MATLAB: How to centre points of interest in an image before it’s cropped and saved

digital image processingimage acquisitionimage analysisimage processingimage segmentationMATLAB

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

Best Answer

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])
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