Parsing ome.tiff for getting channels

ometiff_parser.py

import tifffile
file_name = 'laulab_tma1_file.ome.tiff'

with tifffile.TiffFile(file_name) as tif:
    img = tif.asarray()
    print(f"Image shape: {img.shape}")
    print(f"Image dtype: {img.dtype}")
    print(f"Number of pages: {len(tif.pages)}")
    
    # Check if OME metadata exists
    if tif.ome_metadata:
        print("\nOME metadata found")
        print(tif.ome_metadata[:500])

    # Parse OME metadata to get channel names
    if tif.ome_metadata:
        import xml.etree.ElementTree as ET
        try:
            root = ET.fromstring(tif.ome_metadata)
            ns = {'ome': 'http://www.openmicroscopy.org/Schemas/OME/2016-06'}
            
            # Find all channels
            channels = root.findall('.//ome:Channel', ns)
            print(f"\n=== FOUND {len(channels)} CHANNELS/PROTEINS ===")
            
            for i, ch in enumerate(channels):
                name = ch.get('Name', f'Channel_{i}')
                ch_id = ch.get('ID', 'N/A')
                print(f"  {i}: {name} (ID: {ch_id})")
            
            # Also check image dimensions
            pixels = root.find('.//ome:Pixels', ns)
            if pixels is not None:
                print(f"\nImage dimensions from OME:")
                print(f"  SizeC (channels): {pixels.get('SizeC')}")
                print(f"  SizeX: {pixels.get('SizeX')}")
                print(f"  SizeY: {pixels.get('SizeY')}")
                print(f"  SizeZ: {pixels.get('SizeZ', '1')}")
                
        except Exception as e:
            print(f"Could not parse OME XML: {e}")