Abstract
X-rays offer high penetration with the potential for tomography of centimetre-sized specimens, but synchrotron beamlines often provide illumination that is only millimetres wide. Here an approach is demonstrated termed Tomosaic for tomographic imaging of large samples that extend beyond the illumination field of view of an X-ray imaging system. This includes software modules for image stitching and calibration, while making use of existing modules available in other packages for alignment and reconstruction. The approach is compatible with conventional beamline hardware, while providing a dose-efficient method of data acquisition. By using parallelization on a distributed computing system, it provides a solution for handling teravoxel-sized or larger datasets that cannot be processed on a single workstation in a reasonable time. Using experimental data, the package is shown to provide good quality three-dimensional reconstruction for centimetre-sized samples with sub-micrometre pixel size.
Highlights
Computed tomography (CT) allows one to obtain internal structure of a three-dimensional sample from of a series of two-dimensional projection images collected around a common rotation axis
If one instead uses a synchrotron radiation source for its higher spectral flux and its parallel-beam geometry, relativistic effects limit the angular extent of the beam so that even at the 20–50 m distance of many experimental enclosures from the X-ray source one often has a beam that is at most a millimetre or two in width (Weitkamp et al, 2010)
In order to obtain tomographic reconstructions of an object that is larger than the field of view of the illuminating beam and the detector without sacrificing spatial resolution, several approaches have been described previously (Kyrieleis et al, 2009); we describe three main ones here: a local tomography acquisition approach, a projection-oriented acquisition approach, and a sinogram-oriented acquisition approach
Summary
Computed tomography (CT) allows one to obtain internal structure of a three-dimensional sample from of a series of two-dimensional projection images collected around a common rotation axis. When using X-rays rather than visiblelight or electron microscopy, CT is especially powerful because of the ability to image centimetre-sized or larger objects (Stock, 2008a). Illuminating centimetre-sized objects is straightforward when using cone-beam illumination from laboratory-based electron-impact sources which emit into a solid angle approaching ; with laboratory-based systems it becomes challenging to obtain both submicrometre voxel resolution and centimetre-sized fields of view in reasonable experimental times. While there are a limited number of long wiggler-source beamlines that can provide illumination over much larger specimen widths (Nemoz et al, 2007), they deliver a lower photon density on the specimen so that they are less well suited for micrometre-resolution studies. There is a need for a method for imaging centimetre-sized
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