A phase-retrieval toolbox for X-ray holography and tomography

Lohse, Leon Merten; Robisch, Anna-Lena; Töpperwien, Mareike; Maretzke, Simon; Krenkel, Martin; Hagemann, J.; Salditt, Tim

doi:10.1107/s1600577520002398

Cited by 76 publications

(96 citation statements)

References 53 publications

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“…Note that for a biological cell at the given photon energy, absorption can be neglected, and the cell can essentially be regarded as a pure phase object. In this study, a nonlinear approach of the contrast transfer function (CTF) was used for phase retrieval (47,48). The phase distribution in the object plane fðr t Þ retrieved by the linear form of the CTF is given by…”

Section: X-ray Tomographymentioning

confidence: 99%

X-Ray Structural Analysis of Single Adult Cardiomyocytes: Tomographic Imaging and Microdiffraction

Reichardt¹,

Neuhaus²,

Nicolas³

et al. 2020

Biophysical Journal

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We present a multiscale imaging approach to characterize the structure of isolated adult murine cardiomyocytes based on a combination of full-field three-dimensional coherent x-ray imaging and scanning x-ray diffraction. Using these modalities, we probe the structure from the molecular to the cellular scale. Holographic projection images on freeze-dried cells have been recorded using highly coherent and divergent x-ray waveguide radiation. Phase retrieval and tomographic reconstruction then yield the three-dimensional electron density distribution with a voxel size below 50 nm. In the reconstruction volume, myofibrils, sarcomeric organization, and mitochondria can be visualized and quantified within a single cell without sectioning. Next, we use microfocusing optics by compound refractive lenses to probe the diffraction signal of the actomyosin lattice. Comparison between recordings of chemically fixed and untreated, living cells indicate that the characteristic lattice distances shrink by $10% upon fixation.

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Section: X-ray Tomographymentioning

confidence: 99%

X-Ray Structural Analysis of Single Adult Cardiomyocytes: Tomographic Imaging and Microdiffraction

Reichardt¹,

Neuhaus²,

Nicolas³

et al. 2020

Biophysical Journal

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“…Secondly, a region of interest (ROI) scan was performed at propagation distances of 40, 41, 45 and 50 mm with a final voxel size of 50.21 nm. The phase retrieval and tomographic 3D image reconstruction was performed using the holotomography toolbox 21 in Matlab R2018b (The MathWorks Inc., USA). For each sample, the optimal phase retrieval algorithm was determined based on visual inspection.…”

Section: Methodsmentioning

confidence: 99%

“…For each sample, the optimal phase retrieval algorithm was determined based on visual inspection. These were either based on the contrast transfer function (CTF)-formalism 20,22 or on an implementation of the non-linear Tikhonov approximation 21,23 . Table 1 summarizes the selected algorithm and the ratio between phase shifting (δ) and absorbing (β) components of the index of refraction, i.e.…”

Section: Methodsmentioning

confidence: 99%

Nanotomographic evaluation of precipitate structure evolution in a Mg–Zn–Zr alloy during plastic deformation

Zeller‐Plumhoff

Robisch

Pelliccia³

et al. 2020

Sci Rep

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Magnesium and its alloys attract increasingly wide attention in various fields, ranging from transport to medical solutions, due to their outstanding structural and degradation properties. These properties can be tailored through alloying and thermo-mechanical processing, which is often complex and multi-step, thus requiring in-depth analysis. In this work, we demonstrate the capability of synchrotron-based nanotomographic X-ray imaging methods, namely holotomography and transmission X-ray microscopy, for the quantitative 3D analysis of the evolution of intermetallic precipitate (particle) morphology and distribution in magnesium alloy Mg–5.78Zn–0.44Zr subjected to a complex multi-step processing. A rich history of variation of the intermetallic particle structure in the processed alloy provided a testbed for challenging the analytical capabilities of the imaging modalities studied. The main features of the evolving precipitate structure revealed earlier by traditional light and electron microscopy methods were confirmed by the 3D techniques of synchrotron-based X-ray imaging. We further demonstrated that synchrotron-based X-ray imaging enabled uncovering finer details of the variation of particle morphology and number density at various stages of processing—above and beyond the information provided by visible light and electron microscopy.

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“…Note, that for a biological cell at the given photon energy, absorption can be neglected, and the cell can essentially be regarded as a pure phase object. In this study a nonlinear approach of the contrast transfer function (CTF) was used for phase retrieval (47,48). The phase distribution in the object plane (r ⊥ ) retrieved by the linear form of the CTF is given by…”

Section: X-ray Tomographymentioning

confidence: 99%

“…with natural units = for the (squared) spatial frequencies, measured intensities in the detector plane ( ) (r ⊥ ), ratio of imaginary and real part of the refractive index , N indicated the index of the respective distance and a frequency-dependent regularization parameter (k ⊥ ) (lim 1 for high and lim 2 for low spatial frequencies). The nonlinear approach uses the solution of the CTF as input for an iterative phase retrieval based on a minimization of the Tikhonov functional (47). Thus, the accuracy of the reconstructed phase is not less than the results of the CTF.…”

Section: X-ray Tomographymentioning

confidence: 99%

X-ray structural analysis of single adult cardiomyocytes: tomographic imaging and micro-diffraction

Reichardt¹,

Neuhaus²,

Nicolas³

et al. 2020

Preprint

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ABSTRACTWe present a multi-scale imaging approach to characterize the structure of isolated adult murine cardiomyocytes based on a combination of full-field three-dimensional (3d) coherent x-ray imaging and scanning x-ray diffraction. Using these modalities, we probe the structure from the molecular to the cellular scale. Holographic projection images on freeze-dried cells have been recorded using highly coherent and divergent x-ray waveguide radiation. Phase retrieval and tomographic reconstruction then yield the 3d electron density distribution with a voxel size below 50 nm. In the reconstruction volume, myofibrils, sarcomeric organisation and mitochondria can be visualized and quantified within a single cell without sectioning. Next, we use micro-focusing optics by compound refractive lenses to probe the diffraction signal of the acto-myosin lattice. Comparison between recordings of chemically fixed and untreated, living cells indicate that the characteristic lattice distances shrink by approximately 10% upon fixation.SIGNIFICANCEDiffraction with synchrotron radiation has played an important role to decipher the molecular structure underlying force generation in muscle. In this work, the diffraction signal of the actomyosin contractile unit has for the first time been recorded from living cardiomyocytes, bringing muscle diffraction to the scale of single cells. In addition to scanning diffraction, we use coherent optics at the same synchrotron endstation to perform holographic imaging and tomography on a single cardiomyocyte. By this hard x-ray microscopy modality, we extend the length scales covered by scanning diffraction and reconstruct the electron density of an entire freeze-dried cardiomyocyte, visualizing the 3d architecture of myofibrils, sarcomers, and mitochondria with a voxel size below 50 nm.

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A phase-retrieval toolbox for X-ray holography and tomography

Cited by 76 publications

References 53 publications

X-Ray Structural Analysis of Single Adult Cardiomyocytes: Tomographic Imaging and Microdiffraction

X-Ray Structural Analysis of Single Adult Cardiomyocytes: Tomographic Imaging and Microdiffraction

Nanotomographic evaluation of precipitate structure evolution in a Mg–Zn–Zr alloy during plastic deformation

X-ray structural analysis of single adult cardiomyocytes: tomographic imaging and micro-diffraction

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