Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aefs_v2_0.tar.gz(23 Kbytes)|
|Manuscript Title: Local electron tomography using angular variations of surface tangents: Stomo version 2|
|Authors: T.C. Petersen, S.P. Ringer|
|Program title: STOMO version 2|
|Catalogue identifier: AEFS_v2_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 183(2012)698|
|Programming language: C/C++.|
|Operating system: Windows XP.|
|RAM: Scales as the product of experimental image dimensions multiplied by the number of points chosen by the user in polynomial fitting. Typical runs require between 50 Mb and 100 Mb of RAM.|
|Supplementary material: Sample output files, for the test run provided, are available.|
|Keywords: Electron tomography, Morphology, Differential geometry, Atom probe tomography.|
|PACS: 68.37.Lp, 6.35.bd.|
|Classification: 7.4, 14.|
Does the new version supersede the previous version?: Yes
Nature of problem:
A local electron tomography algorithm of specimens for which conventional back projection may fail and or data for which there is a limited angular range (which would otherwise cause significant 'missing-wedge' artefacts). The algorithm does not solve the tomography back projection problem but rather locally reconstructs the 3D morphology of surfaces defined by varied scattering densities.
Local reconstruction is effected using image-analysis edge and ridge detection computations on experimental tilt series to measure smooth angular variations of surface tangent-line intersections, which generate point clouds decorating the embedded and or external scattering surfaces of a specimen.
Reasons for new version:
The new version was coded to cater for rectangular images in experimental tilt-series, ensure smoother image rotations, provide ridge detection (suitable for sensing phase-contrast Fresnel fringes and other fine-scale structures), faster/larger kernel edge detection and also greatly reduce RAM usage. Specimen surface normals are also explicitly computed from tangent-line and edge intersections, providing new information for potential use in point cloud rendering. Hysteresis thresholding implemented in the version 1 edge-detection algorithm provided only sparse edge-linking. Version 2 now implements edge tracking using recursion to fully link the edges during hysteresis thresholding. Furthermore in version 1 the minimum number of fitted polynomial points (specified in the input file) was not correctly imposed, which has been fixed for version 2. Most of these changes increase the accuracy of 3d morphology surface-tomography reconstructions by facilitating the use of more/finer tilt angles and experimental images of increased spatial-resolution. The ridge detection was incorporated to specifically improve the reconstruction of internal specimen morphology.
Summary of revisions:
The input experimental tilt-series of images must be registered with respect to a common single tilt axis with known orientation and position.
For high quality reconstruction, 2 - 5 mins.
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