Phase-contrast x-ray imaging and tomography of the nematode Caenorhabditis elegans

Imaging cell morphology and physiology using X-rays

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.

Forward model for propagation-based x-ray phase contrast imaging in parallel- and cone-beam geometry

We demonstrate a fast, flexible, and accurate paraxial wave propagation model to serve as a forward model for propagation-based X-ray phase contrast imaging (XPCI) in parallel-beam or cone-beam geometry. This model incorporates geometric cone-beam effects into the multi-slice beam propagation method. It enables rapid prototyping and is well suited to serve as a forward model for propagation-based X-ray phase contrast tomographic reconstructions. Furthermore, it is capable of modeling arbitrary objects, including those that are strongly or multi-scattering. Simulation studies were conducted to compare our model to other forward models in the X-ray regime, such as the Mie and full-wave Rytov solutions.

Single-image phase retrieval for hard X-ray grating interferometry

A single-image method is proposed for quantitative phase retrieval in hard X-ray grating interferometry. This novel method assumes a quasi-homogeneous sample, with a constant ratio between the real and imaginary parts of its complex refractive index. The method is first theoretically derived and presented, and then validated by synchrotron radiation experiments. Compared with the phase-stepping method, the presented approach abandons grating scanning and multiple image acquisition, and is therefore advantageous in terms of its simplified acquisition procedure and reduced data-collection times, which are especially important for applications such as in vivo imaging and phase tomography. Moreover, the sample's phase image, instead of its first derivative, is directly retrieved. In particular, the stripe artifacts encountered in the integrated phase images are significantly suppressed. The improved quality of the retrieved phase images can be beneficial for image interpretation and subsequent processing. Owing to its requirement for a single image and its robustness against noise, the present method is expected to find use in potential investigations in diverse applications.

X-ray imaging of a water bear offers a new look at tardigrade internal anatomy

BACKGROUND

Tardigrades (water bears) are microscopic invertebrates of which the anatomy has been well studied using traditional techniques, but a comprehensive three-dimensional reconstruction has never been performed. In order to close this gap, we employed X-ray computed tomography (CT), a technique that is becoming increasingly popular in zoology for producing high-resolution, three-dimensional (3D) scans of whole specimens. While CT has long been used to scan larger samples, its use in some microscopic animals can be problematic, as they are often too small for conventional CT yet too large for high-resolution, optics-based soft X-ray microscopy. This size gap continues to be narrowed with advancements in technology, with high-resolution imaging now being possible using both large synchrotron devices and, more recently, laboratory-based instruments.

RESULTS

Here we use a recently developed prototype lab-based nano-computed tomography device to image a 152 μm-long tardigrade at high resolution (200-270 nm pixel size). The resulting dataset allowed us to visualize the anatomy of the tardigrade in 3D and analyze the spatial relationships of the internal structures. Segmentation of the major structures of the body enabled the direct measurement of their respective volumes. Furthermore, we segmented every storage cell individually and quantified their volume distribution. We compare our measurements to those from published studies in which other techniques were used.

CONCLUSIONS

The data presented herein demonstrate the utility of CT imaging as a powerful supplementary tool for studies of tardigrade anatomy, especially for quantitative volume measurements. This nanoCT study represents the smallest complete animal ever imaged using CT, and offers new 3D insights into the spatial relationships of the internal organs of water bears.

Single-image phase retrieval using an edge illumination X-ray phase-contrast imaging setup

A method is proposed which enables the retrieval of the thickness or of the projected electron density of a sample from a single input image acquired with an edge illumination phase-contrast imaging setup. The method assumes the case of a quasi-homogeneous sample, i.e. a sample with a constant ratio between the real and imaginary parts of its complex refractive index. Compared with current methods based on combining two edge illumination images acquired in different configurations of the setup, this new approach presents advantages in terms of simplicity of acquisition procedure and shorter data collection time, which are very important especially for applications such as computed tomography and dynamical imaging. Furthermore, the fact that phase information is directly extracted, instead of its derivative, can enable a simpler image interpretation and be beneficial for subsequent processing such as segmentation. The method is first theoretically derived and its conditions of applicability defined. Quantitative accuracy in the case of homogeneous objects as well as enhanced image quality for the imaging of complex biological samples are demonstrated through experiments at two synchrotron radiation facilities. The large range of applicability, the robustness against noise and the need for only one input image suggest a high potential for investigations in various research subjects.

Compound focusing mirror and X-ray waveguide optics for coherent imaging and nano-diffraction

A compound optical system for coherent focusing and imaging at the nanoscale is reported, realised by high-gain fixed-curvature elliptical mirrors in combination with X-ray waveguide optics or different cleaning apertures. The key optical concepts are illustrated, as implemented at the Göttingen Instrument for Nano-Imaging with X-rays (GINIX), installed at the P10 coherence beamline of the PETRA III storage ring at DESY, Hamburg, and examples for typical applications in biological imaging are given. Characteristic beam configurations with the recently achieved values are also described, meeting the different requirements of the applications, such as spot size, coherence or bandwidth. The emphasis of this work is on the different beam shaping, filtering and characterization methods.

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.

Phase retrieval through a one-dimensional ptychographic engine

Ptychographic techniques are currently the subject of increasing scientific interest due to their capability to retrieve the complex transmission function of an object at very high resolution. However, they impose a substantial burden in terms of acquisition time and dimension of the scanned area, which limits the range of samples that can be studied. We have developed a new method that combines the ptychographic approach in one direction with Fresnel propagation in the other by employing a strongly asymmetric probe. This enables scanning the sample in one direction only, substantially reducing exposure times while covering a large field of view. This approach sacrifices ptychographic-related resolution in one direction, but removes any limitation on the probe dimension in the direction orthogonal to the scanning, enabling the scan of relatively large objects without compromising exposure times.

Pulse-resolved multi-photon X-ray detection at 31 MHz based on a quadrant avalanche photodiode

The technical realisation and the commissioning experiments of a high-speed X-ray detector based on a quadrant avalanche silicon photodiode and high-speed digitizers are described. The development is driven by the need for X-ray detectors dedicated to time-resolved diffraction and imaging experiments, ideally requiring pulse-resolved data processing at the synchrotron bunch repetition rate. By a novel multi-photon detection scheme, the exact number of X-ray photons within each X-ray pulse can be recorded. Commissioning experiments at beamlines P08 and P10 of the storage ring PETRA III, at DESY, Hamburg, Germany, have been used to validate the pulse-wise multi-photon counting scheme at bunch frequencies ≥ 31 MHz, enabling pulse-by-pulse readout during the PETRA III 240-bunch mode with single-photon detection capability. An X-ray flux of ≥ 3.7 × 10(9) photons s(-1) can be detected while still resolving individual photons at low count rates.

Reconstruction of wave front and object for inline holography from a set of detection planes

We illustrate the errors inherent in the conventional empty beam correction of full field X-ray propagation imaging, i.e. the division of intensities in the detection plane measured with an object in the beam by the intensity pattern measured without the object, i.e. the empty beam intensity pattern. The error of this conventional approximation is controlled by the ratio of the source size to the smallest feature in the object, as is shown by numerical simulation. In a second step, we investigate how to overcome the flawed empty beam division by simultaneous reconstruction of the probing wavefront (probe) and of the object, based on measurements in several detection planes (multi-projection approach). The algorithmic scheme is demonstrated numerically and experimentally, using the defocus wavefront of the hard X-ray nanoprobe setup at the European Synchrotron Radiation Facility (ESRF).

Versatility of a hard X-ray Kirkpatrick-Baez focus characterized by ptychography

In the past decade Kirkpatrick-Baez (KB) mirrors have been established as powerful focusing systems in hard X-ray microscopy applications. Here a ptychographic characterization of the KB focus in the dedicated nano-imaging setup GINIX (Göttingen Instrument for Nano-Imaging with X-rays) at the P10 coherence beamline of the PETRA III synchrotron at HASLYLAB/DESY, Germany, is reported. More specifically, it is shown how aberrations in the KB beam, caused by imperfections in the height profile of the focusing mirrors, can be eliminated using a pinhole as a spatial filter near the focal plane. A combination of different pinhole sizes and illumination conditions of the KB setup makes the prepared optical setup well suited not only for high-resolution ptychographic coherent X-ray diffractive imaging but also for moderate-resolution/large-field-of-view propagation imaging in the divergent KB beam.

Efficient focusing of 8 keV X-rays with multilayer Fresnel zone plates fabricated by atomic layer deposition and focused ion beam milling

Fresnel zone plates (FZPs) recently showed significant improvement by focusing soft X-rays down to ~10 nm. In contrast to soft X-rays, generally a very high aspect ratio FZP is needed for efficient focusing of hard X-rays. Therefore, FZPs had limited success in the hard X-ray range owing to difficulties of manufacturing high-aspect-ratio zone plates using conventional techniques. Here, employing a method of fabrication based on atomic layer deposition (ALD) and focused ion beam (FIB) milling, FZPs with very high aspect ratios were prepared. Such multilayer FZPs with outermost zone widths of 10 and 35 nm and aspect ratios of up to 243 were tested for their focusing properties at 8 keV and shown to focus hard X-rays efficiently. This success was enabled by the outstanding layer quality thanks to ALD. Via the use of FIB for slicing the multilayer structures, desired aspect ratios could be obtained by precisely controlling the thickness. Experimental diffraction efficiencies of multilayer FZPs fabricated via this combination reached up to 15.58% at 8 keV. In addition, scanning transmission X-ray microscopy experiments at 1.5 keV were carried out using one of the multilayer FZPs and resolved a 60 nm feature size. Finally, the prospective of different material combinations with various outermost zone widths at 8 and 17 keV is discussed in the light of the coupled wave theory and the thin-grating approximation. Al2O3/Ir is outlined as a promising future material candidate for extremely high resolution with a theoretical efficiency of more than 20% for as small an outermost zone width as 10 nm at 17 keV.

Transport of intensity phase reconstruction to solve the twin image problem in holographic x-ray imaging

We have implemented a deterministic method for solving the phase problem in hard x-ray in-line holography which overcomes the twin image problem. The phase distribution in the detector plane is retrieved by using two images with slightly different Fresnel numbers. We then use measured intensities and reconstructed phases in the detection plane to compute the exit wave in the sample plane. No further a priori information like a limited support or the assumption of pure phase objects is necessary so that it can be used for a wide range of complex samples. Using a nano-focused hard x-ray beam half period resolutions better than 30 nm are achieved.