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With several fourth-generation, or diffraction-limited, storage rings and multiple beamlines in operation, the missing range of the spectrum was infrared…until recently.With several fourth-generation, or diffraction-limited, storage rings and multiple beamlines in operation, the missing range of the spectrum was infrared…until recently.

Data volumes collected in many scientific fields have long exceeded the capacity of human comprehension. This is especially true in biomedical research where multiple replicates and techniques are required to conduct reliable studies. Ever-increasing data rates from new instruments compound our dependence on statistics to make sense of the numbers. The currently available data analysis tools lack user-friendliness, various capabilities or ease of access. Problem-specific software or scripts freely available in supplementary materials or research lab websites are often highly specialized, no longer functional, or simply too hard to use. Commercial software limits access and reproducibility, and is often unable to follow quickly changing, cutting-edge research demands. Finally, as machine learning techniques penetrate data analysis pipelines of the natural sciences, we see the growing demand for user-friendly and flexible tools to fuse machine learning with spectroscopy datasets. In our opinion, open-source software with strong community engagement is the way forward. To counter these problems, we develop Quasar, an open-source and user-friendly software, as a solution to these challenges. Here, we present case studies to highlight some Quasar features analyzing infrared spectroscopy data using various machine learning techniques.

Alzheimer’s disease (AD) is the most common cause of dementia, costing about 1% of the global economy. Failures of clinical trials targeting amyloid-β protein (Aβ), a key trigger of AD, have been explained by drug inefficiency regardless of the mechanisms of amyloid neurotoxicity, which are very difficult to address by available technologies. Here, we combine two imaging modalities that stand at opposite ends of the electromagnetic spectrum, and therefore, can be used as complementary tools to assess structural and chemical information directly in a single neuron. Combining label-free super-resolution microspectroscopy for sub-cellular imaging based on novel optical photothermal infrared (O-PTIR) and synchrotron-based X-ray fluorescence (S-XRF) nano-imaging techniques, we capture elemental distribution and fibrillary forms of amyloid-β proteins in the same neurons at an unprecedented resolution. Our results reveal that in primary AD-like neurons, iron clusters co-localize with elevated amyloid β-sheet structures and oxidized lipids. Overall, our O-PTIR/S-XRF results motivate using high-resolution multimodal microspectroscopic approaches to understand the role of molecular structures and trace elements within a single neuronal cell.A new imaging approach that combines two techniques standing at the opposite ends of the electromagnetic spectrum.

Loss of memory during Alzheimer's disease (AD), a fatal neurodegenerative disorder, is associated with neuronal loss and the aggregation of amyloid proteins into neurotoxic β‐sheet enriched structures. However, the mechanism of amyloid protein aggregation is still not well understood due to many challenges when studying the endogenous amyloid structures in neurons or in brain tissue. Available methods either require chemical processing of the sample or may affect the amyloid protein structure itself. Therefore, new approaches, which allow studying molecular structures directly in neurons, are urgently needed. A novel approach is tested, based on label‐free optical photothermal infrared super‐resolution microspectroscopy, to study AD‐related amyloid protein aggregation directly in the neuron at sub‐micrometer resolution. Using this approach, amyloid protein aggregates are detected at the subcellular level, along the neurites and strikingly, in dendritic spines, which has not been possible until now. Here, a polymorphic nature of amyloid structures that exist in AD transgenic neurons is reported. Based on the findings of this work, it is suggested that structural polymorphism of amyloid proteins that occur already in neurons may trigger different mechanisms of AD progression. Molecular mechanisms of amyloid protein aggregation and neuronal loss related to Alzheimer's disease (AD) are not well understood. Using novel label‐free optical photothermal infrared super‐resolution imaging, amyloid protein aggregates can be detected directly in AD‐affected neurons at the subcellular level. This study demonstrates the polymorphic nature of amyloid structures, which may coexist already at the neuronal level.

The photoresponse in the electrical conductivity of a single-walled carbon nanotube (SWNT) film is dramatically enhanced when the nanotube film is suspended in vacuum. We show here that the change in conductivity is bolometric (caused by heating of the SWNT network). Electron-phonon interactions lead to ultrafast relaxation of the photoexcited carriers, and the energy of the incident infrared (IR) radiation is efficiently transferred to the crystal lattice. It is not the presence of photoexcited holes and electrons, but a rise in temperature, that results in a change in resistance; thus, photoconductivity experiments cannot be used to support the band picture over the exciton model of excited states in carbon nanotubes. The photoresponse of suspended SWNT films is sufficiently high that they may function as the sensitive element of an IR bolometric detector.

Fiber Bragg gratings are key components for optical fiber sensing applications in harsh environments. This paper investigates the structural and chemical characteristics of femtosecond laser photo-inscribed microvoids. These voids are at the base of type III fs-gratings consisting of a periodic array of microvoids inscribed at the core of an optical fiber. Using high-resolution techniques such as quantitative phase microscopy, electron transmission microscopy, and scattering-type scanning near-field IR optical microscopy, we examined the structure of the microvoids and the densified shells around them. We also investigated the high-temperature behavior of the voids, revealing their evolution in size and shape under step isochronal annealing conditions up to 1250 °C.

It is well known that infrared microscopy of micrometer sized samples suffers from strong scattering distortions, attributed to Mie scattering. The state-of-the-art preprocessing technique for modelling and removing Mie scattering features from infrared absorbance spectra of biological samples is built on a meta model for perfect spheres. However, non-spherical cell shapes are the norm rather than the exception, and it is therefore highly relevant to evaluate the validity of this preprocessing technique for deformed spherical systems. Addressing these cases, we investigate both numerically and experimentally the absorbance spectra of 3D-printed individual domes, rows of up to five domes, two domes with varying distance, and semi-capsules of varying lengths as model systems of deformed individual cells and small cell clusters. We find that coupling effects between individual domes are small, corroborating previous related literature results for spheres. Further, we point out and illustrate with examples that, while optical reciprocity guarantees the same extinction efficiency for top vs. bottom illumination, a scatterer’s internal field may be vastly different in these two situations. Finally, we demonstrate that the ME-EMSC model for preprocessing infrared spectra from spherical biological systems is valid also for deformed spherical systems.

Material characterization and investigation are the basis for improving the performance of electrochemical devices. However, many compounds with electrochemical applications are sensitive to atmospheric gases and moisture; therefore, even their characterization should be performed in a controlled atmosphere. In some cases, it is impossible to execute such investigations in a glove box, and, therefore, in the present work, an air-tight 3D printed cell was developed that preserves samples in a controlled atmosphere while allowing spectroscopic measurements in reflectance geometry. Equipped with a cheap 1 mm thick CaF2 optical window or a more expensive 0.5 mm thick ZnS window, the cell was used for both optical photothermal infrared and Raman spectroscopy measures; imaging of the samples was also possible. The far-infrared range reflectance measurements were performed with a cell equipped with a diamond window.

This study investigates the structural and optical responses of silica glass to femtosecond (fs) laser irradiation followed by high-energy electron (2.5 MeV, 4.9 GGy) irradiation. Using optical microscopy and spectroscopy techniques, we analyzed retardance, phase shifts, nanograting periodicity, and Raman D2 band intensity, which is an indicator of local glass densification. S-SNOM and nano-FTIR measurements further revealed changes in the Si–O–Si vibrational bands, indicating partial relaxation of the densified nanolayers under electron irradiation. Our findings reveal significant optical modifications due to subsequent electron irradiation, including reduced retardance and phase values, which are in agreement with the relaxation of the local densification. SEM analysis confirmed the preservation of nanogratings’ morphology including their periodicity. Apart from revealing fundamental aspects related to glass densification within nanogratings, this study also underscores the potential of combined fs-laser and electron irradiation techniques in understanding silica glass behavior under high radiation conditions, which is crucial for applications in harsh environments.

Development of sustainable processes for hydrocarbons synthesis is a fundamental challenge in chemistry since these are of unquestionable importance for the production of many essential synthetic chemicals, materials and carbon-based fuels. Current industrial processes rely on non-abundant metal catalysts, temperatures of hundreds of Celsius and pressures of tens of bars. We propose an alternative gas phase process under mild reaction conditions using only atomic carbon, molecular hydrogen and an inert carrier gas. We demonstrate that the presence of CH 2 and H radicals leads to efficient C-C chain growth, producing micron-length fibres of unbranched alkanes with an average length distribution between C 23 -C 33 . Ab-initio calculations uncover a thermodynamically favourable methylene coupling process on the surface of carbonaceous nanoparticles, which is kinematically facilitated by a trap-and-release mechanism of the reactants and nanoparticles that is confirmed by a steady incompressible flow simulation. This work could lead to future alternative sustainable synthetic routes to critical alkane-based chemicals or fuels. There is an urgent need of cleaner and energy-efficient technologies for future sustainable chemicals and fuels. Here the authors report the gas phase synthesis of long hydrocarbon chains from atomic carbon and molecular hydrogen precursors in an inert carrier gas, avoiding the use of metal catalysts.