PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data

A new computer program for analysing ptychographic data combines both high-level simplicity and high-performance computing on large-scale computing clusters. It is available with a royalty-free non-exclusive licence for academic and non-commercial purposes.

[1]  M. A. Oldfield,et al.  Fast Fourier method for the accurate rotation of sampled images , 1997 .

[2]  J. Rodenburg,et al.  An improved ptychographical phase retrieval algorithm for diffractive imaging. , 2009, Ultramicroscopy.

[3]  Jianwei Miao,et al.  Ptychographic imaging with a compact gas-discharge plasma extreme ultraviolet light source. , 2015, Optics letters.

[4]  Brian McMahon,et al.  Definition and exchange of crystallographic data , 2005 .

[5]  J. Rodenburg,et al.  Movable aperture lensless transmission microscopy: a novel phase retrieval algorithm. , 2004, Physical review letters.

[6]  Ondřej Mandula,et al.  PyNX.Ptycho: a computing library for X-ray coherent diffraction imaging of nanostructures , 2016 .

[7]  Tim Salditt,et al.  Hard x-ray nanobeam characterization by coherent diffraction microscopy , 2010 .

[8]  D. Shapiro,et al.  Nanosurveyor 2: A Compact Instrument for Nano-Tomography at the Advanced Light Source , 2017 .

[9]  A. Diaz,et al.  Ptychographic X-ray computed tomography of extended colloidal networks in food emulsions , 2016, 1602.04230.

[10]  Manuel Guizar-Sicairos,et al.  Iterative least-squares solver for generalized maximum-likelihood ptychography. , 2018, Optics express.

[11]  L. Armijo Minimization of functions having Lipschitz continuous first partial derivatives. , 1966 .

[12]  O. Bunk,et al.  Quantitative interior x-ray nanotomography by a hybrid imaging technique , 2015 .

[13]  O. Bunk,et al.  X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution , 2014, Scientific Reports.

[14]  Manuel Guizar-Sicairos,et al.  Element-specific X-ray phase tomography of 3D structures at the nanoscale. , 2015, Physical review letters.

[15]  R. Horstmeyer,et al.  Wide-field, high-resolution Fourier ptychographic microscopy , 2013, Nature Photonics.

[16]  A. Diaz,et al.  Resonant Ptychographic Tomography Facilitates Three-Dimensional Quantitative Colocalization of Catalyst Components and Chemical Elements , 2018, The Journal of Physical Chemistry C.

[17]  Talita Perciano,et al.  SHARP: a distributed, GPU-based ptychographic solver , 2016, 1602.01448.

[18]  Jan Sijbers,et al.  Fast and flexible X-ray tomography using the ASTRA toolbox. , 2016, Optics express.

[19]  A. G. Cullis,et al.  Transmission microscopy without lenses for objects of unlimited size. , 2007, Ultramicroscopy.

[20]  T. Ishikawa,et al.  High-resolution multislice x-ray ptychography of extended thick objects. , 2014, Physical review letters.

[21]  O. Bunk,et al.  High-throughput ptychography using Eiger: scanning X-ray nano-imaging of extended regions. , 2014, Optics express.

[22]  V. Favre-Nicolin,et al.  Fast computation of scattering maps of nanostructures using graphical processing units , 2010, 1010.2641.

[23]  Olimpia D. Onelli,et al.  Evolutionary‐Optimized Photonic Network Structure in White Beetle Wing Scales , 2018, Advanced materials.

[24]  P. Thibault,et al.  Maximum-likelihood refinement for coherent diffractive imaging , 2012 .

[25]  John M. Rodenburg,et al.  Electron ptychography. I. Experimental demonstration beyond the conventional resolution limits , 1998 .

[26]  Stefan Vogt,et al.  Performance and Ongoing Development of the Velociprobe, a Fast Hard X-ray Nanoprobe for High-Resolution Ptychographic Imaging , 2018, Microscopy and Microanalysis.

[27]  J. Fienup,et al.  Phase retrieval with transverse translation diversity: a nonlinear optimization approach. , 2008, Optics express.

[28]  Andreas Menzel,et al.  Reconstructing state mixtures from diffraction measurements , 2013, Nature.

[29]  J. Rodenburg,et al.  Ptychographic transmission microscopy in three dimensions using a multi-slice approach. , 2012, Journal of the Optical Society of America. A, Optics, image science, and vision.

[30]  Message Passing Interface Forum MPI: A message - passing interface standard , 1994 .

[31]  Youssef S. G. Nashed,et al.  Distributed Automatic Differentiation for Ptychography , 2017, ICCS.

[32]  J. Rodenburg,et al.  The theory of super-resolution electron microscopy via Wigner-distribution deconvolution , 1992, Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences.

[33]  Franz Pfeiffer,et al.  Near-field ptychography: phase retrieval for inline holography using a structured illumination , 2013, Scientific Reports.

[34]  O. Bunk,et al.  High-Resolution Scanning X-ray Diffraction Microscopy , 2008, Science.

[35]  David A. Bader,et al.  Hierarchical Data Format , 2011, Encyclopedia of Parallel Computing.

[36]  Manuel Guizar-Sicairos,et al.  X-ray Fourier ptychography , 2019, Science Advances.

[37]  Plamen Stefanov,et al.  Inverse Problems and Applications , 2014 .

[38]  Herbert J. Bernstein,et al.  Specification of the Crystallographic Binary File (CBF/imgCIF) , 2006 .

[39]  Jörg Raabe,et al.  Fast positioning for X-ray scanning microscopy by a combined motion of sample and beam-defining optics , 2019, Journal of synchrotron radiation.

[40]  Christoph Rau,et al.  Sampling in x-ray ptychography , 2013 .

[41]  Franz Pfeiffer,et al.  X-ray ptychography , 2017, Nature Photonics.

[42]  A. Diaz,et al.  A three-dimensional view of structural changes caused by deactivation of fluid catalytic cracking catalysts , 2017, Nature Communications.

[43]  G. Bruun,et al.  Collective modes of a two-dimensional spin-1=2 Fermi gas in a harmonic trap , 2013, 1301.0358.

[44]  Neculai Andrei,et al.  Accelerated scaled memoryless BFGS preconditioned conjugate gradient algorithm for unconstrained optimization , 2010, Eur. J. Oper. Res..

[45]  W. Hoppe Beugung im inhomogenen Primärstrahlwellenfeld. I. Prinzip einer Phasenmessung von Elektronenbeungungsinterferenzen , 1969 .

[46]  W. Brocklesby,et al.  Ptychographic coherent diffractive imaging with orthogonal probe relaxation. , 2016, Optics express.

[47]  B Enders,et al.  A computational framework for ptychographic reconstructions , 2016, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[48]  Tom Peterka,et al.  Parallel ptychographic reconstruction. , 2014, Optics express.

[49]  M. Guizar‐Sicairos,et al.  Three-dimensional magnetization structures revealed with X-ray vector nanotomography , 2017, Nature.

[50]  Gabriel Aeppli,et al.  High-resolution non-destructive three-dimensional imaging of integrated circuits , 2017, Nature.

[51]  Francesco De Carlo,et al.  TomoPy: a framework for the analysis of synchrotron tomographic data , 2014, Journal of synchrotron radiation.

[52]  Mirko Holler,et al.  Alignment methods for nanotomography with deep subpixel accuracy. , 2019, Optics express.

[53]  N. Delen,et al.  Free-space beam propagation between arbitrarily oriented planes based on full diffraction theory: a fast Fourier transform approach , 1998 .

[54]  Gozde Bozdagi Akar,et al.  Digital computation of the fractional Fourier transform , 1996, IEEE Trans. Signal Process..