aligning_code_3

import numpy as np
import tifffile as tiff
from skimage.registration import phase_cross_correlation

# Specify the path to your TIFF file
image_file = "C:/Users/XXXX/sequence.tif"

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

#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(len(img_pre)):  # Use len(img_pre) for actual number of slices
  # Extract the current slice
  imgtest = img_pre[i, :, :]

  # Calculate the shift needed to align the current slice with the reference image
  shift, _, _ = phase_cross_correlation(reference_image, imgtest)

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

# Specify the path to save the aligned TIFF file
save_path = "C:/Users/XXXX/sequence_aligned.tif"

# Save the aligned images
tiff.imsave(save_path, np.array(aligned_images, dtype='uint16'))
print(f"Aligned images saved to {save_path}")