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Color-Based Segmentation Using K-Means Clustering

This example shows how to segment colors in an automated fashion using the L*a*b* color space and K-means clustering.

This example requires Statistics and Machine Learning Toolbox™.

Step 1: Read Image

Read in hestain.png, which is an image of tissue stained with hemotoxylin and eosin (H&E). This staining method helps pathologists distinguish different tissue types.

he = imread('hestain.png');
imshow(he), title('H&E image');
text(size(he,2),size(he,1)+15,...
     'Image courtesy of Alan Partin, Johns Hopkins University', ...
     'FontSize',7,'HorizontalAlignment','right');

Step 2: Convert Image from RGB Color Space to L*a*b* Color Space

How many colors do you see in the image if you ignore variations in brightness? There are three colors: white, blue, and pink. Notice how easily you can visually distinguish these colors from one another. The L*a*b* color space (also known as CIELAB or CIE L*a*b*) enables you to quantify these visual differences.

The L*a*b* color space is derived from the CIE XYZ tristimulus values. The L*a*b* space consists of a luminosity layer 'L*', chromaticity-layer 'a*' indicating where color falls along the red-green axis, and chromaticity-layer 'b*' indicating where the color falls along the blue-yellow axis. All of the color information is in the 'a*' and 'b*' layers. You can measure the difference between two colors using the Euclidean distance metric.

Convert the image to L*a*b* color space using makecform and applycform.

cform = makecform('srgb2lab');
lab_he = applycform(he,cform);

Step 3: Classify the Colors in 'a*b*' Space Using K-Means Clustering

Clustering is a way to separate groups of objects. K-means clustering treats each object as having a location in space. It finds partitions such that objects within each cluster are as close to each other as possible, and as far from objects in other clusters as possible. K-means clustering requires that you specify the number of clusters to be partitioned and a distance metric to quantify how close two objects are to each other.

Since the color information exists in the 'a*b*' space, your objects are pixels with 'a*' and 'b*' values. Use kmeans to cluster the objects into three clusters using the Euclidean distance metric.

ab = double(lab_he(:,:,2:3));
nrows = size(ab,1);
ncols = size(ab,2);
ab = reshape(ab,nrows*ncols,2);

nColors = 3;
% repeat the clustering 3 times to avoid local minima
[cluster_idx, cluster_center] = kmeans(ab,nColors,'distance','sqEuclidean', ...
                                      'Replicates',3);

Step 4: Label Every Pixel in the Image Using the Results from KMEANS

For every object in your input, kmeans returns an index corresponding to a cluster. The cluster_center output from kmeans will be used later in the example. Label every pixel in the image with its cluster_index.

pixel_labels = reshape(cluster_idx,nrows,ncols);
imshow(pixel_labels,[]), title('image labeled by cluster index');

Step 5: Create Images that Segment the H&E Image by Color.

Using pixel_labels, you can separate objects in hestain.png by color, which will result in three images.

segmented_images = cell(1,3);
rgb_label = repmat(pixel_labels,[1 1 3]);

for k = 1:nColors
    color = he;
    color(rgb_label ~= k) = 0;
    segmented_images{k} = color;
end

imshow(segmented_images{1}), title('objects in cluster 1');

imshow(segmented_images{2}), title('objects in cluster 2');

imshow(segmented_images{3}), title('objects in cluster 3');

Step 6: Segment the Nuclei into a Separate Image

Notice that there are dark and light blue objects in one of the clusters. You can separate dark blue from light blue using the 'L*' layer in the L*a*b* color space. The cell nuclei are dark blue.

Recall that the 'L*' layer contains the brightness values of each color. Find the cluster that contains the blue objects. Extract the brightness values of the pixels in this cluster and threshold them with a global threshold using imbinarize.

You must programmatically determine the index of the cluster containing the blue objects because kmeans will not return the same cluster_idx value every time. You can do this using the cluster_center value, which contains the mean 'a*' and 'b*' value for each cluster. The blue cluster has the smallest cluster_center value (determined experimentally).

mean_cluster_value = mean(cluster_center,2);
[tmp, idx] = sort(mean_cluster_value);
blue_cluster_num = idx(1);

L = lab_he(:,:,1);
blue_idx = find(pixel_labels == blue_cluster_num);
L_blue = L(blue_idx);
is_light_blue = imbinarize(L_blue);

Use the mask is_light_blue to label which pixels belong to the blue nuclei. Then display the blue nuclei in a separate image.

nuclei_labels = repmat(uint8(0),[nrows ncols]);
nuclei_labels(blue_idx(is_light_blue==false)) = 1;
nuclei_labels = repmat(nuclei_labels,[1 1 3]);
blue_nuclei = he;
blue_nuclei(nuclei_labels ~= 1) = 0;
imshow(blue_nuclei), title('blue nuclei');


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