Nanosurveyor: a framework for real-time data processing

BackgroundThe ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality.ResultsHere we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis.ConclusionsThe pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.

[1]  Saša Bajt,et al.  Evidence for interstellar origin of seven dust particles collected by the Stardust spacecraft , 2014, Science.

[2]  H. Padmore,et al.  A fast, direct x-ray detection charge-coupled device. , 2009, The Review of scientific instruments.

[3]  Jörg Maser,et al.  A hard X-ray nanoprobe beamline for nanoscale microscopy , 2012, Journal of synchrotron radiation.

[4]  J. Joseph,et al.  Development of a compact fast CCD camera and resonant soft x-ray scattering endstation for time-resolved pump-probe experiments. , 2011, The Review of scientific instruments.

[5]  Pieter Hintjens,et al.  ZeroMQ: Messaging for Many Applications , 2013 .

[6]  H Toyokawa,et al.  The PILATUS 1M detector. , 2006, Journal of synchrotron radiation.

[7]  R. Falcone,et al.  ALS-II, a Potential Soft X-ray, Diffraction Limited Upgrade of the Advanced Light Source* , 2014 .

[8]  Eugenie Samuel Reich,et al.  Ultimate upgrade for US synchrotron , 2013, Nature.

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

[10]  A. Damascelli,et al.  Electronic Structure of MgB 2 from Angle-Resolved Photoemission Spectroscopy , 2002 .

[11]  Electronic structure of MgB2 from angle-resolved photoemission spectroscopy. , 2001, Physical review letters.

[12]  Tom White,et al.  Hadoop: The Definitive Guide , 2009 .

[13]  Anders Eklund,et al.  BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs , 2014, Front. Neuroinform..

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

[15]  A. G. Cullis,et al.  Hard-x-ray lensless imaging of extended objects. , 2007, Physical review letters.

[16]  B. Schmitt,et al.  The PILATUS 1 M detector , 2006 .

[17]  B. Schmitt,et al.  EIGER: Next generation single photon counting detector for X-ray applications , 2011 .

[18]  Matthew Rocklin,et al.  Dask: Parallel Computation with Blocked algorithms and Task Scheduling , 2015, SciPy.

[19]  E. Al-Dmour,et al.  The MAX IV Facility , 2013 .

[20]  Carl Nettelblad,et al.  Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time1 , 2016, Journal of applied crystallography.

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

[22]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

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

[24]  Y S Chu,et al.  Design and performance of a scanning ptychography microscope. , 2014, The Review of scientific instruments.

[25]  J. Rodenburg.  Ptychography and Related Diffractive Imaging Methods , 2008 .

[26]  J. Kirz,et al.  Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source , 2013 .

[27]  Eric Jones,et al.  SciPy: Open Source Scientific Tools for Python , 2001 .

[28]  Rafael Fernandez-Leiro,et al.  A pipeline approach to single-particle processing in RELION , 2016, bioRxiv.

[29]  Finn Verner Jensen,et al.  Introduction to Bayesian Networks , 2008, Innovations in Bayesian Networks.

[30]  Anton Barty,et al.  Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data , 2014, Journal of applied crystallography.

[31]  Timothy L. Foley,et al.  Covalent Small Molecule Inhibitors of Ca2+-Bound S100B , 2014, Biochemistry.

[32]  Scott Shenker,et al.  Spark: Cluster Computing with Working Sets , 2010, HotCloud.

[33]  F. Maia.  The Coherent X-ray Imaging Data Bank , 2012, Nature Methods.