2019
DOI: 10.1364/oe.27.036637
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Alignment methods for nanotomography with deep subpixel accuracy

Abstract: As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits metho… Show more

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Cited by 58 publications
(39 citation statements)
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“…For original tomogram, see Supplementary Materials Figure S4. The reconstructed tomogram had a voxel size of 38.1 nm and an effective spatial resolution of 78.3 nm, estimated by Fourier shell correlation (FSC) as implemented in the reconstruction script of Odstrčil et al [46]. The selected region and the associated FSC are shown in the Supplementary Materials Figure S5 and Figure S6, respectively.…”
Section: Tomography Studiesmentioning
confidence: 99%
See 1 more Smart Citation
“…For original tomogram, see Supplementary Materials Figure S4. The reconstructed tomogram had a voxel size of 38.1 nm and an effective spatial resolution of 78.3 nm, estimated by Fourier shell correlation (FSC) as implemented in the reconstruction script of Odstrčil et al [46]. The selected region and the associated FSC are shown in the Supplementary Materials Figure S5 and Figure S6, respectively.…”
Section: Tomography Studiesmentioning
confidence: 99%
“…The total acquisition of the tomogram took about 19 h. Ptychographic reconstructions were done on a cropped area of 256 × 256 pixels, corresponding to a pixel size of 37 nm, with the PtyREX package [69] to obtain a 2D projection series. This series was aligned and reconstructed into 3D volumes with a reconstructed voxel size of 38.1 nm and effective isotropic resolution of 78.3 nm using the MATLAB script by Odstrcil et al [46].…”
Section: Tomography Studiesmentioning
confidence: 99%
“…The tomograms were aligned and reconstructed using the script of Odstrčil et al. [36] with a resulting voxel size of ca. 37 nm for all samples.…”
mentioning
confidence: 99%
“…As the pixel size of projections depends on the x-ray photon energy, we resized all complex-valued ptychographic projections to a common pixel size of 26.52 nm using an interpolation based on fast fractional Fourier transform ( 58 , 59 ). Next, the phase of the reconstructed 2D projections was extracted by post-processing alignment and removal of constant and linear phase components, and the projections were aligned using a tomographic consistency approach ( 59 ).…”
Section: Methodsmentioning
confidence: 99%