Filling one type of holes in a binary image

Hello, I am trying to obtain a mask from this image, such that the gray represents the walls and the nice plus-shaped channels should be the "holes" to be filled. There are other semi-rectangular holes that are basically grains that I do not want it filled. I tried imfill, imclose, bwareaopen, and combinations of these but still could not reach a satisfying solution. Can you please help me out?

Answer 1

[Steve Eddins]

Based on your description of what you're trying to do, I ask the question: how are the semi-rectangular grains, which you want to keep, different from the channels, which you want to fill? Well, the channels are relatively thin in one dimension, either horizontally or vertically. So, perhaps a morphological erosion can be constructed that will keep a portion of each grain, while completely eliminating the channels.

First, a bit of preprocessing.

rgb = imread("image.jpeg");
A = rgb2gray(rgb);
B = imcomplement(A);
imshow(B)

The channels seem to be approximately 10 pixels thick, while the grains around 50-by-50. Let's erode with a square structuring element with a size that's in between.

C = imerode(B,ones(25,25));
imshow(C)

Next, use morphological reconstruction to restore the original grain shapes.

D = imreconstruct(C,B);
imshow(D)

Finally, complement once more to make the grains dark again.

E = imcomplement(D);
imshow(E)

Is this what you are looking for? If you need to eliminate the partial grains along the image border, see imclearborder.

[Aktham Shoukry]

Steve,

Thank you for your great response. I think this concept will work. However, I want the final image to look something like either of these two images:

Only the channels part are my interest. The grey walls are just to dillineate the channels and the grains.

Thank you again.

[Steve Eddins]

Try subtracting A from E in my solution:

load extra_step A E
F = E - A;
imshow(F)

Follow that up with imbinarize and bwareaopen (or bwareafilt) to clean up the small spots between the channels.

[Aktham Shoukry]

Steve,

Thank you so much! This works really good.

[Steve Eddins]

If this answer works for you, please go ahead and mark it Accepted. Thanks!

[Aktham Shoukry]

Done. This is my first question post here so I am not familiar with this yet... Thank you again.

[Steve Eddins]

Also, would it be OK for me to use this image and example in a MATLAB Central blog post?

[Aktham Shoukry]

Of course! Please go ahead.

[Steve Eddins]

Thanks! And welcome to MATLAB Answers!

[Aktham Shoukry]

Thank you again!