create_masks.py 文件源码

def blob_labels(centers_of_mass, blob_image):
    """
    label nuclei with segmentation - so labels are in the same order as the outer layer

    :param list centers_of_mass: centers of target blobs/cells
    :param np.array blob_image: image of the target cells, or nuclei of cells
    :return segmented_blobs: a labelled image where each index is a different cell
    :return distance: image where each pixel's value is related to how far away from a blob center it is
    """

    image = np.abs(blob_image-1)
    distance = ndimage.distance_transform_edt(np.abs(image-1))
    local_maxi = np.zeros_like(image)
    for c in centers_of_mass:
        local_maxi[int(c[0]), int(c[1])] = 1
    markers = ndimage.label(local_maxi)[0]
    segmented_blobs = segmentation.random_walker(distance, markers, beta=20)

    return segmented_blobs, distance