        pyramid=True,
        tile=True,
        tile_width=256,
        tile_height=256,
        compression='jpeg',
        resunit=pyvips.enums.ForeignTiffResunit.CM,
        xres=1. / (pixel_size * 1e-4),
        yres=1. / (pixel_size * 1e-4)
    )

def process_all_czi_files(input_dir: str, output_dir: str, pixel_size: float, bigtiff: bool = False) -> None:
    """Process all CZI files in the specified directory and save outputs.

    Args:
        input_dir (str): Directory containing CZI files.
        output_dir (str): Directory where the output files will be saved.
        pixel_size (float): Pixel size (in um/px) that will be embedded in the TIFF.
        bigtiff (bool, optional): Save as BigTiff if the image exceeds 4.1 GB. Defaults to False.
    """
    for filename in os.listdir(input_dir):
        if filename.endswith('.czi'):
            czi_file = os.path.join(input_dir, filename)
            process_czi_file(czi_file, output_dir, pixel_size, bigtiff)

# Example usage
input_dir = '/.surgen/'
output_dir = './processed'
pixel_size = 0.44
bigtiff = False

process_all_czi_files(input_dir, output_dir, pixel_size, bigtiff)

[huangtinglin]

Thanks Guillaume! It works. I think it can also be used to convert JPG to TIFF.