neutron-radiography-computed-tomography-biological-systems-at-oak

Neutron Radiography and Computed Tomography of Biological Systems at the Oak Ridge National Laboratory's High Flux Isotope Reactor

Neutrons have historically been used for a broad range of biological applications employing techniques such as small-angle neutron scattering, neutron ...

Oak Ridge National Laboratory

Xi-cam is an extensible platform for data management, analysis and visualization. Xi-cam aims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core of Xi-cam is an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. With Xi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data. Xi-cam's plugin-based architecture targets cross-facility and cross-technique collaborative development, in support of multi-modal analysis. Xi-cam is open-source and cross-platform, and available for download on GitHub.

Xi-cam: a versatile interface for data visualization and analysis.

Cryo-Electron Tomography (cryo-ET) has become an essential technique in revealing cellular and macromolecular assembly structures in their native states. However, due to radiation damage and the limited tilt range, cryo-ET suffers from low contrast and missing wedge artifacts, which limits the tomograms to low resolution and hinders further biological interpretation. In this study, we applied the Model-Based Iterative Reconstruction (MBIR) method to obtain tomographic 3D reconstructions of experimental cryo-ET datasets and demonstrated the advantages of MBIR in contrast improvement, missing wedge artifacts reduction, missing information restoration, and subtomogram averaging compared with other reconstruction approaches. Considering the outstanding reconstruction quality, MBIR has a great potential in the determination of high resolution biological structures with cryo-ET.

Article	Year
Xi-cam: a versatile interface for data visualization and analysis. Journal of synchrotron radiation\| PubMed ID: 29979189	2018
MBIR: A cryo-ET 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information. Journal of structural biology\| PubMed ID: 30872095	2019

Singanallur Venkatakrishnan

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