block_reduce от skimage_measure работал у меня. Вот фрагмент кода:
import numpy as np
from skimage.measure import block_reduce
import skimage.io as tiffio
#read original 2k x 2k image
original_image = tiffio.imread(read_path+"/RawImage_00000.tif", plugin = 'tifffile')
#bin image by factor of 2 along both axes, summing pixel values in 2x2 blocks
sum2bin_image = block_reduce(original_image, block_size=(2, 2), func=np.sum)
#Numpy arrays are 64-bit float variables, so the following step restores the original unsigned 16-bit format
sum2bin_image = np.round(sum2bin_image).astype(np.uint16)
#save generated image
tiffio.imsave(save_path+'/'+'sum2bin_00000.tif', sum2bin_image, plugin='tifffile')