Counting the squama of lizards

Question

A biologist friend of mine asked me if I could help him make a program to count the squama (is this the right translation?) of lizards. He sent me some images and I tried some things on Matlab. For some images it's much harder than other, for example when there are darker(black) regions. At least with my method. I'm sure I can get some useful help here. How should I improve this? Have I taken the right approach? These are some of the images. I got the best results by following Image Processing and Counting using MATLAB. It's basically turning the image into Black and white and then threshold it. But I did add a bit of erosion. Here's the code: ``` img0=imread('C:...\pic.png'); img1=rgb2gray(img0); %The output image BW replaces all pixels in the input image with luminance greater than level with the value 1 (white) and replaces all other pixels with the value 0 (black). Specify level in the range [0,1]. img2=im2bw(img1,0.65);%(img1,graythresh(img1)); imshow(img2) figure; %erode se = st…

Accepted Answer

There is one route you should consider: watershed segmentation. Here is a quick and dirty example with your first image (it assumes you have the IP toolbox):

```
raw=rgb2gray(imread('lCeL8.jpg'));

Icomp = imcomplement(raw);
I3 = imhmin(Icomp,20);
L = watershed(I3);
%%
imagesc(L);
axis image
```

Result shown with a colormap:

You can then count the cells as follows:

```
count = numel(unique(L));
```

One of the advantages is that it can be directly fed to `regionprops` and give you all the nice details about the individual 'squama':

```
r=regionprops(L, 'All');
imshow(raw);

for k=2:numel(r)
    if r(k).Area>100 % I chose 100 to filter out the objects with a small are.
        rectangle('Position',r(k).BoundingBox, 'LineWidth',1, 'EdgeColor','b', 'Curvature', [1 1]); 
    end
end
```

Which you could use to monitor over/under segmentation:

Note: special thanks to @jucestain for helping with the proper access to the fields in the `r` structure here

Counting the squama of lizards

Solution

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