CODEWITHSUNDEEP
pythonimage-processing3dvoxelpython-napari
Paul_Dx
Paul_Dx

Reputation: 15

How to convert multiple single-channel 2d images to 3d volume and keep the Z-axis spacing?

I have multiple images taken from the microscope with different Z-axis planes and converted them into single-channel images, and now I want to convert these single-channel images into 3d volume, but directly stack them without Z-axis spacing.

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import tifffile as tiff

images = []
image_paths = ['1712071651.5126085_mask.jpg', '1712071668.4542189_mask.jpg', '1712071679.8891838_mask.jpg',"1712071690.5503793_mask.jpg","1712071701.1270576_mask.jpg",
               "1712071708.6956294_mask.jpg","1712071716.9926243_mask.jpg","1712071725.3603532_mask.jpg","1712071744.5940547_mask.jpg","1712071753.896742_mask.jpg",
               "1712071762.3356335_mask.jpg","1712071774.8131661_mask.jpg","1712071788.2660403_mask.jpg"]  # 替换为你的图像路径

for path in image_paths:
    image = plt.imread(path)
    if len(image.shape) == 3: 
        image = np.mean(image, axis=-1)
    images.append(image)

height, width = images[0].shape

stacked_image = np.zeros((len(images), height, width), dtype=np.uint8)

z_values = [50,50,50,50,50,50,50,50,50,50,50,50,50]

for i, (image, z) in enumerate(zip(images, z_values)):
    stacked_image[i] = image

tiff.imsave('stacked_image.tif', stacked_image)

The 3d volume is presented by napari, and the 3d volume displayed is very flat. enter image description here

Upvotes: 0

Views: 39

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