pythonimage-processingscikit-imagemedicalmedical-imaging

Select area (square) with specific measure from an image using skimage python


I'm trying to extract 3 areas from the image (lungs image) these areas are indicated in the soft tissues, each area will be a square of specific height and width e.g. 10mm for width and height, as shown in the image below,

Lungs image with extracted 3 areaes of 10mm

as seen in the image also the area is Homogeneous which mean it is only include the same color (soft tissues in the case)

How to do it using python lib like skimage or cv2?


Solution

  • The following code will extract the region of interest (ROI) within the red rectangular annotations. Adjust the color as needed.

    import requests
    from io import BytesIO
    
    import numpy as np
    import scipy.ndimage as ndimage
    from PIL import Image
    
    # replace with your image loading routines
    img = Image.open(BytesIO(requests.get('https://i.sstatic.net/7k5VO.png').content))
    np_img = np.asarray(img)
    
    red_parts = (np_img == (255, 0, 0, 255)).all(axis=-1)  # find red parts of RGBA image
    filled_rects = ndimage.binary_fill_holes(red_parts)  # fill the rects to get a binary mask of ROI
    rects_inner = filled_rects ^ red_parts  # remove the red border
    labelled_rects, num_rects = ndimage.label(rects_inner)  # label/number each individual rect
    
    ROIs = []
    for i in range(1, num_rects + 1):  # 0 is background
        current_mask = labelled_rects == i
        x, y = np.where(current_mask)  # indices where current_mask is True (= area of interest)
        sub_image = np_img[x.min():x.max(), y.min():y.max()]  # extract image data inside rects
        sub_image = sub_image[1:-1, 1:-1]  # remove remaining red border (might be an image compression artefact, needs testing)
        ROIs.append(sub_image)
    pil_imgs = [Image.fromarray(roi) for roi in ROIs]
    

    Which gives you the following images of the marked subcutaneous fatty tissue:

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