Parallel ptychographic reconstruction

Nashed, Youssef S. G.; Vine, D. J.; Peterka, Tom; Deng, Junjing; Ross, Rob; Jacobsen, Chris

doi:10.1364/oe.22.032082

Cited by 120 publications

(104 citation statements)

References 43 publications

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“…Before computing the FRC, the two phase images were aligned with subpixel precision using an efficient image method based on cross-correlation (66) and then were multiplied by a soft-edged mask (Tukey window) to avoid correlation from the image field boundaries. See Nashed et al (67).…”

Section: Methodsmentioning

confidence: 99%

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

Deng

Vine

Chen

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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159

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Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolution beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ∼90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context. ptychography | X-ray fluorescence microscopy | cryogenic biological samples X -ray fluorescence microscopy (XFM) offers unparalleled sensitivity for quantitative mapping of elements, especially trace metals which play a critical role in many biological processes (1-3). It is complementary to light microscopy, which can study some elemental content in live cells (with superresolution techniques possible) but which is more difficult to quantitate because it depends on the binding affinities of fluorophores. However, XFM does not usually show much cellular ultrastructure, because the light elements (such as H, C, N, and O, which are the main constituents of biological materials) have low fluorescence yield (4). At the multi-keV X-ray energies needed to excite most X-ray fluorescence lines of interest, these light elements show little absorption contrast, but phase contrast can be used to image cellular structure (5, 6) and this can be combined with scanned-beam XFM (7-11).One can also acquire phase-contrast X-ray images with a resolution beyond X-ray lens limits by recording the diffraction pattern from a coherently illuminated, noncrystalline sample in an approach called coherent diffraction imaging (CDI) (12). This approach has been used to image isolated dried cells (13-15), and 3-nm resolution has been achieved when imaging silver nanocubes (16). The traditional CDI approach requires that samples meet a so-called "finite support" (17) requirement with no observable scattering outside of a defined region; although some limited success has been obtained (18,19), this finite support condition has proven difficult to achieve with single cells surrounded by ice layers. Ptychography (20-22) is a recently realized CDI method [with an older history (23)] that circumvents this isolated cell requirement by instead scanning a limitedsize coherent illumination spot across the sample. Ptychography has been used to image freeze-dried diatoms at 30-nm resolution (24) and bacter...

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Section: Methodsmentioning

confidence: 99%

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

Deng

Vine

Chen

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

159

131

View full text Add to dashboard Cite

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“…Finally, we note that increased experimental throughput should be coupled with fast computing; one example is to use efficient parallelization schemes for ptychographic image reconstruction (Nashed et al, 2014).…”

Section: à4mentioning

confidence: 99%

Strategies for high-throughput focused-beam ptychography

Jacobsen

Deng

Nashed

2017

J Synchrotron Radiat

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X-ray ptychography is being utilized for a wide range of imaging experiments with a resolution beyond the limit of the X-ray optics used. Introducing a parameter for the ptychographic resolution gain G p (the ratio of the beam size over the achieved pixel size in the reconstructed image), strategies for data sampling and for increasing imaging throughput when the specimen is at the focus of an X-ray beam are considered. The tradeoffs between large and small illumination spots are examined.

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“…Data sets can be quite large and timeconsuming to process (ranging up to a Terabyte total for experiments carried out to date), so that unoptimized single-processor Python reconstruction codes could take up to 20 days for reconstruction. More recently, ptychographic reconstruction software has been developed at Argonne that uses graphical processing units (GPUs) to obtain about a hundred-fold speed-up processing data subsets, and a cluster of up to 128 GPU-equipped nodes to provide up to a 18,000-fold speed-up in aggregate reconstruction of a ptychographic image [10]. This allows reconstructed images to be made available to the experimenter within a few minutes, so that one can plan what region to image next (or change samples if the one under study is found to be problematic) while at the beamline.…”

Section: Ptychographymentioning

confidence: 99%

“…Unlike GSAS, which only performs fi tting to data, GSAS-II handles all aspects of diffraction data reduction and analysis and extends to small-angle scatter- : Multimode X-ray microscopy requires combinations of data from multiple sources. We show here a frozen hydrated Ostreococcus alga imaged at 5.2 keV, where X-ray fl uorescence maps of elemental composition (potassium, sulfur, and phosphorous) were recorded simulateously with X-ray ptychography data recorded using a pixelated array detector and reconstructed using a fast, parallelized code [10]. The lower right image shows an overlay with the psychographic reconstruction, which shows the light element ultrastructure not visible in X-ray fl uorescence [13].…”

Section: Gsas-ii: Crystallography and Small-angle Scatteringmentioning

confidence: 99%