Write pyramidal ome-tiff using tifffile with channel names and crop positions

tifffile_tiled_pyramid_ome_tif.py

import tifffile
import numpy as np

def per_channel_per_tile(img, tile=(1024, 1024)):
    num_channels, num_rows, num_columns = img.shape
    h, w = tile
    for c in range(num_channels):
        for y in range(0, num_rows, h):
            for x in range(0, num_columns, w):
                yield img[c, y:y+h, x:x+w]

img = (
    np
    .arange(1000*1000*10, dtype='uint8')
    .reshape((10, 1000, 1000))
)
num_channels, _, _ = img.shape
tile_shape = (256, 256)
options = dict(
    dtype=img.dtype,
    tile=tile_shape
)
metadata = {
    'Pixels': {'PhysicalSizeX': 0.65, 'PhysicalSizeXUnit': '\u00b5m', 'PhysicalSizeY': 0.65, 'PhysicalSizeYUnit': '\u00b5m'},
    'Channel': {'Name': [f'Channel {i+1}' for i in range(num_channels)]},
    'Plane': {'PositionX': [123]*num_channels, 'PositionY': [456]*num_channels}
}

with tifffile.TiffWriter('temp.ome.tif', bigtiff=True) as tif:
    tif.write(
        data=per_channel_per_tile(img, tile=tile_shape),
        metadata=metadata,
        software='Software name',
        shape=img.shape,
        subifds=2,
        **options
    )
    tif.write(
        data=per_channel_per_tile(img[:, ::2, ::2], tile=tile_shape),
        shape=img[:, ::2, ::2].shape,
        subfiletype=1,
        **options
    )
    tif.write(
        data=per_channel_per_tile(img[:, ::4, ::4], tile=tile_shape),
        shape=img[:, ::4, ::4].shape,
        subfiletype=1,
        **options
    )