Multi-graph matching is an important problem in computer vision. Our task comes from bioimaging, where a set of 29 3D-microscopic images of worms have to be brought into correspondence. Surprisingly, virtually all existing methods are not applicable to this large-scale, real-world problem since they either assume a complete or dense problem setting, and they have so far only been applied to small-scale, toy or synthetic problems. Despite claims in literature that methods addressing complete multi-graph matching are applicable in an incomplete setting, our first contribution is to prove that their runtime would be excessive and impractical. Our second contribution is a new method for incomplete multi-graph matching that applies to real-world, larger-scale problems.We experimentally show that for our bioimaging application we are able to attain results in less than two minutes, whereas the only competing approach requires at least half an hour while producing far worse results. Furthermore, even for small-scale, dense or complete problem instances we achieve results that are at least on par with the leading methods, but an order of magnitude faster.