Help or suggestions with Line detection in microscopy images

Question

I'm doing a personal project in which I want to select some very specific lines in a microscopy image. The first picture is the raw image, the second picture is the image for the lines (in yellow) I would like to detect. Not straight lines yes, but lines indeed.

Now, I made a very basic code for line detection that kind of "works" detecting lines, but it takes a lot of undesired detected lines in the process. See an example with another image (and the code below it, in Python, using OpenCV).

import cv2 as cv
import numpy as np

#Load and normalize .tif image:
img = 'imagenes.tif'
img = cv.imread(img, 0)
img_scaled = cv.normalize(img,  np.zeros((800, 800)), 0, 255, cv.NORM_MINMAX)

#Resizing images:
pct = 30
w = int(img.shape[1] * pct / 100)
h = int(img.shape[0] * pct / 100)
dim = (w, h)
resized = cv.resize(img_scaled, dim, interpolation = cv.INTER_AREA)

# First stage: Gaussian blur.
gaussian = cv.GaussianBlur(resized,(5, 5),0)
# Second Stage: edge detection with Canny.
low_threshold = 90
high_threshold = 150
edges = cv.Canny(gaussian, low_threshold, high_threshold)
# Third stage: Hough Line transform.
rho = 1
theta = np.pi / 180
threshold = 15
minLineLenght = 15
maxLineGap = 15
myBlankLines = resized.copy()
lines = cv.HoughLinesP(edges, rho, theta, threshold, np.array([]),
                    minLineLenght, maxLineGap)
for line in lines:
    for x1,y1,x2,y2 in line:
        cv.line(myBlankLines,(x1,y1),(x2,y2),(255,0,0),5)


cv.imshow('image_resized', resized)
cv.imshow('Stage 1: Gaussian', gaussian)
cv.imshow('Stage 2: Edges', edges)
cv.imshow('Stage 3: Lines', myBlankLines)
cv.waitKey(0)
cv.destroyAllWindows()

Now. I don't mind building a filter from zero and avoid using OpenCV or any other image processing/computer vision library. But I feel a bit lost on what direction I should go. I'm not sure if:

1. Doing more pre-filtering.
2. Adjust parameters for Hough Lines Transform.
3. Something else related with Machine Learning perhaps.

What would you suggest? Thanks for any heads up you might have on this interesting task.

Answer 1

Instead of using a homegrown amalgamation of algorithms, I suggest you look in the scientific literature for existing solutions. People have solved the same problem over and over again, there exist many algorithms to detect lines.

One very popular such method is Frangi's vesselness measure (A.F. Frangi et al, “Multiscale Vessel Enhancement Filtering”, MICCAI 1998). There is an implementation in DIPlib (disclaimer: I wrote this implementation).

You can install DIPlib with pip install diplib. This code shows how to use it, including a second step where the (gray-scale) vesselness measure is thresholded:

import diplib as dip

img = dip.ImageRead('cfqZG.png')(1)

vesselness = dip.FrangiVesselness(img, sigmas=2.0, polarity='black')
out = dip.HysteresisThreshold(vesselness, 0.01, 0.15)

dip.Overlay(img, out).Show()

Tweaking parameters in the code will give you more or fewer of the lines.

If you need thinner lines, simply add a thinning step (dip.ConditionalThinning2D).

Answer 2

• I used Median Blur instead of Gaussian Blur, and used Sobel Filter to detect the edges, the results are not perfect, but you can improve them if you tuned the parameters well(and they are many!)

#==================
# Import Libraries
#==================
import numpy as np
import cv2
import matplotlib.pyplot as plt

# Read Image
img = cv2.imread('1.png', 0)

# Median Blur
img = cv2.medianBlur(img, 3)

# Sobel filter for Edge detection
sobelx = cv2.Sobel(img,cv2.CV_64F,1,0,ksize=5)
sobely = cv2.Sobel(img,cv2.CV_64F,0,1,ksize=5)
sobel = np.sqrt(sobelx**2+sobely**2)

# Threshold Sobel to locate the lines
maxi = 0.30*sobel.max()
sobel[sobel<maxi] = 0

# Normalize
sobel = (255*sobel) / (sobel.max()-sobel.min())
sobel = sobel.astype('uint8')

# Hough Line transform.
rho = 1
theta = np.pi / 180
threshold = 15
minLineLenght = 18
maxLineGap = 13
myBlankLines = img.copy()
lines = cv2.HoughLinesP(sobel, rho, theta, threshold, np.array([]),
                    minLineLenght, maxLineGap)
for line in lines:
    for x1,y1,x2,y2 in line:
        cv2.line(myBlankLines,(x1,y1),(x2,y2),(255,0,0),1)

# Visualize Results
plt.imshow(myBlankLines, cmap='gray')
plt.axis('off')
plt.show()