Literature DB >> 33820138

Adorym: a multi-platform generic X-ray image reconstruction framework based on automatic differentiation.

Ming Du, Saugat Kandel, Junjing Deng, Xiaojing Huang, Arnaud Demortiere, Tuan Tu Nguyen, Remi Tucoulou, Vincent De Andrade, Qiaoling Jin, Chris Jacobsen.   

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.

Entities:  

Year:  2021        PMID: 33820138      PMCID: PMC8237934          DOI: 10.1364/OE.418296

Source DB:  PubMed          Journal:  Opt Express        ISSN: 1094-4087            Impact factor:   3.894


  51 in total

1.  Invited article: a [corrected] unified evaluation of iterative projection algorithms for phase retrieval.

Authors:  S Marchesini
Journal:  Rev Sci Instrum       Date:  2007-01       Impact factor: 1.523

2.  Phase retrieval and Zernike decomposition using measured intensity data and the estimated electric field.

Authors:  John C Zingarelli; Stephen C Cain
Journal:  Appl Opt       Date:  2013-11-01       Impact factor: 1.980

3.  Continuous scanning mode for ptychography.

Authors:  Jesse N Clark; Xiaojing Huang; Ross J Harder; Ian K Robinson
Journal:  Opt Lett       Date:  2014-10-15       Impact factor: 3.776

4.  Parallel ptychographic reconstruction.

Authors:  Youssef S G Nashed; David J Vine; Tom Peterka; Junjing Deng; Rob Ross; Chris Jacobsen
Journal:  Opt Express       Date:  2014-12-29       Impact factor: 3.894

5.  Noise models for low counting rate coherent diffraction imaging.

Authors:  Pierre Godard; Marc Allain; Virginie Chamard; John Rodenburg
Journal:  Opt Express       Date:  2012-11-05       Impact factor: 3.894

6.  An annealing algorithm to correct positioning errors in ptychography.

Authors:  A M Maiden; M J Humphry; M C Sarahan; B Kraus; J M Rodenburg
Journal:  Ultramicroscopy       Date:  2012-06-13       Impact factor: 2.689

7.  Fly-scan ptychography.

Authors:  Xiaojing Huang; Kenneth Lauer; Jesse N Clark; Weihe Xu; Evgeny Nazaretski; Ross Harder; Ian K Robinson; Yong S Chu
Journal:  Sci Rep       Date:  2015-03-13       Impact factor: 4.379

8.  Multi-slice ptychographic tomography.

Authors:  Peng Li; Andrew Maiden
Journal:  Sci Rep       Date:  2018-02-01       Impact factor: 4.379

9.  Three-dimensional single-cell imaging with X-ray waveguides in the holographic regime.

Authors:  Martin Krenkel; Mareike Toepperwien; Frauke Alves; Tim Salditt
Journal:  Acta Crystallogr A Found Adv       Date:  2017-06-29       Impact factor: 2.290

10.  The Bionanoprobe: hard X-ray fluorescence nanoprobe with cryogenic capabilities.

Authors:  S Chen; J Deng; Y Yuan; C Flachenecker; R Mak; B Hornberger; Q Jin; D Shu; B Lai; J Maser; C Roehrig; T Paunesku; S C Gleber; D J Vine; L Finney; J VonOsinski; M Bolbat; I Spink; Z Chen; J Steele; D Trapp; J Irwin; M Feser; E Snyder; K Brister; C Jacobsen; G Woloschak; S Vogt
Journal:  J Synchrotron Radiat       Date:  2013-12-12       Impact factor: 2.616

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  3 in total

1.  Efficient ptychographic phase retrieval via a matrix-free Levenberg-Marquardt algorithm.

Authors:  Saugat Kandel; S Maddali; Youssef S G Nashed; Stephan O Hruszkewycz; Chris Jacobsen; Marc Allain
Journal:  Opt Express       Date:  2021-07-19       Impact factor: 3.833

2.  Single-shot ptychography at a soft X-ray free-electron laser.

Authors:  Konstantin Kharitonov; Masoud Mehrjoo; Mabel Ruiz-Lopez; Barbara Keitel; Svea Kreis; Seung-Gi Gang; Rui Pan; Alessandro Marras; Jonathan Correa; Cornelia B Wunderer; Elke Plönjes
Journal:  Sci Rep       Date:  2022-08-24       Impact factor: 4.996

3.  Using a modified double deep image prior for crosstalk mitigation in multislice ptychography.

Authors:  Ming Du; Xiaojing Huang; Chris Jacobsen
Journal:  J Synchrotron Radiat       Date:  2021-05-19       Impact factor: 2.616

  3 in total

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