Imager does it too. Use the same i1.png and i2.png files from my example above, and this script will give the same output as ImageMagick.

#!/usr/bin/perl
use warnings;
use strict;
use Imager;

my $img = Imager->new;
$img->read(file=>'i1.png', type=>'png')
           or die "Cannot read: ", $img->errstr;

my $img1 = Imager->new;
$img1->read(file=>'i2.png', type=>'png')
           or die "Cannot read: ", $img1->errstr;

my $out = $img->difference( other => $img1 );

$out->write(file=>"$0-diff.png", type=>'png')
           or die "Cannot write: ",$out->errstr;
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