How can I centre points of interest in an image before it's cropped and saved?

Hi folks,

I've successfully managed to crop segmented elements from an image into several images, but I'm now trying to reduce as much of the black background as possible. Below are my code, the base image with the segmented mesh and an example of a cropped section. Any help would be appreciated!

clc; close all;
img = imread('29_11_2019_164105.jpg');
pathName = "C:\Users\ezxtg4\Downloads\JPEG pics\crops\";

[counts, ~] = imhist(rgb2gray(img), 255);
T = otsuthresh(counts);
BW = imbinarize(rgb2gray(img), T);

BW2 = bwareaopen(BW, 3000);
BW2 = imfill(BW2, 'holes');
BW2 = bwperim(BW2);
BW2 = imdilate(BW2, ones(5));
BW2 = imerode(BW2, ones(3));

[L, n] = bwlabel(BW2);

for i = 1:n
    
    I4 = L==i;                      
    I5 = imfill(I4,'holes');    
    I6 = img.*repmat(uint8(I5),[1 1 3]);
    I6 = imclearborder(~I6);
    imwrite(I6, fullfile(pathName, sprintf('crop %d.jpeg', i)));
    
end

[darova]

Red and blues matrices (Red one is bigger?) have different size. Does it work?

[Teshan Rezel]

hiya, sorry about that. The code I pasted was an older experiment. I've copied across the correct code now

[darova]

You want to crop the image or to center?

[Teshan Rezel]

sorry I wasn't clear about that! I'd like to perform the former operation, so cropping please

Answer 1

[darova]

You previous code was ok i think. Just made some changes

[ii,jj] = find(I5);
    % calculate boundaries
i1 = min(ii);       % min row
i2 = max(ii);       % max row
j1 = min(jj);       % min column
j2 = max(jj);       % max column
% ...
I7 = imcrop(I6,[j1 i1 j2-j1 i2-i1]);      % cropped image

EDITED: made a mistake in imcrop(I,[xmin ymin width height])

[Teshan Rezel]

thank you!

[darova]

Made a mistake. Look at the script