Isolate the root image from the background

I want to create a good binary image with root(white) and background(black) from this image. Problem is that in binary image of this picture, top part is all white(similar to root color) and lower part has more contrast between root and background. How should I edit this image with white root and dark background?

Answer 1

[Prabhan Purwar]

Hey,

Color Thresholder app can be used to segment out the roots and background as illustrated (using colorThresholder command) with spectrum settings as shown

• https://www.mathworks.com/help/images/ref/colorthresholder-app.html(Color Thresholder)

Further Median Filter along with imbinarize() can be used to remove noise and highlight roots.

% Ir is output from colorThresholder
im=medfilt3(Ir);
im=rgb2gray(im);
ib=imbinarize(im,0.001);
imshow(ib);

Output:

For further insights kindly refer to the following links:

• https://in.mathworks.com/help/images/noise-removal.html (Noise Removal)
• https://in.mathworks.com/help/images/ref/medfilt3.html (MedianFilter)