Registration of phase-contrast images in propagation-based X-ray phase tomography

X-ray in-line holography and holotomography at the NanoMAX beamline

Coherent X-ray imaging techniques, such as in-line holography, exploit the high brilliance provided by diffraction-limited storage rings to perform imaging sensitive to the electron density through contrast due to the phase shift, rather than conventional attenuation contrast. Thus, coherent X-ray imaging techniques enable high-sensitivity and low-dose imaging, especially for low-atomic-number (Z) chemical elements and materials with similar attenuation contrast. Here, the first implementation of in-line holography at the NanoMAX beamline is presented, which benefits from the exceptional focusing capabilities and the high brilliance provided by MAX IV, the first operational diffraction-limited storage ring up to approximately 300 eV. It is demonstrated that in-line holography at NanoMAX can provide 2D diffraction-limited images, where the achievable resolution is only limited by the 70 nm focal spot at 13 keV X-ray energy. Also, the 3D capabilities of this instrument are demonstrated by performing holotomography on a chalk sample at a mesoscale resolution of around 155 nm. It is foreseen that in-line holography will broaden the spectra of capabilities of MAX IV by providing fast 2D and 3D electron density images from mesoscale down to nanoscale resolution.

PyPhase - a Python package for X-ray phase imaging

X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).

X-ray Phase Contrast osteo-articular imaging: a pilot study on cadaveric human hands

X-ray Phase Contrast Imaging (PCI) is an emerging modality whose availability in clinics for mammography and lung imaging is expected to materialize within the coming years. In this study, we evaluate the PCI Computed Tomography (PCI-CT) performances with respect to current conventional imaging modalities in the context of osteo-articular disorders diagnosis. X-ray PCI-CT was performed on 3 cadaveric human hands and wrists using a synchrotron beam. Conventional CT, MRI and Ultrasound were also performed on these three samples using routine procedures as well as research protocols. Six radiologists and rheumatologists independently evaluated qualitatively and semi quantitatively the 3D images' quality. Medical interpretations were also made from the images. PCI-CT allows the simultaneous visualization of both the high absorbing and the softer tissues. The 6 reader evaluations characterized PCI-CT as a visualization tool with improved performances for all tissue types (significant p-values), which provides sharper outlines and clearer internal structures than images obtained using conventional modalities. The PCI-CT images contain overall more information, especially at smaller scales with for instance more visible micro-calcifications in our chondrocalcinosis case. Despite a reduced number of samples used, this pilot study highlights the possible medical benefits of PCI for osteo-articular disorders evaluation. Although PCI-CT is not yet available in hospitals, the improved visualization capabilities demonstrated so far and the enhanced tissue measurement quality let suggest strong diagnosis benefits for rheumatology in case of a widespread application of PCI.

Nanoscopic X-ray imaging and quantification of the iron cellular architecture within single fibroblasts of Friedreich's ataxia patients

Friedreich's ataxia (FRDA) is a neurodegenerative disease characterized by an increase in intracytoplasmic iron concentration. Here the nanoscale iron distribution within single fibroblasts from FRDA patients was investigated using synchrotron-radiation-based nanoscopic X-ray fluorescence and X-ray in-line holography at the ID16A nano-imaging beamline of the ESRF. This unique probe was deployed to uncover the iron cellular two-dimensional architecture of freeze-dried FRDA fibroblasts. An unsurpassed absolute detection capability of 180 iron atoms within a 30 nm × 50 nm nanoscopic X-ray beam footprint was obtained using state-of-the-art X-ray focusing optics and a large-solid-angle detection system. Various micrometre-sized iron-rich organelles could be revealed for the first time, tentatively identified as endoplasmic reticulum, mitochondria and lysosomes. Also a multitude of nanoscopic iron hot-spots were observed in the cytosol, interpreted as chaperoned iron within the fibroblast's labile iron pool. These observations enable new hypotheses on the storage and trafficking of iron in the cell and ultimately to a better understanding of iron-storage diseases such as Friedreich's ataxia.

Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography

Propagation-based phase-contrast tomography has become a valuable tool for visualization of three-dimensional biological samples, due to its high sensitivity and its potential in providing increased contrast between materials with similar absorption properties. We present a statistical iterative reconstruction algorithm for this imaging technique in the near-field regime. Under the assumption of a single material, the propagation of the x-ray wavefield-relying on the transport-of-intensity equation-is made an integral part of the tomographic reconstruction problem. With a statistical approach acting directly on the measured intensities, we find an unconstrained nonlinear optimization formulation whose solution yields the three-dimensional distribution of the sample. This formulation not only omits the intermediate step of retrieving the projected thicknesses but also takes the statistical properties of the measurements into account and incorporates prior knowledge about the sample in the form of regularization techniques. We show some advantages of this integrated approach compared to two-step approaches on data obtained using a commercially available x-ray micro-tomography system. In particular, we address one of the most considerable challenges of the imaging technique, namely, the artifacts arising from samples containing highly absorbing features. With the use of statistical weights in our noise model, we can account for these materials and recover features in the vicinity of the highly absorbing features that are lost in the conventional two-step approaches. In addition, the statistical modeling of our reconstruction approach will prove particularly beneficial in the ongoing transition of this imaging technique from synchrotron facilities to laboratory setups.