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Synchrotrons

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Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.

Methods in molecular biology (Clifton, N.J.)
Like an article narrative is deemed by an editor and referees to be worthy of being a version of record on acceptance as a publication, so must the underpinning data also be scrutinized before passing it as a version of record. Indeed without the und...

The synergy of synchrotron imaging and convolutional neural networks towards the detection of human micro-scale bone architecture and damage.

Journal of the mechanical behavior of biomedical materials
The growing health and economic burden of bone fractures, their intricate multiscale features and the existing knowledge gaps in the comprehension of micro-scale bone damage occurrence make fracture diagnosis a challenging issue. In this scenario, de...

On stars and spikes: Resolving the skeletal morphology of planktonic Acantharia using synchrotron X-ray nanotomography and deep learning image segmentation.

Acta biomaterialia
Acantharia (Acantharea) are wide-spread marine protozoa, presenting one of the rare examples of strontium sulfate mineralization in the biosphere. Their endoskeletons consist of 20 spicules arranged according to a unique geometric pattern named Mülle...

BioSAXS at European Synchrotron Radiation Facility - Extremely Brilliant Source: BM29 with an upgraded source, detector, robot, sample environment, data collection and analysis software.

Journal of synchrotron radiation
As part of its Extremely Brilliant Source (EBS) upgrade project, the ESRF's BM29 BioSAXS beamline was subject to a significant upgrade and refurbishment. In addition to the replacement of the beamline's original bending magnet source by a two-pole wi...

Screening the phytotoxicity of micro/nanoplastics through non-targeted metallomics with synchrotron radiation X-ray fluorescence and deep learning: Taking micro/nano polyethylene terephthalate as an example.

Journal of hazardous materials
Microplastics (MPs) and nanoplastics (NPs) are global pollutants with emerging concerns. Methods to predict and screen their toxicity are crucial. Elemental dyshomeostasis can be used to assess toxicity of environmental pollutants. Non-targeted metal...

Deep residual networks for crystallography trained on synthetic data.

Acta crystallographica. Section D, Structural biology
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and tra...

High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III.

Journal of synchrotron radiation
Here, high-throughput tomography (HiTT), a fast and versatile phase-contrast imaging platform for life-science samples on the EMBL beamline P14 at DESY in Hamburg, Germany, is presented. A high-photon-flux undulator beamline is used to perform tomogr...

A Multimodal Transfer Learning Approach for Histopathology and SR-microCT Low-Data Regimes Image Segmentation.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Osteocyte-lacunar bone structures are a discerning marker for bone pathophysiology, given their geometric alterations observed during aging and diseases. Deep Learning (DL) image analysis has showcased the potential to comprehend bone health associat...

Cell quantification at the osteochondral interface from synchrotron radiation phase contrast micro-computed tomography images using a deep learning approach.

Scientific reports
Osteochondral interface consists of two tissues: the calcified cartilage (CC) containing chondrocytes, and subchondral bone (SCB) containing osteocytes that interact with each other. In this study, we propose a new method for the three-dimensional (3...

Enhancing synchrotron radiation micro-CT images using deep learning: an application of Noise2Inverse on bone imaging.

Journal of synchrotron radiation
In bone-imaging research, in situ synchrotron radiation micro-computed tomography (SRµCT) mechanical tests are used to investigate the mechanical properties of bone in relation to its microstructure. Low-dose computed tomography (CT) is used to prese...