Elastic volume reconstruction from series of ultra-thin microscopy sections

The authors describe a method for realigning images from serially sectioned biological specimens that minimizes the effect of artificial deformations in the alignment by applying global elastic constraints. The method is applied to transmission electron microscopy and array tomography image series and is made available through the Fiji platform. Anatomy of large biological specimens is often reconstructed from serially sectioned volumes imaged by high-resolution microscopy. We developed a method to reassemble a continuous volume from such large section series that explicitly minimizes artificial deformation by applying a global elastic constraint. We demonstrate our method on a series of transmission electron microscopy sections covering the entire 558-cell Caenorhabditis elegans embryo and a segment of the Drosophila melanogaster larval ventral nerve cord.