Mark selected pixels in an image with circle

Question

I have an image, and I have to mark pixels whose intensity value is less than threshold value with a circle. How do you do this, Scatter plot wont work as we need two input. Help in this regard is appreciated.

matrix = np.matrix([row1,row2,row3,row4,row5,row6,row7,row8,row9,row10,row11,row12])
matrix_s = matrix<=1 # array containing pixels with value less than threshold
#plotting
plt.imshow(matrix)
plt.colorbar()
plt.plot(matrix_s, marker='o') # this won't work as it will join points with line and is not properly scaled with image 
plt.show()

Answer 1

You can use the Circle patch function from matplotlib (see doc here).

Here is an example inspired by the code you provided:

import numpy as np
import matplotlib.pyplot as plt

matrix = np.random.choice(80,size=(10,10))/20

fig,ax=plt.subplots()
im=ax.imshow(matrix,aspect='equal',interpolation=None,origin='lower')
for i in range(matrix.shape[0]):
  for j in range(matrix.shape[1]):
    if matrix[i,j]<=1:
      ax.add_patch(plt.Circle([j,i], radius=0.5, edgecolor='r',lw=3, fill=False))
cbar=plt.colorbar(im)

And the output gives: