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Is there a way to segment this image into 3 parts, even though the colours are so similar?

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Hi folks, I am trying to segment the following image of a seed. The points of interest look very similar in RGB, HSV, LAB and YCbCr colour spaces. Is there a way to segment out the 3 areas of interest? I am looking specifically to segment out the germ, endosperm (corneus + floury) and pericarp. I need to find an automated way to do this as there are hundreds of images to analyse!
Below is an example of my images, followed by a labelled diagram of the seed.
Thanks in advance!

Accepted Answer

yanqi liu
yanqi liu on 1 Dec 2021
yes,sir,may be use kmeans or watershed
clc;
clear all;
close all;
img = imread('https://www.mathworks.com/matlabcentral/answers/uploaded_files/818419/image.png');
img = imresize(img, 0.3, 'bilinear');
im = rgb2gray(img);
bw = ~imbinarize(im,'adaptive','ForegroundPolarity','dark','Sensitivity',0.6);
bw = imclose(imopen(bw, strel('disk', 2)), strel('disk', 5));
bw = bwareafilt(bw,1);
bw = imfill(bw, 'holes');
bw = imopen(bw, strel('disk', 13));
bw = bwareafilt(bw,1);
im = im .* uint8(bw);
% make segment
im = mat2gray(im);
bw1 = imbinarize(im,'adaptive','ForegroundPolarity','dark','Sensitivity',0.7);
bw1 = imclose(bw1, strel('disk', 5));
bw1 = imopen(bw1, strel('disk', 15));
bw1 = imdilate(bwareafilt(bw1,1), strel('disk', 5));
figure; imshow(img);
hold on;
h=imshow(label2rgb(bwlabel(bw1)),[]);
set(h,'AlphaData', 0.6)
  2 Comments
Teshan Rezel
Teshan Rezel on 10 Dec 2021
@yanqi liu thank you for responding, but I'm looking to segment the top image, not the bottom one! The technique you used doesn't appear to work for that one...
yanqi liu
yanqi liu on 11 Dec 2021
yes,sir,is it to segment 3 parts,may be by color or pixel,such as
clc;
clear all;
close all;
img = imread('https://www.mathworks.com/matlabcentral/answers/uploaded_files/818414/image.png');
J = rgb2lab(img);
im = mat2gray(J(:,:,1));
mk = im2bw(im,0.9);
mk = ~mk;
mk = imfill(mk, 'holes');
mk = bwareafilt(mk,1);
im(~mk) = 0;
thresh = multithresh(im,3);
seg_im = imquantize(im,thresh);
figure; imshow(img);
hold on;
h=imshow(label2rgb(seg_im),[]);
set(h,'AlphaData', 0.6)

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