A geometric partitioning method for distributed tomographic reconstruction

Buurlage, Jan‐Willem; Bisseling, Rob H.; Batenburg, Kees Joost

doi:10.1016/j.parco.2018.12.007

Cited by 6 publications

(5 citation statements)

References 42 publications

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“…Alternatively, weighted back projection (WBP) reconstructions are ideal for quick assessment of specimen morphology due to their fast, non-iterative computation 24 , 25 . Figure 3 shows screenshots taken from a live WBP reconstruction visualized using tomviz—time proceeds from left to right.…”

Section: Resultsmentioning

confidence: 99%

Real-time 3D analysis during electron tomography using tomviz

et al. 2022

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The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

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Section: Resultsmentioning

confidence: 99%

Real-time 3D analysis during electron tomography using tomviz

et al. 2022

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“…Alternatively, weighted back projection (WBP) reconstructions are ideal for quick assessment of specimen morphology due to their fast, non-iterative computation [21,22]. Figure 3 shows screenshots taken from a live WBP reconstruction visualized using tomviz-time proceeds from left to right.…”

Section: Resultsmentioning

confidence: 99%

Real-Time 3D Analysis During Tomographic Experiments using tomviz

Hovden

Schwartz

Harris

et al. 2022

Preprint

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The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. We show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

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“…When more advanced iterative reconstruction algorithms such as the simultaneous iterative reconstruction technique (SIRT) [33] are applied, capable of handling noisy and limited data, significantly longer computation times are required, even when using multiple GPUs. [32,34] The computational load further increases when using stateof-the-art reconstruction algorithms, which exploit prior knowledge about the reconstructed object. The discrete algebraic reconstruction technique (DART), for instance, uses prior knowledge on the discrete density of an object.…”

Section: Real-time Reconstruction Of Arbitrary Slicesmentioning

confidence: 99%

Real‐Time Reconstruction of Arbitrary Slices for Quantitative and In Situ 3D Characterization of Nanoparticles

Vanrompay

Buurlage

Pelt

et al. 2020

Part & Part Syst Charact

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strongly connected to their 3D structure. [1][2][3][4][5][6][7][8][9][10] Heterostructures, in which several compounds are combined within a single nano-object, provide even more flexibility to tune their final properties. For example, bimetallic nanoparticles can display superior properties compared to their monometallic counterparts. [11][12][13] To understand the connection between structure/ composition and properties, nanoparticles are often investigated by transmission electron microscopy (TEM). Although TEM has become an indispensable tool for studying nanomaterials, it remains difficult to perform a 3D characterization. Indeed, conventional TEM provides 2D projection images of 3D objects, therefore missing a wealth of information. Electron tomography was developed to overcome this issue. [14][15][16][17] In 2003, Midgley et al. combined high angle annular dark field scanning TEM (HAADF-STEM) with tomography, [18,19] which has since been successfully applied to investigate a broad variety of nanostructures. [20][21][22][23][24] During a typical electron tomography experiment, a series of 2D projection images are collected along various tilt angles, to cover an angular range that is as large as possible. After alignment of the tilt series, they serve as the input to a mathematical algorithm that reconstructs the 3D structure of the object. Although the acquisition of a tilt series can be automated, it can take (many) hours to obtain all images, depending on the complexity of the experiment. In addition, both the alignment and the reconstruction of the acquired projection images are carried out through offline post-processing procedures, performed at a dedicated workstation. These steps are computationally demanding, leading to a total data processing time of at least 1 h. To dramatically accelerate the acquisition of tilt series, socalled "fast tomography" was recently introduced in both TEM and HAADF-STEM modes. [25][26][27] The methodology is based on continuously tilting the holder and simultaneously acquiring projection images, ideally while focusing and tracking the particle at the same time.Fast HAADF-STEM tomography enables a new range of experiments, during which the dynamic behavior of nanoparticles can be probed in 3D. For example, recently this technique was combined with in situ heating to investigate the thermal stability of Au and Au/Pd nanoparticles. [27,28] These experiments are at the state of the art with respect to acquisition time, and we were able to record a full HAADF-STEM tilt series within about 5 min. However, since the alignment A detailed 3D investigation of nanoparticles at a local scale is of great importance to connect their structure and composition to their properties. Electron tomography has therefore become an important tool for the 3D characterization of nanomaterials. 3D investigations typically comprise multiple steps, including acquisition, reconstruction, and analysis/quantification. Usually, the latter two steps are performed offline, at a dedicated workstation. This...

show abstract

A geometric partitioning method for distributed tomographic reconstruction

Cited by 6 publications

References 42 publications

Real-time 3D analysis during electron tomography using tomviz

Real-time 3D analysis during electron tomography using tomviz

Real-Time 3D Analysis During Tomographic Experiments using tomviz

Real‐Time Reconstruction of Arbitrary Slices for Quantitative and In Situ 3D Characterization of Nanoparticles

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