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Aidukas T, Phillips NW, Diaz A, Poghosyan E, Müller E, Levi AFJ, Aeppli G, Guizar-Sicairos M, Holler M. High-performance 4-nm-resolution X-ray tomography using burst ptychography. Nature 2024; 632:81-88. [PMID: 39085541 DOI: 10.1038/s41586-024-07615-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 05/28/2024] [Indexed: 08/02/2024]
Abstract
Advances in science, medicine and engineering rely on breakthroughs in imaging, particularly for obtaining multiscale, three-dimensional information from functional systems such as integrated circuits or mammalian brains. Achieving this goal often requires combining electron- and photon-based approaches. Whereas electron microscopy provides nanometre resolution through serial, destructive imaging of surface layers1, ptychographic X-ray computed tomography2 offers non-destructive imaging and has recently achieved resolutions down to seven nanometres for a small volume3. Here we implement burst ptychography, which overcomes experimental instabilities and enables much higher performance, with 4-nanometre resolution at a 170-times faster acquisition rate, namely, 14,000 resolution elements per second. Another key innovation is tomographic back-propagation reconstruction4, allowing us to image samples up to ten times larger than the conventional depth of field. By combining the two innovations, we successfully imaged a state-of-the-art (seven-nanometre node) commercial integrated circuit, featuring nanostructures made of low- and high-density materials such as silicon and metals, which offer good radiation stability and contrast at the selected X-ray wavelength. These capabilities enabled a detailed study of the chip's design and manufacturing, down to the level of individual transistors. We anticipate that the combination of nanometre resolution and higher X-ray flux at next-generation X-ray sources will have a revolutionary impact in fields ranging from electronics to electrochemistry and neuroscience.
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Affiliation(s)
| | - Nicholas W Phillips
- Paul Scherrer Institute, Villigen, Switzerland
- Mineral Resources, CSIRO, Clayton, Victoria, Australia
| | - Ana Diaz
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | - A F J Levi
- Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Gabriel Aeppli
- Paul Scherrer Institute, Villigen, Switzerland
- Department of Physics, Eidgenössische Technische Hochschule Zürich (ETH Zürich), Zurich, Switzerland
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Quantum Center, Eidgenössische Technische Hochschule Zürich (ETH Zürich), Zurich, Switzerland
| | - Manuel Guizar-Sicairos
- Paul Scherrer Institute, Villigen, Switzerland
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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2
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Vom Scheidt A, Krug J, Goggin P, Bakker AD, Busse B. 2D vs. 3D Evaluation of Osteocyte Lacunae - Methodological Approaches, Recommended Parameters, and Challenges: A Narrative Review by the European Calcified Tissue Society (ECTS). Curr Osteoporos Rep 2024:10.1007/s11914-024-00877-z. [PMID: 38980532 DOI: 10.1007/s11914-024-00877-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/10/2024]
Abstract
PURPOSE OF REVIEW Quantification of the morphology of osteocyte lacunae has become a powerful tool to investigate bone metabolism, pathologies and aging. This review will provide a brief overview of 2D and 3D imaging methods for the determination of lacunar shape, orientation, density, and volume. Deviations between 2D-based and 3D-based lacunar volume estimations are often not sufficiently addressed and may give rise to contradictory findings. Thus, the systematic error arising from 2D-based estimations of lacunar volume will be discussed, and an alternative calculation proposed. Further, standardized morphological parameters and best practices for sampling and segmentation are suggested. RECENT FINDINGS We quantified the errors in reported estimation methods of lacunar volume based on 2D cross-sections, which increase with variations in lacunar orientation and histological cutting plane. The estimations of lacunar volume based on common practice in 2D imaging methods resulted in an underestimation of lacunar volume of up to 85% compared to actual lacunar volume in an artificial dataset. For a representative estimation of lacunar size and morphology based on 2D images, at least 400 lacunae should be assessed per sample.
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Affiliation(s)
- Annika Vom Scheidt
- Division of Macroscopic and Clinical Anatomy, Gottfried Schatz Research Center, Medical University of Graz, Auenbruggerplatz 25, Graz, 8036, Austria.
| | - Johannes Krug
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 55a, 22529, Hamburg, Germany
- Interdisciplinary Competence Center for Interface Research, University Medical Center Hamburg-Eppendorf, Butenfeld 34, 22529, Hamburg, Germany
| | - Patricia Goggin
- Biomedical Imaging Unit, Laboratory and Pathology Block, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Astrid Diana Bakker
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), Amsterdam Movement Sciences, University of Amsterdam and Vrije Universiteit Amsterdam, Gustav Mahlerlaan, Amsterdam, 3004, 1081 LA, The Netherlands
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 55a, 22529, Hamburg, Germany
- Interdisciplinary Competence Center for Interface Research, University Medical Center Hamburg-Eppendorf, Butenfeld 34, 22529, Hamburg, Germany
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3
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Loetgering L, Du M, Boonzajer Flaes D, Aidukas T, Wechsler F, Penagos Molina DS, Rose M, Pelekanidis A, Eschen W, Hess J, Wilhein T, Heintzmann R, Rothhardt J, Witte S. PtyLab.m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and Fourier ptychography. OPTICS EXPRESS 2023; 31:13763-13797. [PMID: 37157257 DOI: 10.1364/oe.485370] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Conventional (CP) and Fourier (FP) ptychography have emerged as versatile quantitative phase imaging techniques. While the main application cases for each technique are different, namely lens-less short wavelength imaging for CP and lens-based visible light imaging for FP, both methods share a common algorithmic ground. CP and FP have in part independently evolved to include experimentally robust forward models and inversion techniques. This separation has resulted in a plethora of algorithmic extensions, some of which have not crossed the boundary from one modality to the other. Here, we present an open source, cross-platform software, called PtyLab, enabling both CP and FP data analysis in a unified framework. With this framework, we aim to facilitate and accelerate cross-pollination between the two techniques. Moreover, the availability in Matlab, Python, and Julia will set a low barrier to enter each field.
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4
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Towards routine 3D characterization of intact mesoscale samples by multi-scale and multimodal scanning X-ray tomography. Sci Rep 2022; 12:16924. [PMID: 36209291 PMCID: PMC9547857 DOI: 10.1038/s41598-022-21368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
Non-invasive multi-scale and multimodal 3D characterization of heterogeneous or hierarchically structured intact mesoscale samples is of paramount importance in tackling challenging scientific problems. Scanning hard X-ray tomography techniques providing simultaneous complementary 3D information are ideally suited to such studies. However, the implementation of a robust on-site workflow remains the bottleneck for the widespread application of these powerful multimodal tomography methods. In this paper, we describe the development and implementation of such a robust, holistic workflow, including semi-automatic data reconstruction. Due to its flexibility, our approach is especially well suited for on-the-fly tuning of the experiments to study features of interest progressively at different length scales. To demonstrate the performance of the method, we studied, across multiple length scales, the elemental abundances and morphology of two complex biological systems, Arabidopsis plant seeds and mouse renal papilla samples. The proposed approach opens the way towards routine multimodal 3D characterization of intact samples by providing relevant information from pertinent sample regions in a wide range of scientific fields such as biology, geology, and material sciences.
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5
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Holler M, Aidukas T, Heller L, Appel C, Phillips NW, Müller-Gubler E, Guizar-Sicairos M, Raabe J, Ihli J. Environmental control for X-ray nanotomography. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1223-1231. [PMID: 36073881 PMCID: PMC9455200 DOI: 10.1107/s1600577522006968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
The acquisition speed and spatial resolution of X-ray nanotomography have continuously improved over the last decades. Coherent diffraction-based techniques breach the 10 nm resolution barrier frequently and thus pose stringent demands on sample positioning accuracy and stability. At the same time there is an increasing desire to accommodate in situ or operando measurements. Here, an environmental control system for X-ray nanotomography is introduced to regulate the temperature of a sample from room temperature up to 850°C in a controlled atmospheric composition. The system allows for a 360° sample rotation, permitting tomographic studies in situ or operando free of missing wedge constraints. The system is implemented and available at the flOMNI microscope at the Swiss Light Source. In addition to the environmental control system itself, the related modifications of flOMNI are described. Tomographic measurements of a nanoporous gold sample at 50°C and 600°C at a resolution of sub-20 nm demonstrate the performance of the device.
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Affiliation(s)
- Mirko Holler
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
| | - Tomas Aidukas
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
| | - Lars Heller
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
| | - Christian Appel
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
| | - Nicholas W. Phillips
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
| | | | | | - Jörg Raabe
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
| | - Johannes Ihli
- Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, Aargau 5232, Switzerland
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Deng J, Yao Y, Jiang Y, Chen S, Mooney TM, Klug JA, Marin FS, Roehrig C, Yue K, Preissner C, Cai Z, Lai B, Vogt S. High-resolution ptychographic imaging enabled by high-speed multi-pass scanning. OPTICS EXPRESS 2022; 30:26027-26042. [PMID: 36236801 DOI: 10.1364/oe.460232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
As a coherent diffraction imaging technique, ptychography provides high-spatial resolution beyond Rayleigh's criterion of the focusing optics, but it is also sensitively affected by the decoherence coming from the spatial and temporal variations in the experiment. Here we show that high-speed ptychographic data acquisition with short exposure can effectively reduce the impact from experimental variations. To reach a cumulative dose required for a given resolution, we further demonstrate that a continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is shown to be more dose-efficient, and has potential for radiation-sensitive sample studies and time-resolved imaging.
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7
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Pande K, Donatelli JJ, Parkinson DY, Yan H, Sethian JA. Joint iterative reconstruction and 3D rigid alignment for X-ray tomography. OPTICS EXPRESS 2022; 30:8898-8916. [PMID: 35299332 PMCID: PMC8970703 DOI: 10.1364/oe.443248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.
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Affiliation(s)
- K. Pande
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - J. J. Donatelli
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Mathematics, Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - D. Y. Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - H. Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - J. A. Sethian
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Mathematics, Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Mathematics, University of California, Berkeley, CA 94720, USA
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8
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Renders J, Sijbers J, De Beenhouwer J. Adjoint image warping using multivariate splines with application to four-dimensional computed tomography. Med Phys 2021; 48:6362-6374. [PMID: 34407210 PMCID: PMC9291926 DOI: 10.1002/mp.14765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 11/11/2022] Open
Abstract
Purpose Adjoint image warping is an important tool to solve image reconstruction problems that warp the unknown image in the forward model. This includes four‐dimensional computed tomography (4D‐CT) models in which images are compared against recorded projection images of various time frames using image warping as a model of the motion. The inversion of these models requires the adjoint of image warping, which up to now has been substituted by approximations. We introduce an efficient implementation of the exact adjoints of multivariate spline based image warping, and compare it against previously used alternatives. Methods Using symbolic computer algebra, we computed a list of 64 polynomials that allow us to compute a matrix representation of trivariate cubic image warping. By combining an on‐the‐fly computation of this matrix with a parallelized implementation of columnwise matrix multiplication, we obtained an efficient, low memory implementation of the adjoint action of 3D cubic image warping. We used this operator in the solution of a previously proposed 4D‐CT reconstruction model in which the image of a single subscan was compared against projection data of multiple subscans by warping and then projecting the image. We compared the properties of our exact adjoint with those of approximate adjoints by warping along inverted motion. Results Our method requires halve the memory to store motion between subscans, compared to methods that need to compute and store an approximate inverse of the motion. It also avoids the computation time to invert the motion and the tunable parameter of the number of iterations used to perform this inversion. Yet, a similar and often better reconstruction quality was obtained in comparison with these more expensive methods, especially when the motion is large. When compared against a simpler method that is similar to ours in computational demands, our method achieves a higher reconstruction quality in general. Conclusions Our implementation of the exact adjoint of cubic image warping improves efficiency and provides accurate reconstructions.
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Affiliation(s)
- Jens Renders
- imec-Vision Lab, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Jan Sijbers
- imec-Vision Lab, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Jan De Beenhouwer
- imec-Vision Lab, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
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Du M, Kandel S, Deng J, Huang X, Demortiere A, Nguyen TT, Tucoulou R, De Andrade V, Jin Q, Jacobsen C. Adorym: a multi-platform generic X-ray image reconstruction framework based on automatic differentiation. OPTICS EXPRESS 2021; 29:10000-10035. [PMID: 33820138 PMCID: PMC8237934 DOI: 10.1364/oe.418296] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 05/09/2023]
Abstract
We describe and demonstrate an optimization-based X-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Saugat Kandel
- Applied Physics Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Junjing Deng
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Arnaud Demortiere
- Laboratoire de Réactivité et Chimie des Solides (LRCS), CNRS UMR 7314, Université de Picardie Jules Verne, Hub de l’Energie, 15 Rue Baudelocque, 80039 Amiens Cedex, France
| | - Tuan Tu Nguyen
- Laboratoire de Réactivité et Chimie des Solides (LRCS), CNRS UMR 7314, Université de Picardie Jules Verne, Hub de l’Energie, 15 Rue Baudelocque, 80039 Amiens Cedex, France
| | - Remi Tucoulou
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Vincent De Andrade
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Qiaoling Jin
- Department of Physics & Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Department of Physics & Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
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10
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Improving image quality in fast, time-resolved micro-CT by weighted back projection. Sci Rep 2020; 10:18029. [PMID: 33093571 PMCID: PMC7581769 DOI: 10.1038/s41598-020-74827-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 09/24/2020] [Indexed: 11/29/2022] Open
Abstract
Time-resolved micro-CT is an increasingly powerful technique for studying dynamic processes in materials and structures. However, it is still difficult to study very fast processes with this technique, since fast scanning is typically associated with high image noise levels. We present weighted back projection, a technique applicable in iterative reconstruction methods using two types of prior knowledge: (1) a virtual starting volume resembling the sample, for example obtained from a scan before the dynamic process was initiated, and (2) knowledge on which regions in the sample are more likely to undergo the dynamic process. Therefore, processes on which this technique is applicable are preferably occurring within a static grid. Weighted back projection has the ability to handle small errors in the prior knowledge, while similar 4D micro-CT techniques require the prior knowledge to be exactly correct. It incorporates the prior knowledge within the reconstruction by using a weight volume, representing for each voxel its probability of undergoing the dynamic process. Qualitative analysis on a sparse subset of projection data from a real micro-CT experiment indicates that this method requires significantly fewer projection angles to converge to a correct volume. This can lead to an improved temporal resolution.
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11
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Goethals W, Vanbillemont B, Lammens J, De Beer T, Vervaet C, Boone MN. In-Situ X-ray Imaging Of Sublimating Spin-Frozen Solutions. MATERIALS 2020; 13:ma13132953. [PMID: 32630310 PMCID: PMC7378758 DOI: 10.3390/ma13132953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 11/28/2022]
Abstract
Spin-freeze-drying is a promising technique to enable long-term storage of pharmaceutical unit doses of aqueous drug solutions. To investigate the sublimation of the ice during the primary phase of freeze-drying, X-ray imaging can yield crucial temporally resolved information on the local dynamics. In this paper, we describe a methodology to investigate the sublimation front during single unit-dose freeze-drying using 4D in-situ X-ray imaging. Three spin-frozen samples of different solutions were imaged using this methodology and the process characteristics were analysed and reduced to two-dimensional feature maps.
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Affiliation(s)
- Wannes Goethals
- Department of Physics and Astronomy, Radiation Physics, Ghent University, Proeftuinstraat 86/N12, B-9000 Gent, Belgium;
- Centre for X-ray Tomography (UGCT), Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
- Correspondence:
| | - Brecht Vanbillemont
- Laboratory of Pharmaceutical Process Analytical Technology (LPPAT), Department of Pharmaceutical Analysis, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (B.V.); (T.D.B.)
| | - Joris Lammens
- Laboratory of Pharmaceutical Technology, Department of Pharmaceutics, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (J.L.); (C.V.)
| | - Thomas De Beer
- Laboratory of Pharmaceutical Process Analytical Technology (LPPAT), Department of Pharmaceutical Analysis, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (B.V.); (T.D.B.)
| | - Chris Vervaet
- Laboratory of Pharmaceutical Technology, Department of Pharmaceutics, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (J.L.); (C.V.)
| | - Matthieu N. Boone
- Department of Physics and Astronomy, Radiation Physics, Ghent University, Proeftuinstraat 86/N12, B-9000 Gent, Belgium;
- Centre for X-ray Tomography (UGCT), Ghent University, Proeftuinstraat 86, B-9000 Gent, Belgium
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12
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Odstrčil M, Holler M, Raabe J, Guizar-Sicairos M. Alignment methods for nanotomography with deep subpixel accuracy. OPTICS EXPRESS 2019; 27:36637-36652. [PMID: 31873438 DOI: 10.1364/oe.27.036637] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits methods with deep-subpixel accuracy combined with a multi-resolution scheme. This leads to robust and accurate alignment with significantly reduced computational and memory requirements. The performance of the presented methods is demonstrated on simulated and measured datasets for tomography and also laminography acquisition geometries. A GPU accelerated implementation of our alignment framework is publicly available.
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