Elastic volume reconstruction from series of ultra-thin microscopy sections

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
Nature Methods (Impact Factor: 32.07). 06/2012; 9(7):717-20. DOI: 10.1038/nmeth.2072
Source: PubMed


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.

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Available from: Albert Cardona
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    • "Corresponding SIFT features between adjacent sections were used to determine a rigid linear transformation between sections, which was applied to all sections in the dataset to achieve a coarse, 3D rigid alignment of the data. Then, we applied elastic registration (Saalfeld et al., 2012) to further improve the alignment accuracy between adjacent sections while minimizing the global deformation of the entire image block. The warping transforms generated in these steps were applied to all conventional fluorescence and STORM channels. "
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    • "One promising approach is (three-dimensional) reconstruction from serial section transmission electron microscopy (TEM), which is nowadays a well-established way of analyzing circuitry of neural networks [1–3]. However, several hundreds of sections or even more have to be cut without any loss of sections, inspected and photographed with the TEM, resulting in an enormous data volume, which is followed by a complex elastic alignment to compensate inevitable image distortions using an elastic alignment program (for example, TrakEM2 [4,5]). Hence, the main criterion in selecting a suitable subject for such a study is a small size. "
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