It appears that there is no solution to do it in full JS in IE curently... A solution is available here, using a php query :
http://danielmclaren.com/node/90
<?php
/**
* an example URL for viewing a base64-encoded image:
* http://example.com/decode.php?image/png;base64,iVBORw0KGgoAAAANS...
*/
$data = split(";", $_SERVER["QUERY_STRING"]);
$type = $data[0];
$data = split(",", $data[1]);
header("Content-type: ".$type);
echo base64_decode($data[1]);
?>