Influence of finite spatial coherence on ptychographic reconstruction

Stachnik, Karolina; Mohácsi, István; Vartiainen, Ismo; Stuebe, Nicolas; Meyer, Jan; Warmer, Martin; Dávid, Christian; Meents, A.

doi:10.1063/1.4926328

Cited by 18 publications

(10 citation statements)

References 25 publications

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“…The characteristics of the three MX beamlines at PETRA III are summarized in Table 1. 2.2. Beamline P11 @ DESY DESY beamline P11 provides two state-of-the-art endstations for structural investigations of biological samples at different length scales: an X-ray microscope with a resolution of up to 10 nm [9,10,11] and a crystallography experiment. The crystallography endstation (shown in Figure 2) is operated between 5.5 keV and 30 keV and provides full SAD/MAD capability.…”

Section: 1overviewmentioning

confidence: 99%

Status of the crystallography beamlines at PETRA III

et al. 2016

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Since 2013, three beamlines for macromolecular crystallography are available to users at the thirdgeneration synchrotron PETRA III in Hamburg: P11, P13 and P14, the latter two operated by EMBL. Beamline P11 is operated by DESY and is equipped with a Pilatus 6M detector. Together with the photon flux of 2 × 10 13 ph/s provided by the very brilliant X-ray source of PETRA III, a full data set can be typically collected in less than 2 min. P11 provides state-of-the-art microfocusing capabilities with beam sizes down to 1 × 1 µm 2 , which makes the beamline ideally suited for investigation of microcrystals and serial crystallography experiments. An automatic sample changer allows fast sample exchange in less than 20 s, which enables high-throughput crystallography and fast crystal screening. For sample preparation, an S2 biosafety laboratory is available in close proximity to the beamline.

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Section: 1overviewmentioning

confidence: 99%

Status of the crystallography beamlines at PETRA III

et al. 2016

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“…We used a self-developed scanning transmission X-ray microscope at photon energies slightly above Fe K absorption edge (7.112 keV), which is explained in detail in Supplementary Method 5. Horizontal spatial coherence was enhanced by defocussing the X-ray beam with convexly bent horizontally deflecting X-ray mirrors that are components of P11 optics 57 .…”

Section: Methodsmentioning

confidence: 99%

Multimodal X-ray imaging of nanocontainer-treated macrophages and calcium distribution in the perilacunar bone matrix

Stachnik

Warmer

Mohácsi

et al. 2020

Sci Rep

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Studies of biological systems typically require the application of several complementary methods able to yield statistically-relevant results at a unique level of sensitivity. Combined X-ray fluorescence and ptychography offer excellent elemental and structural imaging contrasts at the nanoscale. They enable a robust correlation of elemental distributions with respect to the cellular morphology. Here we extend the applicability of the two modalities to higher X-ray excitation energies, permitting iron mapping. Using a long-range scanning setup, we applied the method to two vital biomedical cases. We quantified the iron distributions in a population of macrophages treated with Mycobacteriumtuberculosis-targeting iron-oxide nanocontainers. Our work allowed to visualize the internalization of the nanocontainer agglomerates in the cytosol. From the iron areal mass maps, we obtained a distribution of antibiotic load per agglomerate and an average areal concentration of nanocontainers in the agglomerates. In the second application we mapped the calcium content in a human bone matrix in close proximity to osteocyte lacunae (perilacunar matrix). A concurrently acquired ptychographic image was used to remove the mass-thickness effect from the raw calcium map. The resulting ptychographyenhanced calcium distribution allowed then to observe a locally lower degree of mineralization of the perilacunar matrix. Metal ions play an important role in the vital functions of living organisms. They are present in various biological systems in a vast range of concentrations as structural, electrolyte (minor), and trace elements. From being major tissue components (e.g. Ca in bones) to constituents of essential biological molecules (e.g. Fe in hemoglobin), metals take part in the majority of extra-and intracellular processes. In particular, first-row transition metals (Mn, Fe, Cu, Ni, Zn)-despite their minute concentrations-are involved in sub-cellular processes. Moreover, their abnormal accumulation in human brain was correlated with mechanisms leading to neurodegeneration diseases such as Parkinson's and Alzheimer's 1-3. Metal compounds have also been utilized as novel drug delivery systems by addressing metabolic properties of bacterial agents 4,5 or as more efficient medical imaging markers tracking tissue of interest 6-8. In all aforementioned cases, studies of metal contributions require knowledge of their quantitative spatial distributions with respect to the sub-cellular structure. Electron-probe Energy-Dispersive Spectroscopy offers elemental mapping at nanometer-range spatial resolutions and high excitation efficiency in the low-Z-element

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“…However, low coherence, similarly to setup vibrations or insufficient diffraction sampling, leads to loss of speckle visibility. Therefore the actual quality improvement provided by the additional flux of a low coherence illumination could be smaller than the expected value or even counterproductive 38 . On the other hand, one should not use more coherence than needed 32 as this leads to unnecessary filtering of the incoming intensity and decrease of the signal-to-noise ratio, an optimum has to be found.…”

Section: Scanning Precisionmentioning

confidence: 96%

High resolution 3D imaging of integrated circuits by x-ray ptychography

Odstrčil

Holler

Raabe

et al. 2018

Image Sensing Technologies: Materials, Devices, Systems, and Applications V

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Significant advances in lithography and chip manufacturing in recent years have resulted in new challenges in metrology of electronic microdevices. Manufacturing process for the 10 nm node is already available and in combination with complex three-dimensional structured interconnections, there is a lack of methods for verification that the final products correspond to the original specifications. X-ray ptycho-tomography is a locally nondestructive imaging method that could potentially help to fill the gap between electron microscopy and conventional X-ray tomography. Quantitativeness of ptycho-tomography provides detailed device geometries and corresponding sensitivity to elemental composition through the complex-valued refractive index. In order to tackle the experimental challenges and improve the imaging quality, new computational methods need to be developed for both ptychography and tomography that can account for a wide range of imperfections such as sample drifts, illumination changes or sample changes during the scan. Here, we will mention the most important of them and possible ways how to deal with them.

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Influence of finite spatial coherence on ptychographic reconstruction

Cited by 18 publications

References 25 publications

Status of the crystallography beamlines at PETRA III

Status of the crystallography beamlines at PETRA III

Multimodal X-ray imaging of nanocontainer-treated macrophages and calcium distribution in the perilacunar bone matrix

High resolution 3D imaging of integrated circuits by x-ray ptychography

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