Select largest object in an image

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Use bwconncomp instead since it returns the coordinate indexes for region in a separate cell, where the size of each is easily discerned:

>> BW = [1 0 0; 0 0 0; 0 1 1]; % two regions
>> CC = bwconncomp(BW)
CC = 
    Connectivity: 8
       ImageSize: [3 3]
      NumObjects: 2
    PixelIdxList: {[1]  [2x1 double]}

The PixelIdxList field is a cell array with the indexes of coordinates for each region. The length of each array is the size of each region:

>> numPixels = cellfun(@numel,CC.PixelIdxList)
numPixels =
     1     2
>> [biggestSize,idx] = max(numPixels)
biggestSize =
     2
idx =
     2

Then you can easily make a new image with just this component:

BW2 = false(size(BW));
BW2(CC.PixelIdxList{idx}) = true;

EDIT: From the comments, the need to crop the output image so that the region comes to the edges can be addressed with regionprops using the ‘BoundingBox’ option:

s  = regionprops(BW2, 'BoundingBox');

which gives you a rectangle s.BoundingBox which you can use to crop with BW3 = imcrop(BW2,s.BoundingBox);.

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