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Magnetic Resonance Imaging (MRI) exams provide imaging data of high importance to various medical fields including that of neuro-oncology [1]. Beyond the technological aspect of this imaging technique, the assessment of this data is crucial and specialists are necessary. Recent trends aim at developing software systems for the automation of certain tasks [2]. The advances of artificial intelligence and in specific that of neural networks allowed for the automation of processes like that of segmentation based [3] on modern mathematical instruments, their software implementations and deployment in suitable hardware. Due to their complexity such systems are hard to be accessed by groups of specialists not belonging to the original research team and affiliated institutes. Even at premature stages such systems could provide useful insights to the broader medical community. This is especially the case when cross-facility experiments are necessary and novel approaches to research are implemented like virtual trials [ref]. This short manuscript communicates the design and development of a web-based system [Fig.1 and Fig.2] that allows for easier access to advanced methods of automated MRI assessment [4] while it allows for data management and feedback collection for further research. The system permits the inclusion of multiple imaging methods including systems that provide quantitative information [5] for the automatically segmented data. Last but not least, the outcome of this project suggests that such systems can be prototyped fast and render important radiomic advances [6] available to a larger audience. While funds allow it a publicly available beta is in www.rmn.ai

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this article, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicity, the software leverages GPU accelerated processing through the PyTorch CUDA interface. This is essential for designing new methods that can readily be employed. As an example, we present an improved position refinement method based on Adam and a new version of the rPIE algorithm, adapted for partial coherence setups. Results are shown on both synthetic and real datasets. The software is released as open-source.

The advancement of quantum technologies is expected to pave the way for what we refer to as practical Quantum Computing (pQC). pQC should provide solutions to certain problems, superior to those offered by the classical computational paradigm. The QC field is in development but has not taken its final form yet. In an attempt to define requirements for its practical use, this research reviews the current state of QC services as provided by IBM, Google, Microsoft , Rigetti and D-Wave, and proposes potential applications in the synchrotron radiation facility Elettra Sincrotrone Trieste. This research has concentrated its focus on potential applications that may benefit from using QC for Optimization problems even if it acknowledges other uses in fields like those of simulation modelling and information theory. In specific, this work starts by hinting on the optimisation needs for accelerator control till beamline end-station uses in scientific applications like X-ray Fluorescence data fitting and Ptychography reconstructions. The connection of QC to specific practical optimisation problems in a synchrotron and a Free Electron Laser may serve as a partial guideline for the future development of the field.

Code and data for a publication on a fast tomography alignment algorithm. Raw data have been kindly provided by Prof. Dr. Francesco Brun (University of Trieste, Elettra Sincrotrone Trieste)

Two dataset for XRF alignment experiments. Contents: dataset 1 (raw signals, manual alignment, automatic alignment) dataset 2 (raw signals , manual alignment, automatic alignment) &nbsp

The report summarises the views expressed by the Italian Computing and Data Initiative (ICDI) in response to the open consultation for the EOSC Strategic Research and Innovation Agenda (SRIA), closed on the 31st of August. It provides insightful input and suggestions about the current draft of the SRIA document shared with the wider EOSC community, with the aim of helping to shape the future vision of the European Open Science Cloud.

An improved understanding of an ovary’s structures is highly desirable to support advances in folliculogenesis knowledge and reproductive medicine, with particular attention to fertility preservation options for prepubertal girls with malignant tumors. Although currently the golden standard for structural analysis is provided by combining histological sections, staining, and visible 2D microscopic inspection, synchrotron radiation phase-contrast microtomography is becoming a new challenge for three-dimensional studies at micrometric resolution. To this aim, the proper use of contrast agents can improve the visualization of internal structures in ovary tissues, which normally present a low radiopacity. In this study, we report a comparison of four staining protocols, based on iodine or tungsten containing agents, applied to bovine ovarian tissues fixed in Bouin’s solution. The microtomography (microCT) analyses at two synchrotron facilities under different set-ups were performed at different energies in order to maximize the image contrast. While tungsten-based agents allow large structures to be well identified, Iodine ones better highlight smaller features, especially when acquired above the K-edge energy of the specific metal. Further scans performed at lower energy where the setup was optimized for overall quality and sensitivity from phase-contrast still provided highly resolved visualization of follicular and intrafollicular structures at different maturation stages, independent of the staining protocol. The analyses were complemented by X-ray Fluorescence mapping on 2D sections, showing that the tungsten-based agent has a higher penetration in this type of tissues.

Significance Here we establish femtosecond covariance spectroscopy as a technique that uses ultrashort stochastic light pulses to measure nonlinear material responses. By using pulses with spectrally uncorrelated fluctuations we can leverage on the noise and consider each repetition of the experiment as a measurement under different conditions. In this limit we demonstrate that nonlinear processes in the sample can be retrieved by measuring the spectral correlations in different pulses. We validate the approach by studying stimulated Raman scattering in α-quartz. This concept can be applied to reveal low-energy modes of electronic, spin, and vibrational origin and adapted to different techniques and wavelength ranges, from optical to X-ray free-electron lasers, where strong stochastic fluctuations are unavoidable., The success of nonlinear optics relies largely on pulse-to-pulse consistency. In contrast, covariance-based techniques used in photoionization electron spectroscopy and mass spectrometry have shown that a wealth of information can be extracted from noise that is lost when averaging multiple measurements. Here, we apply covariance-based detection to nonlinear optical spectroscopy, and show that noise in a femtosecond laser is not necessarily a liability to be mitigated, but can act as a unique and powerful asset. As a proof of principle we apply this approach to the process of stimulated Raman scattering in α-quartz. Our results demonstrate how nonlinear processes in the sample can encode correlations between the spectral components of ultrashort pulses with uncorrelated stochastic fluctuations. This in turn provides richer information compared with the standard nonlinear optics techniques that are based on averages over many repetitions with well-behaved laser pulses. These proof-of-principle results suggest that covariance-based nonlinear spectroscopy will improve the applicability of fs nonlinear spectroscopy in wavelength ranges where stable, transform-limited pulses are not available, such as X-ray free-electron lasers which naturally have spectrally noisy pulses ideally suited for this approach.

Despite the rhizotoxicity of aluminum (Al) being identified over 100 years ago, there is still no consensus regarding the mechanisms whereby root elongation rate is initially reduced in the approximately 40% of arable soils worldwide that are acidic. We used high-resolution kinematic analyses, molecular biology, rheology, and advanced imaging techniques to examine soybean (Glycine max) roots exposed to Al. Using this multidisciplinary approach, we have conclusively shown that the primary lesion of Al is apoplastic. In particular, it was found that 75 µm Al reduced root growth after only 5 min (or 30 min at 30 µm Al), with Al being toxic by binding to the walls of outer cells, which directly inhibited their loosening in the elongation zone. An alteration in the biosynthesis and distribution of ethylene and auxin was a second, slower effect, causing both a transient decrease in the rate of cell elongation after 1.5 h but also a longer term gradual reduction in the length of the elongation zone. These findings show the importance of focusing on traits related to cell wall composition as well as mechanisms involved in wall loosening to overcome the deleterious effects of soluble Al.

Nanotoxicology and nanomedicine investigations often require the probing of nano-objects such as fibres and particles in biological samples and cells, whilst internalization and intracellular destiny are the main issues for in vitro cellular studies. Various high resolution microscopy techniques are well suited for providing this highly sought-after information. However, sample preparation, nanomaterial composition and sectioning challenges make it often difficult to establish whether the fibres or particles have been internalized or they are simply overlaying or underlying the biological matter. In this paper we suggest a novel suitable combination of two different microscopic techniques to reveal in intact cells the uptake of asbestos fibres by mesothelial cells. After exposure to asbestos fibres and fixation, cells were first analysed under the AFM instrument and then imaged under the TwinMic soft X-ray microscope at Elettra Sincrotrone. The suggested approach combines standard soft X-ray microscopy imaging and AFM microscopy, with a common non-invasive sample preparation protocol which drastically reduces the experimental uncertainty and provides a quick and definitive answer to the nanoparticle cellular and tissue uptake.

Understanding the lateral variations in the elemental and chemical state of constituents induced by electrochemical reactions at nanoscales is crucial for the advancement of electrochemical materials science. This requires in situ studies to provide observables that contribute to both modeling beyond the phenomenological level and exactly transducing the functionally relevant quantities. A range of X-ray coherent diffraction imaging (CDI) approaches have recently been proposed for imaging beyond the diffraction limit with potentially dramatic improvements in time resolution with chemical sensitivity. In this paper, we report a selection of ptychography results obtained in situ during the electrodeposition of a metal–polymer nanocomposite. Our selection includes dynamic imaging during electrochemically driven growth complemented with absorption and phase spectroscopy with high lateral resolution. We demonstrate the onset of morphological instability feature formation and correlate the chemical state of Mn with the local growth rate controlled by the current density distribution resulting from morphological evolution.

This paper describes two novel in situ microspectroscopic approaches to the dynamic study of electrodeposition processes: x-ray fluorescence (XRF) mapping with submicrometric space resolution and keyhole coherent diffractive imaging (kCDI) with nanometric lateral resolution. As a case study, we consider the pulse-plating of nanocomposites with polypyrrole matrix and Mn x Co y O z dispersoids, a prospective cathode material for zinc-air batteries. This study is centred on the detailed measurement of the elemental distributions developing in two representative subsequent growth steps, based on the combination of in situ identical-location XRF microspectroscopy—accompanied by soft-x ray absorption microscopy—and kCDI. XRF discloses space and time distributions of the two electrodeposited metals and kCDI on the one hand allows nanometric resolution and on the other hand provides complementary absorption as well as phase contrast modes. The joint information derived from these two microspectroscopies allows measurement of otherwise inaccessible observables that are a prerequisite for electrodeposition modelling and control accounting for dynamic localization processes.