connected-components-3d

import cc3d import numpy as np # Create a sample 3D binary image labels_in = np.zeros((10, 10, 10), dtype=np.int32) labels_in[2:5, 2:5, 2:5] = 1 labels_in[6:8, 6:8, 6:8] = 1 labels_in[4,4,4] = 0 # Introduce a gap for demonstration print(f"Input shape: {labels_in.shape}, dtype: {labels_in.dtype}") # Perform connected component labeling with 26-connectivity (default) # Also return the number of connected components (N) labels_out, N = cc3d.connected_components(labels_in, return_N=True, connectivity=26) print(f"\nOutput labeled image (slice 5):\n{labels_out[:,:,5]}") print(f"Number of connected components found: {N}") # Example of extracting a single component # for segid in range(1, N + 1): # extracted_component = (labels_out == segid).astype(labels_in.dtype) # print(f"Component {segid} volume: {np.sum(extracted_component)}")