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Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments.

ABSTRACT: Hard X-ray nanotomography enables 3D investigations of a wide range of samples with high resolution (<100?nm) with both synchrotron-based and laboratory-based setups. However, the advantage of synchrotron-based setups is the high flux, enabling time resolution, which cannot be achieved at laboratory sources. Here, the nanotomography setup at the imaging beamline P05 at PETRA III is presented, which offers high time resolution not only in absorption but for the first time also in Zernike phase contrast. Two test samples are used to evaluate the image quality in both contrast modalities based on the quantitative analysis of contrast-to-noise ratio (CNR) and spatial resolution. High-quality scans can be recorded in 15?min and fast scans down to 3?min are also possible without significant loss of image quality. At scan times well below 3?min, the CNR values decrease significantly and classical image-filtering techniques reach their limitation. A machine-learning approach shows promising results, enabling acquisition of a full tomography in only 6?s. Overall, the transmission X-ray microscopy instrument offers high temporal resolution in absorption and Zernike phase contrast, enabling in situ experiments at the beamline.

SUBMITTER: Flenner S

PROVIDER: S-EPMC7467338 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments.

Flenner Silja S Storm Malte M Kubec Adam A Longo Elena E Döring Florian F Pelt Daniël M DM David Christian C Müller Martin M Greving Imke I

Journal of synchrotron radiation 20200730 Pt 5

Hard X-ray nanotomography enables 3D investigations of a wide range of samples with high resolution (<100 nm) with both synchrotron-based and laboratory-based setups. However, the advantage of synchrotron-based setups is the high flux, enabling time resolution, which cannot be achieved at laboratory sources. Here, the nanotomography setup at the imaging beamline P05 at PETRA III is presented, which offers high time resolution not only in absorption but for the first time also in Zernike phase co ...[more]

PMID: 32876609

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Project description:Object retrieval systems measure the degree of similarity of the shape of 3D models. They search for the elements of the 3D model databases that resemble the query model. In structural bioinformatics, the query model is a protein tertiary/quaternary structure and the objective is to find similarly shaped molecules in the Protein Data Bank. With the ever-growing size of the PDB, a direct atomic coordinate comparison with all its members is impractical. To overcome this problem, the shape of the molecules can be encoded by fixed-length feature vectors. The distance of a protein to the entire PDB can be measured in this low-dimensional domain in linear time. The state-of-the-art approaches utilize Zernike-Canterakis moments for the shape encoding and supply the retrieval process with geometric data of the input structures. The BioZernike descriptors are a standard utility of the PDB since 2020. However, when trying to calculate the ZC moments locally, the issue of the deficiency of libraries readily available for use in custom programs (i.e., without relying on external binaries) is encountered, in particular programs written in Python. Here, a fast and well-documented Python implementation of the Pozo-Koehl algorithm is presented. In contrast to the more popular algorithm by Novotni and Klein, which is based on the voxelized volume, the PK algorithm produces ZC moments directly from the triangular surface meshes of 3D models. In particular, it can accept the molecular surfaces of proteins as its input. In the presented PK-Zernike library, owing to Numba's just-in-time compilation, a mesh with 50,000 facets is processed by a single thread in a second at the moment order 20. Since this is the first time the PK algorithm is used in structural bioinformatics, it is employed in a novel, simple, but efficient protein structure retrieval pipeline. The elimination of the outlying chain fragments via a fast PCA-based subroutine improves the discrimination ability, allowing for this pipeline to achieve an 0.961 area under the ROC curve in the BioZernike validation suite (0.997 for the assemblies). The correlation between the results of the proposed approach and of the 3D Surfer program attains values up to 0.99.

Dataset Information

Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments.

Publications

Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments.

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