Effects of missing low-frequency information on ptychographic and plane-wave coherent diffraction imaging

Recovery of spatial frequencies in coherent diffraction imaging in the presence of a central obscuration

Coherent diffraction imaging (CDI) and its scanning version, ptychography, are lensless imaging approaches used to iteratively retrieve a sample's complex scattering amplitude from its measured diffraction patterns. These imaging methods are most useful in extreme ultraviolet (EUV) and X-ray regions of the electromagnetic spectrum, where efficient imaging optics are difficult to manufacture. CDI relies on high signal-to-noise ratio diffraction data to recover the phase, but increasing the flux can cause saturation effects on the detector. A conventional solution to this problem is to place a beam stop in front of the detector. The pixel masking method is a common solution to the problem of missing frequencies due to a beam stop. This paper describes the information redundancy in the recorded data set and expands on how the reconstruction algorithm can exploit this redundancy to estimate the missing frequencies. Thereafter, we modify the size of the beam stop in experimental and simulation data to assess the impact of the missing frequencies, investigate the extent to which the lost portion of the diffraction spectrum can be recovered, and quantify the effect of the beam stop on the image quality. The experimental findings and simulations conducted for EUV imaging demonstrate that when using a beam stop, the numerical aperture of the condenser is a crucial factor in the recovery of lost frequencies. Our thorough investigation of the reconstructed images provides information on the overall quality of reconstruction and highlights the vulnerable frequencies if the beam stop size is larger than the extent of the illumination NA. The outcome of this study can be applied to other sources of frequency loss, and it will contribute to the improvement of experiments and reconstruction algorithms in CDI.

Soft X-ray spectro-ptychography of boron nitride nanobamboos, carbon nanotubes and permalloy nanorods

Spectro-ptychography offers improved spatial resolution and additional phase spectral information relative to that provided by scanning transmission X-ray microscopes. However, carrying out ptychography at the lower range of soft X-ray energies (e.g. below 200 eV to 600 eV) on samples with weakly scattering signals can be challenging. Here, results of soft X-ray spectro-ptychography at energies as low as 180 eV are presented, and its capabilities are illustrated with results from permalloy nanorods (Fe 2p), carbon nanotubes (C 1s) and boron nitride bamboo nanostructures (B 1s, N 1s). The optimization of low-energy X-ray spectro-ptychography is described and important challenges associated with measurement approaches, reconstruction algorithms and their effects on the reconstructed images are discussed. A method for evaluating the increase in radiation dose when using overlapping sampling is presented.

Initial probe function construction in ptychography based on zone-plate optics

X-ray ptychography is a popular variant of coherent diffraction imaging that offers ultrahigh resolution for extended samples. In x-ray ptychography instruments, the Fresnel zone-plate (FZP) is the most commonly used optical probe system for both soft x-ray and hard x-ray. In FZP-based ptychography with a highly curved defocus probe wavefront, the reconstructed image quality can be significantly impacted by the initial probe function form, necessitating the construction of a suitable initial probe for successful reconstruction. To investigate the effects of initial probe forms on FZP-based ptychography reconstruction, we constructed four single-mode initial probe models (IPMs) and three multi-mode IPMs in this study, and systematically compared their corresponding simulated and experimental reconstructions. The results show that the Fresnel IPM, spherical IPM, and Fresnel-based multi-mode IPMs can result in successful reconstructions for both near-focus and defocus cases, while random IPMs and constant IPMs work only for near-focus cases. Consequently, for FZP-based ptychography, the elaborately constructed IPMs that closely resemble real probes in wavefront phase form are more advantageous than natural IPMs such as the random or constant model. Furthermore, these IPMs with high phase similarity to the high-curvature large-sized probe adopted in experiments can help greatly improve ptychography experiment efficiency and decrease radiation damage to samples.

Quantitative toxicological study of dose-dependent arsenic-induced cells via synchrotron-based STXM and FTIR measurement

Inorganic arsenic (iAs) is a well-known naturally occurring metalloid with abundant hazards to our environment, especially being a human carcinogen through arsenic-contaminated drinking water. The iAs-related contamination is usually examined by a chemical assay system or fluorescence staining technique to investigate iAs accumulation and its deleterious effects. In this work, we present a dual-modality measurement and quantitative analysis methods for the overall evaluation of various dose-dependent iAs-related cytotoxicological manifestations by the combination of the synchrotron-radiation-based scanning transmission soft X-ray microscopy (SR-STXM) and Fourier transform infrared micro-spectroscopy (SR-FTIR) techniques. The gray level co-occurrence matrix (GLCM) based machine learning was employed on SR-STXM data to quantify the cytomorphological feature changes and the dose-dependent iAs-induced feature classifications with increasing doses. The infrared spectral absorption peaks and changes of dose-dependent iAs-induced cells were obtained by the SR-FTIR technique and classified by the multi-spectral-variate principle component analysis (PCA-LDA) method, showing the separated spatial distribution of dose-dependent groups. In addition, the quantitative comparisons of trivalent and pentavalent iAs under high dose conditions (iAs^III_H & iAs^V_H) demonstrated that iAs^III_H and its compounds were more toxic than iAs^V_H. This method has a potential in providing the morphological and spectral characteristics evolution of the iAs-related cells or particles, revealing the actual risk of arsenic contamination and metabolism.

X-ray ptychography using randomized zone plates

We have developed a randomized grating condenser zone plate (GCZP) that provides a µm-scale probe for use in x-ray ptychography. This delivers a significantly better x-ray throughput than probes defined by pinhole apertures, while providing a clearly-defined level of phase diversity to the illumination on the sample, and helping to reduce the dynamic range of the detected signal by spreading the zero-order light over an extended area of the detector. The first use of this novel x-ray optical element has been demonstrated successfully for both amplitude and phase contrast imaging using soft x-rays on the TwinMic beamline at the Elettra synchrotron.

Background noise removal in x-ray ptychography

Ptychography is a diffraction-based x-ray microscopy method that removes the resolution limit imposed by image-forming optical elements. However, background noise in the recorded diffraction patterns will degrade the reconstructed images and may cause reconstruction failure. Removal of the background noise from a ptychography dataset is an important but rather ambiguous prereconstruction data processing step because high-spatial-frequency diffraction signals are inevitably partly wiped out along with the noise. In this paper, several newly designed techniques for removing background noise from experimental ptychographic datasets are provided. Meanwhile, effects of residual background noise and high-frequency signal loss on reconstructed image quality are discussed in detail. The image quality is assessed quantitatively by the power spectral density analysis method and spatial resolution calculation. Both the simulated and experimental results indicate that the positive effect of noise removal by these methods clearly exceeds the negative effect of the accompanied high-spatial-frequency signal loss because part of the lost signals can be recovered by the improved consistencies between neighboring diffraction patterns by the noise removal.

Holography-guided ptychography with soft X-rays

Ptychography is a lensless imaging technique that aims to reconstruct an object from a set of coherent diffraction patterns originating from different and partially overlapping sample illumination areas. For a successful convergence of the iterative algorithms used, the sample scan positions have to be known with very high accuracy. Here, we present a method that allows to directly encode this information in the diffraction patterns without the need of accurate position encoders. Our approach relies on combining ptychography with another coherent imaging method, namely Fourier-transform holography. We have imaged two different objects using coherent soft-X-ray illumination and investigate the influence of experimental and numerical position refinement on the reconstruction result. We demonstrate that holographically encoded positions significantly reduce the experimental and numerical requirements. Our ptychographic reconstructions cover a large field of view with diffraction-limited resolution and high sensitivity in the reconstructed phase shift and absorption of the objects.

Spatial, spectral, and polarization multiplexed ptychography

We introduce a novel coherent diffraction imaging technique based on ptychography that enables simultaneous full-field imaging of multiple, spatially separate, sample locations. This technique only requires that diffracted light from spatially separated sample sites be mutually incoherent at the detector, which can be achieved using multiple probes that are separated either by wavelength or by orthogonal polarization states. This approach enables spatially resolved polarization spectroscopy from a single ptychography scan, as well as allowing a larger field of view to be imaged without loss in spatial resolution. Further, we compare the numerical efficiency of the multi-mode ptychography algorithm with a single mode algorithm.

Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs

We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium.

Ptychographic microscope for three-dimensional imaging

Ptychography is a coherent imaging technique that enables an image of a specimen to be generated from a set of diffraction patterns. One limitation of the technique is the assumption of a multiplicative interaction between the illuminating coherent beam and the specimen, which restricts ptychography to samples no thicker than a few tens of micrometers in the case of visible-light imaging at micron-scale resolution. By splitting a sample into axial sections, we demonstrated in recent work that this thickness restriction can be relaxed and whats-more, that coarse optical sectioning can be realized using a single ptychographic data set. Here we apply our technique to data collected from a modified optical microscope to realize a reduction in the optical sectioning depth to 2 μm in the axial direction for samples up to 150 μm thick. Furthermore, we increase the number of sections that are imaged from 5 in our previous work to 34 here. Our results compare well with sectioned images collected from a confocal microscope but have the added advantage of strong phase contrast, which removes the need for sample staining.