simple_colocalisation.py

# Pearson coefficient described at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074624/

# Start with
# $ omero shell --login

conn = omero.gateway.BlitzGateway(client_obj=client)
i = conn.getObject("Image", 62137)
p = i.getPrimaryPixels()

# get 2D planes and reshape to 1D array
r = p.getPlane(0,0,0)
red = r.reshape(r.size)
g = p.getPlane(0,1,0)
green = g.reshape(g.size)

# pearson colocalistion coefficient
from scipy.stats import pearsonr
pearsonr(red, green)
# (0.73771152645247484, 0.0)

# scatter plot
import matplotlib.pyplot as plt
plt.scatter(red, green)
# <matplotlib.collections.PathCollection at 0x117779d50>
plt.show()