What if they are not in a box? Images must be rectangular. If the x and y don't specify a rectangle, then you can use max(x), min(x), max(y), and min(y) to find the bounding box. Then use imcrop. If you want a polygon and not a rectangular crop, then you must mask instead of crop. You can use poly2mask() for that to get a binary image. Then multiply that by the image, or set the inverse of that in the image to zero (there's 2 ways).
out = in * uint8(binaryImage);
or
out = in;
out(binaryImage) = 0;
