Absorption Imaging Research Articles

Tomographic absorption spectroscopy based on dictionary learning

Tomographic absorption spectroscopy (TAS) has an advantage over other optical imaging methods for practical combustor diagnostics: optical access is needed in a single plane only, and the access can be limited. However, practical TAS often suffers from limited projection data. In these cases, priors such as smoothness and sparseness can be incorporated to mitigate the ill-posedness of the inversion problem. This work investigates use of dictionary learning (DL) to effectively extract useful a priori information from the existing dataset and incorporate it in the reconstruction process to improve accuracy. We developed two DL algorithms; our numerical results suggest that they can outperform classical Tikhonov reconstruction under moderate noise conditions. Further testing with experimental data indicates that they can effectively suppress reconstruction artifacts and obtain more physically plausible solutions compared with the inverse Radon transform.

Thermometry of one-dimensional Bose gases with neural networks

We design a neural network to extract and process features from absorption images taken of one-dimensional Bose gases in the quasi-condensate regime. Specifically, the network is trained to predict both the temperature of single realizations of the system and the uncertainty thereof. For multiple realizations, the individual predictions can be combined in an estimate of the mean temperature, improving precision. We benchmark our model on both simulated and experimentally measured data and compare it to the established method of density ripples thermometry. We find the predictions of the two methods compatible, although the neural network reaches similar precision needing much fewer realizations, thus highlighting the efficiency gain achievable when incorporating neural networks into analysis of data from cold gas experiments. Further, we study feature maps to reveal which local features of the condensate are extracted by the network and how said features correlate with properties of the system. A similar analysis could be employed to uncover physical relations in more complex systems.

Phase and dark-field imaging with mesh-based structured illumination and polycapillary optics.

X-ray phase and dark-field (DF) imaging have been shown to improve the diagnostic capabilities of X-ray systems. However, these methods have found limited clinical use due to the need for multiple precision gratings with limited field of view or requirements on X-ray coherence that may not be easily translated to clinical practice. This work aims to develop a practicable X-ray phase and DF imaging system that could be translated and practiced in the clinic. This work employs a conventional source to create structured illumination with a simple wire mesh. A mesh-shifting algorithm is used to allow wider Fourier windowing to enhance resolution. Deconvolution of the source spot width and camera resolution improves accuracy. Polycapillary optics are employed to enhance coherence. The effects of incorporating optics with two different focal lengths are compared. Information apparent in enhanced absorption images, phase images, and DF images of fat embedded phantoms were compared and subjected to a limited receiver operator characteristic (ROC) study. The DF images of the moist and dry porous object (sponges) were compared. The mesh-based phase and DF imaging system constructs images with three different information types: scatter-free absorption images, differential phase images, and scatter magnitude/DF images, simultaneously from the same original image. The polycapillary optic enhances the coherence of the beam. The deblurring technique corrects the phase signal error due to geometrical blur and the limitation of the camera modulation transfer function (MTF) and removes image artifacts to improve the resolution in a single shot. The mesh-shifting method allows the use of a wider Fourier processing window, which gives even higher resolution, at the expense of an increased dose. The limited ROC study confirms the efficacy of the system over the conventional system. DF images of moist and dry porous object show the significance of the system in the imaging of lung infections. The mesh-based X-ray phase and DF imaging system is an inexpensive and easy setup in terms of alignment and data acquisition and can produce phase and DF images in a single shot with wide field of view. The system shows significant potential for use in diagnostic imaging in a clinical setting.

Linear calibration‐free wavelength modulation spectroscopy

AbstractThis article presents a new linear calibration‐free wavelength modulation spectroscopy (LCF‐WMS) technique for gas sensing. By combining the natural logarithms of the transmitted intensity and background signals, this technique eliminates the effects of the intensity, intensity modulation, and the modulation phase to obtain integrable harmonic signals along the line‐of‐sight and thus realize calibration‐free measurements. To illustrate the validity of the LCF‐WMS technique, it was applied to measurement of the water vapor concentration in air at ambient temperature. Because of its specific features of line‐of‐sight integrability and baseline independence, this method will be advantageous in absorption tomography and high‐pressure applications.

In-vivo X-ray dark-field computed tomography for the detection of radiation-induced lung damage in mice.

Radiotherapy of thoracic tumours can lead to side effects in the lung, which may benefit from early diagnosis. We investigated the potential of X-ray dark-field computed tomography by a proof-of-principle murine study in a clinically relevant radiotherapeutic setting aiming at the detection of radiation-induced lung damage. Six mice were irradiated with 20Gy to the entire right lung. Together with five unirradiated control mice, they were imaged using computed tomography with absorption and dark-field contrast before and 16weeks post irradiation. Mean pixel values for the right and left lung were calculated for both contrasts, and the right-to-left-ratio R of these means was compared. Radiologists also assessed the tomograms acquired 16weeks post irradiation. Sensitivity, specificity, inter- and intra-reader accuracy were evaluated. In absorption contrast the group-average of R showed no increase in the control group and increased by 7% (p=0.005) in the irradiated group. In dark-field contrast, it increased by 2% in the control group and by 14% (p=0.005) in the irradiated group. Specificity was 100% for both contrasts but sensitivity was almost four times higher using dark-field tomography. Two cases were missed by absorption tomography but were detected by dark-field tomography. The applicability of X-ray dark-field computed tomography for the detection of radiation-induced lung damage was demonstrated in a pre-clinical mouse model. The presented results illustrate the differences between dark-field and absorption contrast and show that dark-field tomography could be advantageous in future clinical settings.

Quantification of the effects of grid angulation on image quality in single-grid-based phase-contrast x-ray imaging

Single-grid-based phase-contrast x-ray imaging (SG-PCXI) is a single-exposure, non-interferometric method for the simultaneous retrieval of absorption, differential phase-contrast, and dark-field images using a conventional x-ray grid; it requires minimal exposure and minimal system setup for potential medical and industrial imaging applications. However, owing to the Moiré artifact, the retrieved images are often distorted because of the inadequate sampling of the grid strips by the pixel array detector. This attribute can result in the degradation of image quality. Therefore, in this study, we propose a method for effectively removing the Moiré artifact by employing a grid angulation technique to improve image quality in SG-PCXI. We theoretically analyzed the formation of the Moiré artifact in an SG-PCXI setup and quantified the effects of grid angulation on the image quality. We conducted an experiment using a tabletop setup to verify the theoretical quantification of the effects of grid angulation on image quality. The Moiré artifact was completely removed in the retrieved images when the x-ray grid was rotated at θ = 18.2° and 26.3°, which aligned well with the theoretical quantification. Furthermore, the spatial resolution of the retrieved images improved as the grid frequency increased. Thus, the experimental results indicated that the proposed method can effectively eliminate the Moiré artifact; furthermore, it was determined that the size of the window function should be as large as possible to ensure improved image quality. The proposed method significantly improves image quality in SG-PCXI.

Full image reconstruction in frequency-domain photoacoustic microscopy by means of a low-cost I/Q demodulator.

We present a full image reconstruction methodology in frequency-domain photoacoustic (PA) microscopy using a low-cost I/Q demodulator for the recording of the amplitude and phase of the signals. By modulating the intensity of a continuous-wave diode laser at 10 MHz, we have been able to provide accurate optical absorption images and surface reconstructions of phantom samples, comparing also the extracted results with standard time-domain approaches. The findings of the study in this Letter could be utilized towards the development of inexpensive PA microscopes with multispectral capabilities for a wide range of biomedical studies, requiring the sensitive detection of endogenous or exogenous absorbers in tissues.

Measuring densities of cold atomic clouds smaller than the resolution limit

We propose and demonstrate an experimental method to measure by absorption imaging the size and local column density of a cloud of atoms, even when its smallest dimension is smaller than the resolution of the imaging system. To do this, we take advantage of the fact that, for a given total number of atoms, a smaller and denser cloud scatters less photons when the gas is optically thick. The method relies on making an ansatz on the cloud shape along the unresolved dimension(s), and on providing an additional information such as the total number of atoms. We demonstrate the method on \textit{in-situ} absorption images of elongated 87Sr Fermi gases. We find significant non-linear corrections to the estimated size and local density of the cloud compared to a standard analysis. This allows us to recover an un-distorted longitudinal density profile, and to measure transverse sizes as small as one fourth of our imaging resolution. The ultimate limit of our method is the wavelength that is used for imaging.

Observation of photon recoil effects in single-beam absorption spectroscopy with an ultracold strontium gas

We report on observing photon recoil effects in the absorption of a single monochromatic light at 689 nm through an ultracold 88Sr gas, where the recoil frequency is comparable to natural linewidth of the narrow-line transition 5s2 1S0–5s5p 3P1 in strontium. In the regime of high-saturation, the absorption profile becomes asymmetric due to the photon-recoil shift, which is of the same order as the natural linewidth. The lineshape is described by an extension of the optical Bloch equations including the momentum transfers to atoms during emission and absorption of photons. Our work reveals the photon recoil effects in a simplest single-beam absorption setting, which is of significant relevance to other applications such as saturation spectroscopy, Ramsey interferometry, and absorption imaging.

Dual-energy phase retrieval algorithm for inline phase sensitive x-ray imaging system.

Phase retrieval is vital for quantitative x-ray phase contrast imaging. This work presents an iterative method to simultaneously retrieve the x-ray absorption and phase images from a single x-ray exposure. The proposed approach uses the photon-counting detectors' energy-resolving capability in providing multiple spectrally resolved phase contrast images from a single x-ray exposure. The retrieval method is derived, presented, and experimentally tested with a multi-material phantom in an inline phase contrast imaging setup. By separating the contributions of photoelectric absorption and Compton scattering to the attenuation, the authors divide the phase contrast image into two portions, the attenuation map arises from photoelectric absorption and a pseudo phase contrast image generated by electron density. This way one can apply the Phase Attenuation Dualiby (PAD) algorithm and Fresnel propagation for the iteration. The retrieval results from the experimental images show that this iterative method is fast, accurate, robust against noise, and thus yields noticeable enhancement in contrast to noise ratios.

Advances in micro-CT imaging of small animals.

Micron-scale computed tomography (micro-CT) imaging is a ubiquitous, cost-effective, and non-invasive three-dimensional imaging modality. We review recent developments and applications of micro-CT for preclinical research. Based on a comprehensive review of recent micro-CT literature, we summarize features of state-of-the-art hardware and ongoing challenges and promising research directions in the field. Representative features of commercially available micro-CT scanners and some new applications for both in vivo and ex vivo imaging are described. New advancements include spectral scanning using dual-energy micro-CT based on energy-integrating detectors or a new generation of photon-counting x-ray detectors (PCDs). Beyond two-material discrimination, PCDs enable quantitative differentiation of intrinsic tissues from one or more extrinsic contrast agents. When these extrinsic contrast agents are incorporated into a nanoparticle platform (e.g. liposomes), novel micro-CT imaging applications are possible such as combined therapy and diagnostic imaging in the field of cancer theranostics. Another major area of research in micro-CT is in x-ray phase contrast (XPC) imaging. XPC imaging opens CT to many new imaging applications because phase changes are more sensitive to density variations in soft tissues than standard absorption imaging. We further review the impact of deep learning on micro-CT. We feature several recent works which have successfully applied deep learning to micro-CT data, and we outline several challenges specific to micro-CT. All of these advancements establish micro-CT imaging at the forefront of preclinical research, able to provide anatomical, functional, and even molecular information while serving as a testbench for translational research.

Injector Effects on Hybrid Polymethylmethacrylate Combustion Assessed by Thermochemical Tomography

In this work, two representative hybrid rocket injector designs, a single-port and an axial showerhead design, were examined experimentally to determine the comparative influence on the development of the downstream combustion zone with polymethylmethacrylate (PMMA) fuel. One-dimensional laser absorption tomography was employed to obtain the thermochemical structure of the PMMA–gaseous oxygen reaction layer via quantitative in situ species and temperature measurements. Optical measurements were performed with tunable semiconductor lasers in the midwave infrared to target absorption features in the fundamental vibrational bands of CO, , and . Planar measurements were conducted at the exit plane of cylindrical fuel grains () at axial distances () ranging from 2 to 11 with a constant gaseous oxygen flow for each of the injectors. Assuming azimuthal symmetry, a Tikhonov-regularized Abel inversion technique was used to obtain the radially resolved absorption coefficient, from which temperature and mole fractions were extracted. One-dimensional measurements over all fuel-grain lengths were consolidated to obtain spatially resolved two-dimensional images of the reaction layer thermochemical structure in a hybrid rocket motor geometry. Significant variations in experimental results were observed between the two injectors, suggesting the importance of injection fluid dynamics in hybrid rocket combustion performance. Explanations of the variations are offered from both a theoretical and a computational analysis.

Development and application of a tender X-ray ptychographic coherent diffraction imaging system on BL27SU at SPring-8.

Ptychographic coherent diffraction imaging (CDI) allows the visualization of both the structure and chemical state of materials on the nanoscale, and has been developed for use in the soft and hard X-ray regions. In this study, a ptychographic CDI system with pinhole or Fresnel zone-plate optics for use in the tender X-ray region (2-5 keV) was developed on beamline BL27SU at SPring-8, in which high-precision pinholes optimized for the tender energy range were used to obtain diffraction intensity patterns with a low background, and a temperature stabilization system was developed to reduce the drift of the sample position. A ptychography measurement of a 200 nm thick tantalum test chart was performed at an incident X-ray energy of 2.500 keV, and the phase image of the test chart was successfully reconstructed with approximately 50 nm resolution. As an application to practical materials, a sulfur polymer material was measured in the range of 2.465 to 2.500 keV including the sulfur K absorption edge, and the phase and absorption images were successfully reconstructed and the nanoscale absorption/phase spectra were derived from images at multiple energies. In 3 GeV synchrotron radiation facilities with a low-emittance storage ring, the use of the present system will allow the visualization on the nanoscale of the chemical states of various light elements that play important roles in materials science, biology and environmental science.

Hyperspectral absorption microscopy using photoacoustic remote sensing.

An improved method of remote optical absorption spectroscopy and hyperspectral optical absorption imaging is described which takes advantage of the photoacoustic remote sensing detection architecture. A wide collection of photoacoustic excitation wavelengths ranging from 210 nm to 1550 nm was provided by a nanosecond tunable source allowing access to various salient endogenous chromophores such as DNA, hemeproteins, and lipids. Sensitivity of the device was demonstrated by characterizing the infrared absorption spectrum of water. Meanwhile, the efficacy of the technique was explored by recovering cell nuclei and oxygen saturation from a live chicken embryo model and by recovering adipocytes from freshly resected murine adipose tissue. This represents a continued investigation into the characteristics of the hyperspectral photoacoustic remote sensing technique which may represent an effective means of non-destructive endogenous contrast characterization and visualization.

Atom cloud detection and segmentation using a deep neural network

We use a deep neural network (NN) to detect and place region-of-interest (ROI) boxes around ultracold atom clouds in absorption and fluorescence images—with the ability to identify and bound multiple clouds within a single image. The NN also outputs segmentation masks that identify the size, shape and orientation of each cloud from which we extract the clouds’ Gaussian parameters. This allows 2D Gaussian fits to be reliably seeded thereby enabling fully automatic image processing. The method developed performs significantly better than a more conventional method based on a standardized image analysis library (Scikit-image) both for identifying ROI and extracting Gaussian parameters.

Single-shot x-ray phase-contrast and dark-field imaging based on coded binary phase mask

We introduce a coded-mask-based multi-contrast imaging method for high-resolution phase-contrast and dark-field imaging. The method uses a binary phase mask designed to provide an ultra-high-contrast pattern and reference-free single-shot measurement and an algorithm based on maximum-likelihood optimization and automatic differentiation to perform simultaneous reconstruction of absorption, phase, and dark-field object images. Further, we demonstrate that the method has great potential for real-time quantitative phase imaging and wavefront sensing when combined with deep learning.

Physics-trained neural network for sparse-view volumetric laser absorption imaging of species and temperature in reacting flows.

A deep learning method for laser absorption tomography was developed to effectively integrate physical priors related to flow-field thermochemistry and transport. Mid-fidelity reacting flow simulations were coupled with a forward molecular absorption model to train a deep neural network that performs the tomographic inversion of laser absorption images to predict temperature and species fields in flames. The method was evaluated through numerical simulation and experimental testing in benchtop laminar flames. The target flow-fields involved a spatially-convolved laminar ethylene-flame doublet, backlit with tunable radiation from a quantum cascade laser near 4.85 µm probing rovibrational absorption transitions of carbon monoxide. 2D images were collected at 11 different projection angles, yielding an aggregate of 50,688 unique lines of sight capturing the scene with a pixel resolution of approximately 70 µm. A convolutional neural network was introduced to efficiently generate temperature and species profiles and trained with a large dataset of large-eddy simulations of laminar flames at variable conditions. The learning-based approach to the inversion problem was found to more accurately predict species and temperature fields of the flame with fewer projection angles, reduce convergence time, and expand the field domain relative to classical linear tomography.

Snapshot three-dimensional absorption imaging of microscopic specimens.

Snapshot projection optical tomography (SPOT) uses a micro-lens array (MLA) to simultaneously capture the projection images of a three-dimensional (3D) specimen corresponding to different viewing directions. Compared to other light-field imaging techniques using an MLA, SPOT is dual telecentric and can block high-angle stray rays without sacrificing the light collection efficiency. Using SPOT, we recently demonstrated snapshot 3D fluorescence imaging. Here we demonstrate snapshot 3D absorption imaging of microscopic specimens. For the illumination, we focus the incoherent light from a light-emitting diode onto a pinhole, which is placed at a conjugate plane to the sample plane. SPOT allows us to capture the ray bundles passing through the specimen along different directions. The images recorded by an array of lenslets can be related to the projections of 3D absorption coefficient along the viewing directions of lenslets. Using a tomographic reconstruction algorithm, we obtain the 3D map of absorption coefficient. We apply the developed system to different types of samples, which demonstrates the optical sectioning capability. The transverse and axial resolutions measured with gold nanoparticles are 1.3 μm and 2.3 μm, respectively.

Linear multispectral absorption tomography based on regularized iterative methods.

A regularization approach of iterative algorithms was proposed to reconstruct the two-dimensional temperature and concentration distributions based on linear multispectral absorption tomography (MAT). This method introduces a secondary prior into a classical iterative algorithm via regularization to improve the reconstruction accuracy. Numerical studies revealed that the regularized iteration outperformed the classical and superiorized versions under various noisy conditions and with different number of spectral lines. The algorithms were also tested with the existing experimental data of a premixed flat flame produced by a McKenna burner. The comparison between the reconstructions and the measured temperature profile using thermocouples confirmed the superiority of our proposed regularized iterative method.

High-Resolution Imaging of Cold Atoms through a Multimode Fiber

We developed an ultra-compact high-resolution imaging system for cold atoms. Its only in-vacuum element is a multimode optical fiber with a diameter of $230\,\mu$m, which simultaneously collects light and guides it out of the vacuum chamber. External adaptive optics allow us to image cold Rb atoms with a $\sim 1\,\mu$m resolution over a $100 \times 100\,\mu$m$^2$ field of view. These optics can be easily rearranged to switch between fast absorption imaging and high-sensitivity fluorescence imaging. This system is particularly suited for hybrid quantum engineering platforms where cold atoms are combined with optical cavities, superconducting circuits or optomechanical devices restricting the optical access.