I need to extract path/lines from 
import cv2
import matplotlib.pyplot as plt
import numpy as np
# Threshold
img = cv2.imread("subset_comp.tif")
img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
_, img_thr = cv2.threshold(img_gray, 150, 255, cv2.THRESH_BINARY)
fig, axs = plt.subplots(1, 2)
axs[0].set_title("Thresholded")
axs[0].imshow(img_thr, aspect="auto", cmap="gray")
# Find lines
lines = cv2.HoughLinesP(
img_thr, rho=1, theta=np.pi / 180, threshold=128, minLineLength=600, maxLineGap=30,
)
lines = lines.squeeze()
axs[1].set_title("Grayscale with Lines")
axs[1].imshow(img_gray, aspect="auto", cmap="gray")
for x1, y1, x2, y2 in lines:
axs[1].plot([x1, x2], [y1, y2], "r")
fig.show()
