SPlit all ome.tiff images to channels
This is code from chatGPT to split ome.tiff images to separate channels and call them image_c1, image_c2 ... and so on.
The downside of this script is that even if it does not do anything it still exits sucessfully
# run this in command line using python3
import os
import tifffile
# Input and output directories
input_folder = 'path_to_input_folder'
output_folder = 'path_to_output_folder'
# Get a list of all OME-TIFF files in the input folder
tif_files = [f for f in os.listdir(input_folder) if f.endswith('.ome.tif')]
# Loop through each OME-TIFF file
for tif_file in tif_files:
tif_path = os.path.join(input_folder, tif_file)
# Load the OME-TIFF image
image = tifffile.imread(tif_path)
# Split the channels
for channel_idx in range(image.shape[0]):
channel = image[channel_idx]
# Save each channel as a separate image
channel_name = f'{tif_file[:-8]}_c{channel_idx + 1}.tif'
channel_path = os.path.join(output_folder, channel_name)
tifffile.imwrite(channel_path, channel)
print(f'Saved {channel_name}')
print('All channels saved successfully.')
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