ometiff-channel-names.py

ometiff-channel-names.py

import sys
import io
import warnings
import xml.etree.ElementTree
import tifffile

if len(sys.argv) != 2:
    print(f"Usage: ometiff-channel-names.py input.ome.tif")
    print("Print the channel names for the first image in an OME-TIFF file.")
    sys.exit(1)
ometiff_path = sys.argv[1]

tiff = tifffile.TiffFile(ometiff_path)
omexml_string = tiff.pages[0].description

root = xml.etree.ElementTree.parse(io.StringIO(omexml_string))
namespaces = {'ome': 'http://www.openmicroscopy.org/Schemas/OME/2016-06'}
channels = root.findall('ome:Image[1]/ome:Pixels/ome:Channel', namespaces)
channel_names = [c.attrib['Name'] for c in channels]

for n in channel_names:
    print(n)