Extraction of Plankton using Segmentation with Matlab

Question

I am trying to extract plankton from a scanned image.

I segmented the plankton using the technique I found here, http://www.mathworks.com/help/images/examples/detecting-a-cell-using-image-segmentation.html

The outline is not bad, however, now I am not sure how to extract the images so each individual plankton can be saved individually. I tried to use labels but there is a lot of noise and it labels every single spec. I am wondering if there is a better way to do this.

Here is my code:

I = imread('plankton_2.jpg');
figure, imshow(I), title('original image');
[~, threshold] = edge(I, 'sobel');
fudgeFactor = .5;
BWs = edge(I,'sobel', threshold * fudgeFactor);
figure, imshow(BWs), title('binary gradient mask');
se90 = strel('line', 3, 90);
se0 = strel('line', 3, 0);
BWsdil = imdilate(BWs, [se90 se0]);
figure, imshow(BWsdil), title('dilated gradient mask');
BWdfill = imfill(BWsdil, 'holes');
figure, imshow(BWdfill);
title('binary image with filled holes');

BWnobord = imclearborder(BWdfill,1);
figure, imshow(BWnobord), title('cleared border image');
seD = strel('diamond',1);
BWfinal = imerode(BWnobord,seD);
BWfinal = imerode(BWfinal,seD);
figure, imshow(BWfinal), title('segmented image');
BWoutline = bwperim(BWfinal);
Segout = I;
Segout(BWoutline) = 0;
figure, imshow(Segout), title('outlined original image');

label = bwlabel(BWfinal);
max(max(label))


for j = 1:max(max(label))
    [row, col] = find(label == j);
    len = max(row) - min(row)+2;
    breadth = max(col)-min(col) +2;
    target = uint8(zeros([len breadth]));
    sy = min(col)-1;
    sx = min(row)-1;

    for i = 1:size(row,1)
        x = row(i,1)-sx;
        y = col(i,1) - sy;
        target(x,y)=I(row(i,1),col(i,1));
    end
    mytitle =strcat('Object Number:',num2str(j));
    figure, imshow(target);mytitle;
end



for j = 1:max(max(label))
    [row, col] = find(label == j);
    len = max(row) - min(row)+2;
    breadth = max(col)-min(col) +2;
    target = uint8(zeros([len breadth]));
    sy = min(col)-1;
    sx = min(row)-1;

    for i = 1:size(row,1)
        x = row(i,1)-sx;
        y = col(i,1) - sy;
        target(x,y)=I(row(i,1),col(i,1));
    end
    mytitle =strcat('Object Number:',num2str(j));
    figure, imshow(target);mytitle;
end

Answer 1

You should use the regionprops function to filter the detected objects by size and/or shape characteristics.