decode_ground_truth_bbbc039.py

# Example instructions to decode ground truth masks in BBBC039
# Masks available at: https://data.broadinstitute.org/bbbc/BBBC039/masks.zip

import skimage.io
import matplotlib.pyplot as plt
import skimage.morphology

# Load one image after uncompressing masks.zip
gt = skimage.io.imread("IXMtest_A02_s1_w1051DAA7C-7042-435F-99F0-1E847D9B42CB.png")

# Keep first channel only
gt = gt[:,:,0]

# Label independent connected components
gt = skimage.morphology.label(gt)

# Display image or use as needed
plt.imshow(gt)