aligning_code_2

import numpy as np
import tifffile as tiff
from skimage.registration import phase_cross_correlation
#numpy for numerical operations
#tifffile for reading and writing tiff image files
#phase_cross_relation to align the images

#specify the path to tiff file
image_file = "C:/Users/XXXX/sequence.tif"

#read the tiff image
img_pre = tiff.imread(image_file)

#modify the size of the array to fit the size of your image
Dim_size1 = np.array((2000, 2000, 1683), dtype=int)

#empty list to store aligned images
aligned_images = []

#reference image for alignment
reference_image = img_pre[0, :, :]

#loop through each slice to align the images
for i in range(Dim_size1[0]):                                            #start from the first slice
    imgtest = img_pre[i, :, :]                                           #extract the current slice
   

    #calculate the shift needed to align the current slice with the reference image
    shift = phase_cross_correlation(reference_image, imgtest)[0]

    #apply the calculated shift to align the current slice
    aligned_image = np.roll(imgtest, shift.astype(int), axis=(0, 1))
    aligned_images.append(aligned_image)

#specify the path to save the aligned tiff file
save_path = "C:/Users/g202303490/Downloads/archive/72/origin/294/images/sequence_aligned.tif"

#save the aligned images
tiff.imsave(save_path, aligned_images)
print(f"Aligned images saved to {save_path}") #prints a message showing where the aligned images are saved.