Estimating and correcting interference fringes in infrared spectra in infrared hyperspectral imaging.

Short-term acclimation response of individual cells of Thalassiosira weissflogii was monitored by Synchrotron FTIR imaging over the span of 75 minutes. The cells, collected from batch cultures, were maintained in a constant flow of medium, at an irradiance of 120 µmol m-2 s-1 and at 20 °C. Multiple internal reflections due to the micro fluidic channel were modeled, and showed that fringes are additive sinusoids to the pure absorption of the other components of the system. Preprocessing of the hyperspectral cube (x, y, Abs(λ)) included removing spectral fringe using an EMSC approach. Principal component analysis of the time series of hyperspectral cubes showed macromolecular pool variations (carbohydrates, lipids and DNA/RNA) of less than 2% after fringe correction.

3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography.

We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical and morphological localization by determining a complete infrared spectrum for every voxel (millions of spectra determined per sample).

Frequency-Comb Spectrum of Periodic-Patterned Signals.

Using arbitrary periodic pulse patterns we show the enhancement of specific frequencies in a frequency comb. The envelope of a regular frequency comb originates from equally spaced, identical pulses and mimics the single pulse spectrum. We investigated spectra originating from the periodic emission of pulse trains with gaps and individual pulse heights, which are commonly observed, for example, at high-repetition-rate free electron lasers, high power lasers, and synchrotrons. The ANKA synchrotron light source was filled with defined patterns of short electron bunches generating coherent synchrotron radiation in the terahertz range. We resolved the intensities of the frequency comb around 0.258 THz using the heterodyne mixing spectroscopy with a resolution of down to 1 Hz and provide a comprehensive theoretical description. Adjusting the electron's revolution frequency, a gapless spectrum can be recorded, improving the resolution by up to 7 and 5 orders of magnitude compared to FTIR and recent heterodyne measurements, respectively. The results imply avenues to optimize and increase the signal-to-noise ratio of specific frequencies in the emitted synchrotron radiation spectrum to enable novel ultrahigh resolution spectroscopy and metrology applications from the terahertz to the x-ray region.

High-resolution Fourier-transform infrared chemical imaging with multiple synchrotron beams.

Conventional Fourier-transform infrared (FTIR) microspectroscopic systems are limited by an inevitable trade-off between spatial resolution, acquisition time, signal-to-noise ratio (SNR) and sample coverage. We present an FTIR imaging approach that substantially extends current capabilities by combining multiple synchrotron beams with wide-field detection. This advance allows truly diffraction-limited high-resolution imaging over the entire mid-infrared spectrum with high chemical sensitivity and fast acquisition speed while maintaining high-quality SNR.

Diagnosing malaria infected cells at the single cell level using focal plane array Fourier transform infrared imaging spectroscopy.

New methods are needed to rapidly identify malaria parasites in blood smears. The coupling of a Focal Plane Array (FPA) infrared microscope system to a synchrotron light source at IRENI enables rapid molecular imaging at high spatial resolution. The technique, in combination with hyper-spectral processing, enables imaging and diagnosis of early stage malaria parasites at the single cell level in a blood smear. The method relies on the detection of distinct lipid signatures associated with the different stages of the malaria parasite and utilises resonant Mie extended multiplicative scatter correction to pre-process the spectra followed by full bandwidth image deconvolution to resolve the single cells. This work demonstrates the potential of focal plane technology to diagnose single cells in a blood smear. Brighter laboratory based infrared sources, optical refinements and higher sensitive detectors will soon see the emergence of focal plane array imaging in the clinical environment.

High-spatial-resolution mapping of superhydrophobic cicada wing surface chemistry using infrared microspectroscopy and infrared imaging at two synchrotron beamlines.

The wings of some insects, such as cicadae, have been reported to possess a number of interesting and unusual qualities such as superhydrophobicity, anisotropic wetting and antibacterial properties. Here, the chemical composition of the wings of the Clanger cicada (Psaltoda claripennis) were characterized using infrared (IR) microspectroscopy. In addition, the data generated from two separate synchrotron IR facilities, the Australian Synchrotron Infrared Microspectroscopy beamline (AS-IRM) and the Synchrotron Radiation Center (SRC), University of Wisconsin-Madison, IRENI beamline, were analysed and compared. Characteristic peaks in the IR spectra of the wings were assigned primarily to aliphatic hydrocarbon and amide functionalities, which were considered to be an indication of the presence of waxy and proteinaceous components, respectively, in good agreement with the literature. Chemical distribution maps showed that, while the protein component was homogeneously distributed, a significant degree of heterogeneity was observed in the distribution of the waxy component, which may contribute to the self-cleaning and aerodynamic properties of the cicada wing. When comparing the data generated from the two beamlines, it was determined that the SRC IRENI beamline was capable of producing higher-spatial-resolution distribution images in a shorter time than was achievable at the AS-IRM beamline, but that spectral noise levels per pixel were considerably lower on the AS-IRM beamline, resulting in more favourable data where the detection of weak absorbances is required. The data generated by the two complementary synchrotron IR methods on the chemical composition of cicada wings will be immensely useful in understanding their unusual properties with a view to reproducing their characteristics in, for example, industry applications.

Revealing the dynamics of ultrarelativistic non-equilibrium many-electron systems with phase space tomography.

The description of physical processes with many-particle systems is a key approach to the modeling of numerous physical systems. For example in storage rings, where ultrarelativistic particles are agglomerated in dense bunches, the modeling and measurement of their phase-space distribution is of paramount importance: at any time the phase-space distribution not only determines the complete space-time evolution but also provides fundamental performance characteristics for storage ring operation. Here, we demonstrate a non-destructive tomographic imaging technique for the 2D longitudinal phase-space distribution of ultrarelativistic electron bunches. For this purpose, we utilize a unique setup, which streams turn-by-turn near-field measurements of bunch profiles at MHz repetition rates. To demonstrate the feasibility of our method, we induce a non-equilibrium state and show that the phase-space distribution microstructuring as well as the phase-space distribution dynamics can be observed in great detail. Our approach offers a pathway to control ultrashort bunches and supports, as one example, the development of compact accelerators with low energy footprints.

Restoration and spectral recovery of mid-infrared chemical images.

Fourier transform infrared (FTIR) microspectroscopy is a powerful technique for label-free chemical imaging that has supplied important chemical information about heterogeneous samples for many problems across a variety of disciplines. State-of-the-art synchrotron based infrared (IR) microspectrometers can yield high-resolution images, but are truly diffraction limited for only a small spectral range. Furthermore, a fundamental trade-off exists between the number of pixels, acquisition time and the signal-to-noise ratio, limiting the applicability of the technique. The recently commissioned infrared synchrotron beamline, infrared environmental imaging (IRENI), overcomes this trade off and delivers 4096-pixel diffraction limited IR images with high signal-to-noise ratio in under a minute. The spatial oversampling for all mid-IR wavelengths makes the IRENI data ideal for spatial image restoration techniques. Here, we measured and fitted wavelength-dependent point-spread-functions (PSFs) at IRENI for a 74× objective between the sample plane and detector. Noise-free wavelength-dependent theoretical PSFs are deconvoluted from images generated from narrow bandwidths (4 cm(-1)) over the entire mid-infrared range (4000-900 cm(-1)). The stack of restored images is used to reconstruct the spectra. Restored images of metallic test samples with features that are 2.5 µm and smaller are clearly improved in comparison to the raw data images for frequencies above 2000 cm(-1). Importantly, these spatial image restoration methods also work for samples with vibrational bands in the recorded mid-IR fingerprint region (900-1800 cm(-1)). Improved signal-to-noise spectra are reconstructed from the restored images as demonstrated for a mixture of spherical polystyrene beads in a polyurethane matrix. Finally, a freshly thawed retina tissue section is used to demonstrate the success of deconvolution achievable with a heterogeneous, irregularly shaped, biologically relevant sample with distinguishing spectroscopic features across the entire mid-IR spectral range.

From synthetic to biogenic Mg-containing calcites: a comparative study using FTIR microspectroscopy.

The formation mechanism of the thermodynamically unstable calcite phase, very high Mg calcite, in biological organisms such as sea urchin or corallina algae has been an enigma for a very long time. In contrast to conventional methods such as KBr pellet Fourier Transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD), FTIR microspectroscopy (FTIRM) provides additional information about a local disorder such as an amorphous phase or the occlusion of Mg ions in the calcite lattice. In this work, we characterise for the first time systematically synthetic and biogenic Mg-containing calcium carbonate samples (especially sea urchin teeth--SUT) in detail by using two FTIRM instruments and compare these samples with KBr pellet FTIR measurements. Furthermore, we present spectra from geogenic calcite and dolomite minerals, recorded with both FTIRM systems, as well as KBr pellet FTIR spectra as references. We analyse the spectra by applying multi-peak curve fitting on the in-plane-bending (ν(4)) and out-of-plane (ν(2)) bands. Based on the obtained results we attribute the two singlet bands at ∼860-865 cm(-1) and ∼695-704 cm(-1) observed in the SUT FTIRM spectra to the existence of amorphous calcium carbonate (ACC), and report for the first time the existence of ACC at the mature end of SUT. In the other three studied biominerals, however, we did not find any ACC. Also, based on the FTIRM results, we observe that not only ν(4), but also ν(2) shifts to higher wavenumbers if more calcium ions are replaced by magnesium ions in the calcite lattices.

Time lapse synchrotron IR chemical imaging for observing the acclimation of a single algal cell to CO2 treatment.

Algae are the main primary producers in aquatic environments and therefore of fundamental importance for the global ecosystem. Mid-infrared (IR) microspectroscopy is a non-invasive tool that allows in principle studying chemical composition on a single-cell level. For a long time, however, mid-infrared (IR) imaging of living algal cells in an aqueous environment has been a challenge due to the strong IR absorption of water. In this study, we employed multi-beam synchrotron radiation to measure time-resolved IR hyperspectral images of individual Thalassiosira weissflogii cells in water in the course of acclimation to an abrupt change of CO2 availability (from 390 to 5000 ppm and vice versa) over 75 min. We used a previously developed algorithm to correct sinusoidal interference fringes from IR hyperspectral imaging data. After preprocessing and fringe correction of the hyperspectral data, principal component analysis (PCA) was performed to assess the spatial distribution of organic pools within the algal cells. Through the analysis of 200,000 spectra, we were able to identify compositional modifications associated with CO2 treatment. PCA revealed changes in the carbohydrate pool (1200-950 cm[Formula: see text]), lipids (1740, 2852, 2922 cm[Formula: see text]), and nucleic acid (1160 and 1201 cm[Formula: see text]) as the major response of exposure to elevated CO2 concentrations. Our results show a local metabolism response to this external perturbation.

Realistic modeling of the illumination point spread function in confocal scanning optical microscopy.

In this paper we present a rigorous and general theoretical model for the illumination point spread function of a confocal microscope that correctly reproduces the optical setup. The model uses vectorial theory and assumes that monochromatic light with a Gaussian intensity distribution (such as from a laser or a single-mode fiber) is focused by a microscope objective with high numerical aperture and passes through stratified media on its way to the sample. This covers the important practical case of illumination through up to three layers, which is the situation most commonly encountered in biological microscopy (immersion oil, glass coverslip, aqueous sample medium). It also accounts for objectives that are corrected for a certain coverslip thickness and refractive index but operated under non-design conditions. Furthermore, illumination with linearly, circularly, or elliptically polarized light is covered by introducing a Babinet-Soleil compensator into the beam path. The model leads to a set of analytical equations that are readily evaluated. Two-dimensional intensity distributions for particular cases of interest are presented and discussed.

From self-organization in relativistic electron bunches to coherent synchrotron light: observation using a photonic time-stretch digitizer.

In recent and future synchrotron radiation facilities, relativistic electron bunches with increasingly high charge density are needed for producing brilliant light at various wavelengths, from X-rays to terahertz. In such conditions, interaction of electron bunches with their own emitted electromagnetic fields leads to instabilities and spontaneous formation of complex spatial structures. Understanding these instabilities is therefore key in most electron accelerators. However, investigations suffer from the lack of non-destructive recording tools for electron bunch shapes. In storage rings, most studies thus focus on the resulting emitted radiation. Here, we present measurements of the electric field in the immediate vicinity of the electron bunch in a storage ring, over many turns. For recording the ultrafast electric field, we designed a photonic time-stretch analog-to-digital converter with terasamples/second acquisition rate. We could thus observe the predicted link between spontaneous pattern formation and giant bursts of coherent synchrotron radiation in a storage ring.

Evidence of nanocrystalline semiconducting graphene monoxide during thermal reduction of graphene oxide in vacuum.

As silicon-based electronics are reaching the nanosize limits of the semiconductor roadmap, carbon-based nanoelectronics has become a rapidly growing field, with great interest in tuning the properties of carbon-based materials. Chemical functionalization is a proposed route, but syntheses of graphene oxide (G-O) produce disordered, nonstoichiometric materials with poor electronic properties. We report synthesis of an ordered, stoichiometric, solid-state carbon oxide that has never been observed in nature and coexists with graphene. Formation of this material, graphene monoxide (GMO), is achieved by annealing multilayered G-O. Our results indicate that the resulting thermally reduced G-O (TRG-O) consists of a two-dimensional nanocrystalline phase segregation: unoxidized graphitic regions are separated from highly oxidized regions of GMO. GMO has a quasi-hexagonal unit cell, an unusually high 1:1 O:C ratio, and a calculated direct band gap of ∼0.9 eV.