An electron tomography algorithm for reconstructing 3D morphology using surface tangents of projected scattering interfaces

Timothy Petersen, Simon Ringer

Research output: Contribution to journalArticleResearchpeer-review

19 Citations (Scopus)


Upon discerning the mere shape of an imaged object, as portrayed by projected perimeters, the full three-dimensional scattering density may not be of particular interest. In this situation considerable simplifications to the reconstruction problem are possible, allowing calculations based upon geometric principles. Here we describe and provide an algorithm which reconstructs the three-dimensional morphology of specimens from tilt series of images for application to electron tomography. Our algorithm uses a differential approach to infer the intersection of projected tangent lines with surfaces which define boundaries between regions of different scattering densities within and around the perimeters of specimens. Details of the algorithm implementation are given and explained using reconstruction calculations from simulations, which are built into the code. An experimental application of the algorithm to a nano-sized Aluminium tip is also presented to demonstrate practical analysis for a real specimen. Program summary: Program title: STOMO version 1.0. Catalogue identifier: AEFS_v1_0. Program summary URL: Program obtainable from: CPC Program Library, Queen s University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, No. of lines in distributed program, including test data, etc.: 2988. No. of bytes in distributed program, including test data, etc.: 191 605. Distribution format: tar.gz. Programming language: C/C++. Computer: PC. Operating system: Windows XP. RAM: Depends upon the size of experimental data as input, ranging from 200 Mb to 1.5 Gb. Supplementary material: Sample output files, for the test run provided, are available. Classification: 7.4, 14. External routines: Dev-C++ ( Nature of problem: Electron tomography of specimens for which conventional back projection may fail and/or data for which there is a limited angular range. The algorithm does not solve the tomographic back-projection problem but rather reconstructs the local 3D morphology of surfaces defined by varied scattering densities. Solution method: Reconstruction using differential geometry applied to image analysis computations. Restrictions: The code has only been tested with square images and has been developed for only single-axis tilting. Running time: For high quality reconstruction, 5-15 min.
Original languageEnglish
Pages (from-to)676 - 682
Number of pages7
JournalComputer Physics Communications
Issue number3
Publication statusPublished - 2010
Externally publishedYes

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