Your want to fix all your current images to the correct format (See @ Félix Gagnon-Grenier answer), then once you done that you can do something like the following:
//get array of current images
$imgs = glob(UPLOAD_DIR.'*.png');
//select last image in array, strip out all non-alpha's then pad it with 4 0's
$next = str_pad(preg_replace("/[^0-9]/","", end($imgs))+1, 4, "0", STR_PAD_LEFT);
$file = UPLOAD_DIR.'picture_'.$next.'.png';
Edit
See comments - file based counter
$count_file = UPLOAD_DIR.'count.txt'; //or put somewhere else
//make count file if not exists
if(!file_exists($count_file)){
file_put_contents($count_file,0);
}
//get last image count + 1
$next = file_get_contents($count_file)+1;
//set file var
$file = UPLOAD_DIR.'picture_'.sprintf("%04s",$next).'.png';
//update counter
file_put_contents($count_file, $next);
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