Real-time 3D analysis during electron tomography using tomviz

Schwartz, Jonathan; Harris, Chris; Pietryga, Jacob; Zheng, Huihuo; Kumar, Prashant; Visheratina, Anastasiia; Kotov, Nicholas A.; Major, Brianna; Avery, Patrick; Ercius, Peter; Ayachit, Utkarsh; Geveci, Berk; Muller, David A.; Genova, Alessandro; Jiang, Yi; Hanwell, Marcus D.; Hovden, Robert

doi:10.1038/s41467-022-32046-0

Cited by 26 publications

(18 citation statements)

References 40 publications

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“…This approach permits optimizing the scanning tomography experiments and obtaining relevant information from pertinent sample regions in 2D or 3D during a user project. Thanks to recent developments 3 , 22 , 28 , 29 , this method paves the way towards statistically significant 3D studies, similar to those already available in full-field X-ray tomography 30 , and electron tomography 25 .…”

Section: Introductionmentioning

confidence: 91%

“…Indeed, the two orders of magnitude larger flux available at 4th generation hard X-ray nanoprobes boosts the speed of scanning tomography measurements proportionally, paving the way towards high-throughput scanning X-ray tomography of mesoscale samples 24 . Hence, the implementation of robust, user-friendly scanning tomography workflow is crucial for the routine application of these techniques, similarly as has been published recently for high-throughput electron tomography 25 . Such workflow imposes flexible and fast on-site data processing and tomographic reconstruction adapted to the different number of projections (sparse and high-resolution tomography), diverse data quality (e.g., high and low-level elemental abundances, missing wedge), different imaging modalities (e.g., XRF, X-ray absorption, X-ray diffraction), and the possibility of adapting the field of view and spatial resolution to the examined phenomenon by using multi-scale or local tomography.…”

Section: Introductionmentioning

confidence: 99%

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Towards routine 3D characterization of intact mesoscale samples by multi-scale and multimodal scanning X-ray tomography

Guo

Somogyi

Bazin

et al. 2022

Sci Rep

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Non-invasive multi-scale and multimodal 3D characterization of heterogeneous or hierarchically structured intact mesoscale samples is of paramount importance in tackling challenging scientific problems. Scanning hard X-ray tomography techniques providing simultaneous complementary 3D information are ideally suited to such studies. However, the implementation of a robust on-site workflow remains the bottleneck for the widespread application of these powerful multimodal tomography methods. In this paper, we describe the development and implementation of such a robust, holistic workflow, including semi-automatic data reconstruction. Due to its flexibility, our approach is especially well suited for on-the-fly tuning of the experiments to study features of interest progressively at different length scales. To demonstrate the performance of the method, we studied, across multiple length scales, the elemental abundances and morphology of two complex biological systems, Arabidopsis plant seeds and mouse renal papilla samples. The proposed approach opens the way towards routine multimodal 3D characterization of intact samples by providing relevant information from pertinent sample regions in a wide range of scientific fields such as biology, geology, and material sciences.

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Section: Introductionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Towards routine 3D characterization of intact mesoscale samples by multi-scale and multimodal scanning X-ray tomography

Guo

Somogyi

Bazin

et al. 2022

Sci Rep

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“…Alternatively, acquisition and processing of data from transmission electron microscopy (TEM) tomography enables real-time 3D tomographic visualization of chiral specimens in real time, as data are collected in an electron microscope. Volumetric interpretation and calculation of chirality measures can begin in less than 10 min and a high-quality tomogram can be available within 30 min, as demonstrated for twisted bowtie assemblies 218 . Here, the calculation of chirality should be incorporated into the tomography software, including the open source package tomviz.…”

Section: Tomographic and Crystallographic Analysismentioning

confidence: 99%

Bioinspired chiral inorganic nanomaterials

et al. 2023

Self Cite

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From small molecules to entire organisms, evolution has refined biological structures at the nanoscale, microscale and macroscale to be chiral-that is, mirror dissymmetric. Chirality results in biological, chemical and physical properties that can be influenced by circularly polarized electromagnetic fields. Chiral nanoscale materials can be designed that mimic, refine and advance biological chiral geometries, to engineer optical, physical and chemical properties for applications in photonics, sensing, catalysis and biomedicine. In this Review, we discuss the mechanisms underlying chirality transfer in nature and provide design principles for chiral nanomaterials. We highlight how chiral features emerge in inorganic materials during the chemical synthesis of chiral nanostructures, and outline key applications for inorganic chiral nanomaterials, including promising designs for biomedical applications, such as biosensing and immunomodulation. We conclude Nature Reviews Bioengineering Review article nanostructures). We describe hierarchical multiscale chirality in biological systems (for example, cytoskeleton hypothesis and chirality in biominerals), and analyse the most abundant chirality transfer mechanisms in biology, including enantioselective interaction between surfaces and chiral molecules, template-induced synthesis and chirality transfer, and photon-induced chiral nanomaterials. However, as in many natural systems 54 , these transfer mechanisms cannot be analysed separately because a concomitance of effects is responsible for the resulting chiral morphologies, in particular for highly crystalline nanomaterials, for which template-induced and photon-induced syntheses cannot be entirely decoupled from enantioselective interactions at high Miller index surfaces. Finally, we present potential applications in photonics (for example, polarization-control, non-linear optics), sensing (enantiomer discrimination), catalysis (chemical and pharmaceutical) and biomedicine (for example, photothermal and photodynamic therapies). Chirality in biologyChirality exists across multiple size scales in biological entities, dictating their geometries, properties and behaviour. For example, aminoacyl-tRNA synthases, enzymes involved in the selection of amino acids in protein synthesis, preferentially bind to l-amino acids by steric exclusion of d-amino acids 55 . Peptide elongation of d-amino acids at the ribosomes is slow owing to the large distance between the reaction sites 56 , limiting the production of peptides with incorporated d-amino acids 57,58 . The incorporation of some d-amino acids, such as d-Asp and d-Ser, has been linked to amyloid-β peptides present in the brains of patients with Alzheimer disease 59 , indicating that chirality at the molecular level could extend its influence to the organism and its behaviour.Chirality also offers survival advantage(s) for organisms. Fan-like petal arrangements of mutated Arabidopsis thaliana show left-handed chirality and clockwise twisting. The handedness of their asymmetric g...

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“…The method opens a pathway to the real-time understanding of countless BCP processes. In addition, progress in real-time 3D analysis can allow rapid interpretation of the data 145 and enable further tuning of the rapid TEMT.…”

Section: Rapid Temtmentioning

confidence: 99%

Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions

Weisbord

Segal‐Peretz

2023

ACS Appl. Mater. Interfaces

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Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method’s principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.

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Real-time 3D analysis during electron tomography using tomviz

Cited by 26 publications

References 40 publications

Towards routine 3D characterization of intact mesoscale samples by multi-scale and multimodal scanning X-ray tomography

Towards routine 3D characterization of intact mesoscale samples by multi-scale and multimodal scanning X-ray tomography

Bioinspired chiral inorganic nanomaterials

Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions

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