Oldrich Svec - 5 months ago 57

C# Question

I am new to image analysis. Do you know how to binarize this image in such a way to get the fibers only?

I have tried different threshold techniques etc, but I was not successful. I do not mind what tool I should use but I prefer

`.NET`

`Matlab`

PS: I did not know where to put my answer, so I put it at StackOverflow.

Answer

Based on the comments, it seems you are having difficulty translating the proposed Mathematica solutions into MATLAB. Here is my attempt:

```
%# read image
I = im2double(imread('http://i.stack.imgur.com/6KCd1.jpg'));
%# ImageAdjust[]
II = I;
for k=1:size(II,3)
mn = min(min( II(:,:,k) )); mx = max(max( II(:,:,k) ));
II(:,:,k) = ( II(:,:,k) - mn ) ./ (mx-mn);
end
%# Sharpen[]
II = imfilter(II, fspecial('unsharp'));
%# MinDetect[], MaxDetect[]
II = rgb2gray(II);
mn = imextendedmin(II,0.3,8);
mx = imextendedmax(II,0.7,8);
%# pad image because Mathematica handles border cases differently than MATLAB
pad = 30;
q = padarray(mn, [pad pad], 'symmetric', 'both');
q = medfilt2(q, [5 5]*2+1, 'symmetric'); %# MedianFilter[]
q = ordfilt2(q, 1, ones(2*5+1), 'symmetric'); %# MinFilter[]
q = ordfilt2(q, (25*2+1)^2, ones(25*2+1), 'symmetric'); %# MaxFilter[]
q = ordfilt2(q, 1, ones(20*2+1), 'symmetric'); %# MinFilter[]
%# un-pad image
q = q(pad+1:end-pad, pad+1:end-pad, :);
%# ImageSubtract[], ImageMultiply[], ImageAdd[]
a = imsubtract(mn,q)==1; %# a = mn; a(q) = false;
b = immultiply(mx,q); %# b = mx & q;
c = imadd(a,b); %# c = a | b;
%# show images
figure(1)
subplot(121), imshow(mn)
subplot(122), imshow(mx)
figure(2), imshow(q)
figure(3)
subplot(121), imshow(a)
subplot(122), imshow(b)
figure(4), imshow(c)
```

Note that there are differences at the edges. In the Mathematica documentation, it vaguely says:

At the edges of an image, MedianFilter/MinFilter/MaxFilter uses smaller neighborhoods.

But there is no direct match for this behavior, instead MATLAB gives you the option to customize the padding at the boundaries of the images.

```
%# read image
I = im2double(imread('http://i.stack.imgur.com/6KCd1.jpg'));
%# LaplacianGaussianFilter[]
II = imfilter( I , fspecial('log', [2 2]*2+1, (2*2+1)/2) );
%# ImageAdjust[]
for k=1:size(II,3)
mn = min(min( II(:,:,k) )); mx = max(max( II(:,:,k) ));
II(:,:,k) = ( II(:,:,k) - mn ) ./ (mx-mn);
end
%# Binarize[]
BW = im2bw(II, 0.6);
%# DeleteSmallComponents[]
BW = bwareaopen(BW, 2, 8);
%# show images
figure
subplot(121), imshow(BW)
subplot(122), imshow( imoverlay(I,BW,[0 1 0]) )
```