Thanks to Stephan Saalfeld, TrakEM2 has been upgraded to version 0.9a which includes the new elastic spring-mesh image registration for elastic montages and elastic alignment of serial sections. The new system is capable of correcting folds and tears in the sections, as well as independent section-wise deformations, by exploiting the information in the set of adjacent sections.
Additionally, TrakEM2 0.9a brings enhancements in the rendering and export of images, reading and saving compressed XML files, and many others. See the TrakEM2 website for the complete release notes.