I use Epson scan. Works a treat. Not open source, but it does what it's supposed to do.
Epson scan allows batch-scanning as long as the negatives are together on the platen. However, I always simply select the entire image area and scan it in one go, then split it out in GIMP etc. Or rather, I even don't split it out and just save the whole thing and take from it what I need, when I need it.
On Linux you'd be looking at xsane, but that may/will not support all of your scanner's functionality. I doubt it even allows you to use the transparency adapter in the first place, making it useless for film scanning.