AI@ ALS Workshop Report: Machine Learning Needs at the Advanced Light Source   [Tag-6, Tag-7]

2024, Taylor & Francis  

Parkinson, Dilworth Y, Chavez, Tanny, Choudhary, Monika, English, Damon, Hao, Guanhua, Hellert, Thorsten, Leemann, Simon C, Nemsak, Slavomir, Rotenberg, Eli, Taylor, Andrea 

qlty: Handling large tensors in scientific imaging deep-learning workflows   [Tag-6, Tag-7]

2024, Software Impacts  

Zwart, Petrus H

Towards Autonomous Synchrotron Fourier Transform Infrared Microscopy  [Tag-14]

2024, Microscopy and Microanalysis  

Zwart, Petrus, Tas, Neslihan, Noack, Marcus, Holman, HoiYing

Long-Term, Non-Invasive Detection of Low-Dose Ionizing Radiation Exposure [Tag-6]

2024, Electrochemical Society Meeting Abstracts 245  

Inman, Jamie, Wu, Yulun, Chen, Liang, Ghosh, Dhruba, Wan, Kenneth, DeChant, Jared, Obst-Huebl, Lieselotte, Nakamura, Kei, Ralston, Corie, Celniker, Susan

DLSIA: Deep Learning for Scientific Image Analysis   [Tag-6, Tag-7]

2024, Journal of Applied Crystallography  

Roberts, Eric J, Chavez, Tanny, Hexemer, Alexander, Zwart, Petrus H

Benchmarking topic models on scientific articles using BERTeley [Tag-7]

2024, Journal of Natural Language Processing

Chagnon, E., Pandolfi, R., Donatelli, J., Ushizima, D.

RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs [Tag-7,14]

2024, Nature Scientific Reports

Sordo, Z., Andeer, P., Sethian, J., Northen, T., Ushizima, D.

Optimizing and Scaling the 3D Reconstruction of Single-Particle Imaging [Tag-1]

2024 IEEE International Parallel and Distributed Processing Symposium

N. Shah, C. Sweeney, V. Ramakrishnaiah, J. Donatelli, W.C. Feng.

Methods and Applications of Autonomous Experimentation [Tag-7,14]

2024, CRC Press

Noack, Marcus M and Ushizima, Daniela

A substitutional quantum defect in WS2 discovered by high-throughput computational screening and fabricated by site-selective STM manipulation [Tag-14]

2024, Nature Communications

John C Thomas, Wei Chen, Yihuang Xiong, Bradford A Barker, Junze Zhou, Weiru Chen, Antonio Rossi, Nolan Kelly, Zhuohang Yu, Da Zhou, Shalini Kumari, Edward S Barnard, Joshua A Robinson, Mauricio Terrones, Adam Schwartzberg, D Frank Ogletree, Eli Rotenberg, Marcus M Noack, Sinéad Griffin, Archana Raja, David A Strubbe, Gian-Marco Rignanese, Alexander Weber-Bargioni, Geoffroy HautierZ

A unifying perspective on non-stationary kernels for deeper Gaussian processes [Tag-7]

2024, APL Machine Learning

Noack, Marcus M and Luo, Hengrui and Risser, Mark D

Benchmarking topic models on scientific articles using BERTeley [Tag-7]

Natural Language Processing Journal

E. Chagnon, R. Pandolfi, J. Donatelli, D. Ushizima

tomoCAM: Fast Model-based Iterative Reconstruction via GPU Acceleration and Non-Uniform Fast Fourier Transforms [Tag-3,8]

Journal of Synchrotron Radiation

D. Kumar, D. Parkinson, J.J. Donatelli

Deploying machine learning based segmentation for scientific imaging analysis at synchrotron facilities [Tag-6, Tag-7]

2023, IS&T International Symposium on Electronic Imaging

Hao, Guanhua, Roberts, Eric J, Chavez, Tanny, Zhao, Zhuowen, Holman, Elizabeth A, Yanxon, Howard, Green, Adam, Krishnan, Harinarayan, Ushizima, Daniela, McReynolds, Dylan

Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder [Tag-1]

Ultramicroscopy

J.P.J. Chen, K. Pande, J.J. Donatelli, A.V. Martin, K. Ayyer, H.N. Chapman, R. Bean, K.E. Schmidt, R.A. Kirian

Autonomous x-ray scattering [Tag-7, Tag-14]

Nanotechnology

K.G. Yager, P.W. Majewski, M.M. Noack, M. Fukuto

Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels [Tag-7]

Scientific reports

M.M. Noack, H. Krishnan, M.D. Risser, K.G. Reyes

Mathematical nuances of Gaussian process-driven autonomous experimentation [Tag-14]

MRS Bulletin

M.M. Noack, K.G. Reyes

Autonomous discovery of emergent morphologies in directed self-assembly of block copolymer blends [Tag-14]

Science Advances

G.S. Doerk, A. Stein, S. Bae, M.M. Noack, M. Fukuto, K.G. Yager

Surface enrichment dictates block copolymer orientation [Tag-14]

Nanoscale

S. Bae, M.M. Noack, K.G. Yager

Detecting Lithium Plating Dynamics in a Solid-State Battery with Operando x-Ray Computed Tomography Using Machine Learning [Tag-3,7,12]

Nature Partner Journal

Y. Huang, D. Perlmutter, A. Su, J. Quenum, I. Zenyuk, D. Ushizima 

Advancing the capabilities of polymer blend directed self-assembly [Tag-14]

Novel Patterning Technologies

G.S. Doerk, A. Stein, S. Bae, M. Noack, M. Fukuto, A.A. Kulkarni, K. Toth, C. Osuji, K. Yager

Improve neutron measurement performance with AI and machine learning [Tag-14]

Acta Crystallographica Section A: Foundations of Crystallography

P. Mutti, M. Boehm, Y. Le Goc, T. Weber, M. Noack, J. Sethian

Artificial Intelligence (AI) and Machine Learning (ML) at Experimental Facilities [Tag-7,14]

Artificial Intelligence for Science: A Deep Learning Revolution

J. A. Sethian, J. J. Donatelli, A. Hexemer, M. M. Noack, D. M. Pelt, D. M. Ushizima, P. H. Zwart. 

Iterative projection algorithms for phasing diffraction from crystals with conformational disorder [Tag-1]

in preparation

K. Pande, J. P. Chen, J. J. Donatelli, and R. A. Kirian

Image segmentation using u-net architecture for powder x-ray diffraction images [Tag-6,7]

Proceedings of the IEEE/CVF international conference on computer vision

H. Yanxon, E.J. Roberts, H. Parraga, J. Weng, W. Xu, U. Ruett, A. Hexemer, P.H. Zwart, N. Schwarz

Deploying machine learning based segmentation for scientific imaging analysis at synchrotron facilities [Tag-7]

Society for Imaging Science and Technology, Electronic Imaging

G. Hao, E.J. Roberts, T. Chavez, Z. Zhao, E. Holman, H. Yanxon, A. Green, H. Krishnan, D. Ushizima, D. McReynolds, N. Schwarz, P.H. Zwart, A. Hexemer, D.Y. Parkinson

Using Machine Learning Algorithms for Water Segmentation in Gas Diffusion Layers of Polymer Electrolyte Fuel Cells [Tag-6,7]

Transport in Porous Media

A.D. Shum, C.P. Liu, W.H. Lim, D.Y. Parkinson, I.V. Zenyuk

tomoCAM: Fast Model-based Iterative Reconstruction via GPU Acceleration and Non-Uniform Fast Fourier Transforms [Tag-3]

arXiv/in review

D. Kumar, D. Parkinson, J.J. Donatelli

Advanced stationary and nonstationary kernel designs for domain-aware Gaussian processes [Tag-7]

Communications in Applied Mathematics and Computational Science

M.M. Noack, J.A. Sethian

Autonomous scanning probe microscopy investigations over WS2 and Au{111} [Tag-14]

npj Computational Materials

J.C. Thomas, A. Rossi, D. Smalley, L. Francaviglia, Z. Yu, T. Zhang, S. Kumari, J.A. Robinson, M. Terrones, M. Ishigami, E. Rotenberg, E.S. Barnard, A. Raja, E. Wong, D.F. Ogletree, M.M. Noack, A. Weber-Bargioni

Machine-learning for designing nanoarchitectured materials by dealloying [Tag-14]

Communications Materials

C Zhao, CC Chung, S Jiang, MM Noack, JH Chen, K Manandhar, J Lynch, H. Zhong, W. Zhu, P. Maffettone, D. Olds, M. Fukuto, I. Takeuchi, S. Ghose, T. Caswell, K.G. Yager, Y.K. Chen-Wiegart

Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of Toxoplasma invasion machinery [Tag-6,7]

Proceedings of the National Academy of Sciences Nexus

L. Segev-Zarko, P.D. Dahlberg, S.Y. Sun, D.M. Pelt, C.Y. Kim, E.S. Egan, J.A. Sethian, W. Chiu, J.C. Boothroyd

Validation of Deep Learning Segmentation of CT Images of Fiber-Reinforced Composites [Tag-6,7]

Journal of Composites Science

A. Badran, D. Parkinson, D. Ushizima, D. Marshall, E. Maillet

Validation of Deep Learning Segmentation of CT Images of Fiber-Reinforced Composites [Tag-6,7]

Journal of Composites Science

A. Badran, D. Parkinson, D. Ushizima, D. Marshall, E. Maillet

Unraveling the effect of collagen damage on bone fracture using in situ synchrotron microtomography with deep learning [Tag-7]

Communications Materials

M. Sieverts, Y. Obata, J. L. Rosenberg, W. Woolley, D. Y. Parkinson, H. S. Barnard, D. M. Pelt, C. Acevedo

Structure Determination from Multiple-Scattering Electron Crystallography [Tag-15]

Microscopy and Microanalysis

J.J. Donatelli, J.C.H. Spence

Deep learning-based identification of sub-nuclear structures in FIB-SEM images [Tag-7]

 arXiv

N. Gupta, E. J. Roberts, S. Pang, C. S. Xu, H. F. Hess, F. Wu, A. Dernburg, D. Jorgens, P. H. Zwart, V. Kasinath

The case for data science in experimental chemistry: examples and recommendations [Tag-12]

Nature Reviews, Chemistry

Y. Yano, K. J. Gaffney, J. Gregoire, L. Hung, A. Ourmazd, J. Schrier, J. A. Sethian, F. M. Toma 

A comparison of deep-learning-based inpainting techniques for experimental X-ray scattering [Tag-7]

Proceedings of the IEEE/CVF International Conference on Computer Vision

T. Chavez, E. Roberts, P.H. Zwart, A. Hexemer

MLExchange: A web-based platform enabling exchangeable machine learning workflows for scientific studies [Tag-7]

IEEE, 2022, 4th Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP)

Z. Zhao, T. Chavez, E. A. Holman, G. Hao, A. Green, H. Krishnan, D. McReynolds, R. Pandolfi, E. J. Roberts, P. H. Zwart, H. Yanxon, N. Schwarz, S. Sankaranarayanan, S. V. Kalinin, A. Mehta, S. Campbell, A. Hexemer

Benchmarking autonomous scattering experiments illustrated on TAS [Tag-14] 

Frontiers in Materials

M.T. Parente, A. Schneidewind, G. Brandl, C. Franz, M. Noack, M. Boehm, M. Ganeva

Unveiling characteristic proteins for the structural development of beetle elytra [Tag-3] 

Acta Biomaterialia

S. Murata, J. Rivera, M.Y. Noh, N. Hiyoshi, W. Yang, D.Y. Parkinson, H.S. Barnard, Y. Arakane, D. Kisailus, A. Arakaki

Comparing the Purity of Rolled versus Evaporated Lithium Metal Films Using X-ray Microtomography [Tag-3] 

ACS Energy Letters

A.S. Ho, A.S. Westover, K. Browning, J.A. Maslyn, D.Y. Parkinson, R. Sahore, N. Dudney, N.P. Balsara

Elucidating effects of catalyst loadings and porous transport layer morphologies on operation of proton exchange membrane water electrolyzers [Tag-3] 

Applied Catalysis B: Environmental

D. Kulkarni, A. Huynh, P. Satjaritanun, M. O’Brien, S. Shimpalee, D. Parkinson, P. Shevchenko, F. DeCarlo, N. Danilovic, K.E. Ayers, C. Capuano, I.V. Zenyuk

Towards Data-Informed Motion Artifact Reduction in Quantitative CT Using Piecewise Linear Interpolation [Tag-3] 

IEEE Transactions on Computational Imaging

E. Boigné, D.Y. Parkinson, M. Ihme

Failure Mechanisms at the Interfaces between Lithium Metal Electrodes and a Single-Ion Conducting Polymer Gel Electrolyte [Tag-3] 

ACS Applied Materials & Interfaces

L. Frenck, P. Lennartz, D.Y. Parkinson, M. Winter, N.P. Balsara, G. Brunklaus

A workflow for segmenting soil and plant X-ray CT images with deep learning in Googles Colaboratory [Tag-3,5] 

arXiv

D.A. Rippner, P. Raja, J.M. Earles, A. Buchko, M. Momayyezi, F. Duong, D. Parkinson, E. Forrestel, K. Shackel, J. Neyhart, A.J. McElrone

Failure Mechanisms at the Interfaces between Lithium Metal Electrodes and a Single-Ion Conducting Polymer Gel Electrolyte [Tag-3] 

IEEE Transactions on Computational Imaging

E. Boigné, D.Y. Parkinson, M. Ihme

Cross-correlation Analysis of X-ray Photon Correlation Spectroscopy to Extract Rotational Diffusion Coefficients [Tag-13]

Proceedings of the National Academy of Sciences 

Zixi Hu, J.J. Donatelli, and J.A. Sethian

Scaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL [Tag,1,8]

In Parallel Application Workshop, Alternatives to MPI+X (PAW-ATM)

H.Y. Chang, E. Slaughter, S. Mirchandaney, J. Donatelli, C.H. Yoon

Gaussian Processes for Autonomous Data Acquisition at Large-Scale Synchrotron and Neutron Scattering Facilities  [Tag-14]

Nature Review Physics, July, 2021 [read the paper here]

Marcus M. Noack, Petrus H. Zwart, Daniela M. Ushizima, Masafumi Fukuto, Kevin G. Yager, Katherine C. Elbert, Christopher B. Murray, Aaron Stein, Gregory S. Doerk, Esther H. R. Tsai, Ruipeng Li, Guillaume Freychet, Mikhail Zhernenkov, Hoi-Ying N. Holman, Steven Lee, Liang Chen, Eli Rotenberg, Tobias Weber, Yannick Le Goc, Martin Bohm, Paul Steffens, Paolo Mutti, and James A.  Sethian

Cric searchable image database as a public platform for conventional pap smear cytology data [Tag-6]

Nature Scientific Data, June, 2021

M. Rezende, R. Silva, F. Bernardo, A. Tobias, P. Oliveira, T. Machado, C. Costa, F. Medeiros, D. Ushizima, C. Carneiro, A. Bianchi

Inversion of dynamical Bragg intensities to complex structure factors by iterated projections [TAG-15]

Ultramicroscopy, 222, 113214, 2021

John C.H. Spence and Jeffrey J. Donatelli

GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering [TAG-1, TAG-8]

J. Appl. Cryst. 54, 2021

Pranay Reddy Kommera, Vinay Ramakrishnaiah, Christine Sweeney, Jeffrey Donatelli, and Petrus H. Zwart

Microstructure and Water Absorption of Ancient Concrete from Pompeii: An Integrated Synchrotron Microtomography and Neutron Radiography Characterization [Tag-6]

Cement and Concrete Research, January, 2021

K. Xu, A. Tremsin, J. Li, D. Ushizima, C. Davy, A. Bouterf, Y. Su, M. Marroccoli, A. Mauro, M. Osanna, A. Telesca, P. Monteiro

Deep Density: circumventing the Kohn-Sham equations via symmetry preserving neural networks [Tag-2, Tag-7]

J. Comput. Phys. 443, 110523, 2021

L. Zepeda-Nunez, Y. Chen, J. Zhang, W. Jia, L. Zhang, L. Lin

Numerical solution of large scale Hartree-Fock-Bogoliubov equations [TAG-2]

ESIAM: Math. Model. Numer. Anal. (M2AN), 55, 763, 2021

L. Lin and X. Wu  

Time-dependent unbounded Hamiltonian simulation with vector norm scaling [TAG-11]

Quantum 5, 459, 2021 

D. An, D. Fang, L. Lin

Hierarchical Median Narrow Band for Level Set Segmentation of Cervical Cell Nuclei [TAG-6]

Applied Sciences

A. Braga, R.C.P. Marques, F.N.S. Medeiros, J.F.S. Rocha Neto, A.G.C. Bianchi, C.M. Carneiro, D.M. Ushizima 

A Hierarchical Feature-Based Methodology to Perform Cervical Cancer Classification [TAG-6]

Applied Sciences

D.N. Diniz, M.T. Rezende, A.G.C. Bianchi, C.M. Carneiro, D.M. Ushizima, F.N.S. de Medeiros, M.J.F. Souza

Active Contours for Overlapping Cervical Cell Segmentation [TAG-6]

International Journal of Biomedical Engineering and Technology

F.H.D. Araújo, R.R.V. Silva, F.N.S. Medeiros, J.F. Rocha Neto, P.H.C. Oliveira, A.G.C. Bianchi, D. Ushizima 

Cric searchable image database as a public platform for conventional pap smear cytology data [TAG-6]

Nature Scientific Data

M.T. Rezende, R. Silva, F.O. Bernardo, A.H.G. Tobias, P.H.C. Oliveira, T.M. Machado, C.S. Costa, F.N.S. Medeiros, D.M. Ushizima, C.M. Carneiro, A.G.C. Bianchi

Microstructure and Water Absorption of Ancient Concrete from Pompeii: An Integrated Synchrotron Microtomography and Neutron Radiography Characterization [TAG-3,6]

Cement and Concrete Research

K. Xu, A.S. Tremsin, J. Li, D.M. Ushizima, C.A. Davy, A. Bouterf, Y.T. Su, M. Marroccoli, A.M. Mauro, M. Osanna, A. Telesca

3D Nanotomography of Calcium Silicate Hydrates by Transmission Electron Microscopy [TAG-3]

Journal of the American Ceramic Society

P. Viseshchitra, P. Panod, P. Ercius, P. J. M. Monteiro, M. Scott, D. Ushizima, J. Li, K. Xu, H.R. Wenk 

Persistent and partially mobile oxygen vacancies in Li-rich layered oxides [TAG-4]

Nature Energy 6, pages 642–652 (2021) doi.org/10.1038/s41560-021-00832-7

Peter M. Csernica, Samanbir S. Kalirai, William E. Gent, Kipil Lim, Young-Sang Yu, Yunzhi Liu1, Sung-Jin Ahn, Emma Kaeli, Xin Xu, Kevin H. Stone, Ann F. Marshall, Robert Sinclair, David A. Shapiro, Michael F. Toney and William C. Chueh

Autonomous materials discovery driven by Gaussian process regression with inhomogeneous measurement noise and anisotropic kernels [TAG-14]

Scientific Reports,10, 17663, 2020

Marcus M. Noack, Gregory S. Doerk, Ruipeng Li, Jason K. Streit, Richard A. Vaia, Kevin G. Yager, Masafumi Fukuto

Workflows are the New Applications: Challenges in Performance, Portability, and Productivity [TAG-5]

2020 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC), doi:10.1109/P3HPC51967.2020.00011.

T. Ben-Nun, T. Gamblin, D. S. Hollman, H. Krishnan and C. J. Newburn

Towards a BES Light Source Wide Event-triggered Tomography Data Analysis Pipeline Using a Sustainable Software Stack [TAG-5]

Microscopy and Microanalysis, doi:10.1017/S143192762002379X

H. Krishnan, T. Caswell, D. Allan, 2020

3D Nanotomography of Calcium Silicate Hydrates by Transmission Electron Microscopy [Tag-6]

Journal of the American Ceramic Society, November, 2020

P. Viseshchitra, P. Ercius, P. Monteiro, M. Scott, D. Ushizima, Y. Li, K. Xu, H. Wenk

Sparse matrix-based hpc tomography [Tag-3, Tag-8]

International Conference on Computational Science (pp. 248-261)

Marchesini, S., Trivedi, A., Enfedaque, P., Perciano, T., & Parkinson, D.

Iterative X-ray spectroscopic ptychography [Tag-4, Tag-8]

Journal of Applied Crystallography

Huibin Chang, Ziqin Rong, Pablo Enfedaque, Stefano Marchesini

AI-enabled high-resolution scanning coherent diffraction imaging [Tag-4, Tag-7]

Applied Physics Letters

Mathew J Cherukara, Tao Zhou, Youssef Nashed, Pablo Enfedaque, Alex Hexemer, Ross J Harder, Martin V Holt

An ultrahigh-resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nanomaterials [Tag-4]

Science advances

David A Shapiro, Sergey Babin, Richard S Celestre, Weilun Chao, Raymond P Conley, Peter Denes, Bjoern Enders, Pablo Enfedaque, Susan James, John M Joseph, Harinarayan Krishnan, Stefano Marchesini, Krishna Muriki, Kasra Nowrouzi, Sharon R Oh, Howard Padmore, Tony Warwick, Lee Yang, Valeriy V Yashchuk, Young-Sang Yu, Jiangtao Zhao

Scientific Reports,10,  1325, 2020

Advances in Kriging-Based Autonomous X-Ray Scattering Experiments

Marcus M Noack,  Gregory S Doerk,  Ruipeng Li, Masafumi Fukuto, Kevin G Yager

Inversion of many-beam bragg intensities for phasing by iterated projections: Removal of multiple scattering artifacts from diffraction data [TAG-15]

Physical Review Letters 125.6, 065502, 2020

Jeffrey J. Donatelli and John C.H. Spence

Interactive parallel workflows for synchrotron tomography   [TAG-3, TAG-5, TAG-6, TAG-7] 

SC20, 2020 IEEE/ACM 2nd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP), 2020

Dilworth Y Parkinson, Harinarayan Krishnan, Daniela Ushizima, Matthew Henderson, Shreyas Cholia 

Accelerating Microstructural Analytics with Dask for Volumetric X-ray Images  [TAG-3,TAG-5,TAG-6,TAF-7] 

SC20, 2020 IEEE/ACM 9th Workshop on Python for High-Performance and Scientific Computing (PyHPC) , 2020

Daniela Ushizima, Matthew McCormick, Dilworth Parkinson 

Evaluating crystallographic likelihood functions using numerical quadratures [TAG-1] 

Acta Cryst. D76, 736–750, 2020

Petrus H. Zwart, Elliott D. Perryman 

Randomized Algorithms for Scientific Computing (RASC) [TAG-14]

Workshop Report - U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research Program

Aydin Buluc, Tamara G. Kolda, Stefan M. Wild, Mihai Anitescu, Anthony DeGennaro, John Jakeman, Chandrika Kamath, Ramakrishnan (Ramki)Kannan, Miles E. Lopes, Per-Gunnar Martinsson, Kary Myers, Jelani Nelson, Juan M. Restrepo, C. Seshadhri, Draguna Vrabie, Brendt Wohlberg, Stephen J. Wright, Chao Yang, Peter Zwart

Fluctuation X-ray Scattering real-time app [TAG-1, TAG-8] 

Proc. of the 19th PYTHON in Science Conf. (SCIPY 2020)

Dujardin, Antoine, Elliott Slaugther, Jeffrey Donatelli, Peter Zwart, Amedeo Perazzo, and Chun Hong Yoon 

Materials Data Science for Microstructural Characterization of Archaeological Concrete [Tag-6]

MRS Advances, February 2020.

D. Ushizima, K. Xu, P. Monteiro

Learning the mapping $\mathbf{x}\mapsto \sum_{i=1}^d x_i^2$: the cost of finding the needle in a haystack [Tag-7]

Commun. Appl. Math. Comput. 2020

J. Zhang, L. Zepeda-Nunez, Y. Yao and L. Lin

Enhancing robustness and efficiency of density matrix embedding theory via semidefinite programming and local correlation potential fitting [Tag-2]

Phys. Rev. B, 102, 085123, 2020 (Editor's Suggestion)

X. Wu, M. Lindsey, T. Zhou, Y. Tong and L. Lin 

Near-optimal ground state preparation [Tag-11]

Quantum, 4, 372, 2020

L. Lin and Y. Tong 

Using models to improve optimizers for variational quantum algorithms [TAG-7, TAG-11]

Quantum Sci. Tech. 5, 044008, 2020 

K. J. Sung, J. Yao, M. P. Harrigan, N. C. Rubin, Z. Jiang, L. Lin, R. Babbush, J. R. McClean

An ultra-high resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nano-materials [TAG-None]

Science Advances, 6 (51), eabc4904 (2020)

David A. Shapiro, Sergey Babin, Richard Celestre, Weilun Chao, Raymond P. Conley, Peter Denes, Bjoern Enders, Pablo Enfedaque, Susan James, John Joseph, Harinarayan Krishnan, Stefano Marchesini, Krishna Muriki, Kasra Nowrouzi, Sharon Oh, Howard Padmore, Tony Warwick, Lee Yang, Valeriy. V. Yashchuk, Young-Sang Yu, and Jiangtao Zhao

Distributed Global Digital Volume Correlation by Optimal Transport   [TAG-3,TAG-6,TAG-7]

2019 IEEE/ACM 1st Annual Workshop on Large-scale Experiment-in-the-Loop Computing (XLOOP), 2019 

John Michael L MacNeil, Dmitriy Morozov, Francesco Panerai, Dilworth Parkinson, Harold Barnard, Daniela Ushizima 

Interactive volumetric segmentation for textile micro‐tomography data using wavelets and nonlocal means   [TAG-3,TAG-6,TAG-7]

2019 Statistical Analysis and Data Mining: The ASA Data Science Journal, v12 p338-353, 2019

J Michael L MacNeil, Daniela M Ushizima, Francesco Panerai, Nagi N Mansour, Harold S Barnard, Dilworth Y Parkinson 

Evaluating fiber detection models using neural networks   [TAG-3,TAG-6,TAG-7]

2019 International Symposium on Visual Computing , 2019

Silvia Miramontes, Daniela M Ushizima, Dilworth Y Parkinson 

Reconstructing the three-dimensional latent image of extreme ultraviolet resists with resonant soft x-ray scattering  [TAG-10]

J. Micro/Nanolith. MEMS MOEMS 18(2), 024003, Apr–Jun,  2019

Guillaume Freychet, Isvar A. Cordova, Terry McAfee, Dinesh Kumar, Ronald J. Pandolfi, Chris Anderson, Scott D. Dhuey, Patrick Naulleau, Cheng Wang,  and Alexander Hexemer 

Estimation of Line Cross Sections Using Critical-Dimension Grazing-Incidence Small-Angle X-Ray Scattering [TAG-10]

Phys. Rev. Applied 12, 044026 – Published 11 October 2019

Guillaume Freychet, Dinesh Kumar, Ron J. Pandolfi, Patrick Naulleau, Isvar Cordova, Peter Ercius, Chengyu Song, Joseph Strzalka, and Alexander Hexemer

An Efficient Algorithm for Automatic Structure Optimization in X ray Standing-Wave Experiments  [TAG-7]

Journal of Electron Spectrocopy and Related Phenomena, Oct., 2019

Karslioglu, O., Gehlmann, M., Muller, J., Nemsak, S., Sethian, J.A., Kaduwela, A., Bluhm, H., Fadley, C.

Blind Ptychographic Phase Retrieval via Convergent Alternating Direction Method of Multipliers  [TAG-4]

SIAM J. Imaging Sci., 12, 1,  2019 

Huibin Chang, Pablo Enfedaque, and Stefano Marchesini

Advanced denoising for X-ray ptychography  [TAG-4]

Optics express 27, no. 8 (2019): 10395-10418

Chang, H., Enfedaque, P., Zhang, J., Reinhardt, J., Enders, B., Yu, Y.S., Shapiro, D., Schroer, C.G., Zeng, T. and Marchesini, S.

High performance partial coherent x-ray ptychography [TAG-4, TAG-8]

International Conference on Computational Science (pp. 46-59)

Enfedaque, P., Chang, H., Enders, B., Shapiro, D., & Marchesini, S.

Iterative Joint Ptychography-Tomography with Total Variation Regularization [TAG-3, TAG-4, TAG-8]

IEEE International Conference on Image Processing (ICIP)

Chang, H., Enfedaque, P., & Marchesini, S.

Shape transform phasing of edgy nanocrystals [TAG-1]

Acta Crystallographica A. A75, 239-259, January 2019

Chen J.P., Donatelli J.J., Schmidt K.E., and Kirian R.A.

Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity [TAG-1]

2019 IEEE International Conference on Image Processing (ICIP). IEEE, 2019

Chen, J. P., Schmidt, K. E., Kirian, R. A., & Donatelli, J. J.  

A multiscale neural network based on hierarchical matrices [Tag-2, Tag-7]

SIAM Multiscale Model. Simul. 17, 1189, 2019 

Y. Fan, L. Lin, L. Ying and L. Zepeda-Nunez

Correlative conventional scanning and ptychographic soft x-ray microscopy [TAG-None]

SPIE: X-Ray Nanoimaging: Instruments and Methods IV, 11112 (2019)

Jiangtao Zhao, Kasra Nowrouzi, Richard Celestre, Matthew Marcus, Young-Sang Yu, David A Shapiro

 Accelerating Optical Absorption Spectra and Exciton Energy Computation via Interpolative Separable Density Fitting  [TAG-2]

Intern. Conf. Computational Science, 2018

W. Hu, M. Shao, A. Cepellotti, F. H. da Jornada, L. Lin, K. ?icke, C. Yang and S. G. Louie

 PSelInv: A distributed memory parallel algorithm for selected inversion: the non-symmetric case  [TAG-2, TAG-8]

Parallel Comput. 74, 84, 2018 

M.  Jacquelin, L. Lin and C. Yang

 Gradient Boosting Decision Trees for Echocardiogram Images [TAG-6, TAG-7]

2018 International Joint Conference on Neural Networks (IJCNN), 2018 

V. V. de Melo, D. M. Ushizima, S. F. Baracho and R. C. Coelho

 Computational Analysis of Grazing Incidence Small Angle X-Ray Scattering Data [TAG-10]

Submitted to J. Applied Crystallography, 2018 (in revision). 

A. Sarje, S. Chourou, D. Kumar, S. Venkatakrishnan, X. Li, and A. Hexemer 

 Pursuing the critical dimension using Grazing Incidence Small Angle X-ray Scattering  [TAG-10]

Proc. Vol. 10585, Metrology, Inspection, and Process Control for Microlithography XXXII, SPIE Advanced Lithography 2018.

G. Freychet, D.  Kumar, R. Pandol?, P. Naulleau, I. Cordova, J. Strzalka, M. Fukuto, and A. Hexemer 

 Programmed LWR metrology by multi-techniques approach  [TAG-10]

Proceeding SPIE Advanced Lithography, Vol. 10585, pp. 105850F, 2018.  

J. Reche, M. Besacier, P. Gergaud, Y. Blancquaert, G. Freychet and T. Labbaye 

 Pursuing the critical dimension in etched patterns using x-ray scattering   [TAG-10]

Proceedings SPIE Advanced Lithography, Vol. 10585, pp. 10585-7, 2018. 

G. Freychet, D. Kumar, R. Pandol, D. Staacks, P. Naulleau, R. J. Kline, D. Sunday, M. Fukuto, J. Strzalka and A. Hexemer  

 Ring artifact reduction in synchrotron X-ray tomography through helical acquisition  [TAG-6, TAG-7]

Measurement Science and Technology, Volume 29, Number 3, 2018,

D.M. Pelt, and D. Y.  Parkinson 

 Improving Tomographic Reconstruction from Limited Data Using Mixed-Scale Dense Convolutional Neural Networks   [TAG-6, TAG-7]

Journal of Imaging, 4(11), 128, 2018 

Pelt, D. M., Batenburg, K. J., & Sethian, J. A.

 DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives   [TAG-6]

8th IEEE Symposium on Large Data Analysis and Visualization in conjunction with IEEE VIS 2018, Berlin, Germany, October 21, 2018. 

Brenton Lessley, Talita Perciano, Colleen Heinemann, David Camp, Hank Childs, E. Wes Bethel 

 A mixed-scale dense convolutional neural network for image analysis     [TAG-6,TAG-7]

Proceedings of the National Academy of Sciences, 2018

D.M. Pelt and J.A. Sethian 

 Xi-cam: A versatile interface for data visualization and analysis        [TAG-5,TAG-9]

J. Synchrotron Radiation, Jan., 2018.

Ronald J Pandolfi, Daniel B Allan, Elke Arenholz, Luis Barroso-Luque, Stuart I Campbell, Thomas A Caswell, Austin Blair, Francesco De Carlo, Sean Fackler, Amanda P Fournier, Guillaume Freychet, Masafumi Fukuto, Doga Gürsoy, Zhang Jiang, Harinarayan Krishnan, Dinesh Kumar, R Joseph Kline, Ruipeng Li, Christopher Liman, Stefano Marchesini, Apurva Mehta, Alpha T N'Diaye, Dilworth Y Parkinson, Holden Parks, Lenson A Pellouchoud, Talita Perciano, Fang Ren, Shreya Sahoo, Joseph Strzalka, Daniel Sunday, Christopher J Tassone, Daniela Ushizima, Singanallur Venkatakrishnan, Kevin G Yager, Peter Zwart, James A Sethian, Alexander Hexemer

Dataflow at the COSMIC Beamline-Stream Processing and Supercomputing   [TAG-4, TAG-5]

Microscopy and Microanalysis, 24(S2), 58-59, 2018

Enders, B., Nowrouzi, K., Krishnan, H., Marchesini, S., Park, J., Yu, Y. S., & Shapiro, D. A 

GPU-Based Implementation of Ptycho-ADMM for High Performance X-Ray Imaging [TAG-4, TAG-8]

International Conference on Computational Science, 540-553. 2018 

Enfedaque, P., Chang, H., Krishnan, H. and Marchesini, S. 

Partially coherent ptychography by gradient decomposition of the probe [TAG-4]

Acta Crystallographica Section A: Foundations and Advances, 74(3), 157-169, 2018)

Chang, H., Enfedaque, P., Lou, Y., & Marchesini, S 

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography  [TAG-4]

Nature communications, 9(1), 921, 2018

Yu, Y. S., Farmand, M., Kim, C., Liu, Y., Grey, C. P., Strobridge, F.  C., Krishnan, H., Maia FRNC., Kilcoyne ALD., Marchesini S., Perciano Costa Leite T, Warwick T, Padmore H.,  Cabana J. & Shapiro, DA. 

Variational Phase Retrieval with Globally Convergent Preconditioned Proximal Algorithm  [TAG-4]

SIAM Journal on Imaging Sciences, 11(1), 2018 

Huibin Chang, Stefano Marchesini, Yifei Lou, and Tieyong Zeng 

Mathematics in Pattern Recognition for Scientific Investigations  [TAG-6]

DOE Scientific Machine Learning Workshop, 2018.

T. Perciano, B. Loring, H. Krishnan, J.  Michael L. MacNeil, D. Ushizima,  

Total variation based phase retrieval for Poisson noise removal  [TAG-4]

SIAM Journal on Imaging Sciences, 11(1), 2018 

Huibin Chang, Yifei Lou, Yuping Duan, and Stefano Marchesini  

Denoising Poisson Phaseless Measurements via Orthogonal Dictionary Learning  [TAG-4]

Optics Express, 26, 16, 2018

Huibin Chang and Stefano Marchesini

Free-electron laser data for multiple-particle fluctuation scattering analysis [TAG-1]

Nature Scientific Data, 5, 180201, October 2018

Pande K., Donatelli J.J., Malmerberg E., Foucar L.M., Poon B.K., Sutter M., Botha, S., Basu S., Doak R.B., Dorner K., Epp S.W., Englert L., Fromme R., Hartmann E., Hartmann R., Hauser G., Hattne J., Hosseinizadeh A., Kassemeyer S., Lomb L., Montero S.F.C., Menzel A., Rolles D., Rudenko A., Seibert M.M., Sierra R.G., Schwander P., Ourmazd A., Fromme P., Sauter N.K., Bogan M., Bozek J., Bostedt C., Schlichting I., Kerfeld C.A., and Zwart P.H.

Structure determination from experimental fluctuation X-ray scattering [TAG-1]

PNAS, 115(45), 11772-11777, November 2018

Pande K., Donatelli J.J., Malmerberg E., Foucar L., Bostedt C., Schlichting I., and Zwart P.H.,

Nanoscale Visualization of Magnetic Contrasts with Soft X-ray Spectro-Ptychography at the Advanced Light Source [TAG-None]

Microscopy and Microanalysis 24 (S2), 530-531 (2018)

Young-Sang Yu, Richard Celestre, Bjoern Enders, Kasra Nowrouzi, Howard Padmore, Tony Warwick, Jong-Ryul Jeong, David A Shapiro

Three dimensional localization of nanoscale battery reactions using soft X-ray tomography [TAG-None]

Nature Communications, 9, 921 (2018)

Young-Sang Yu, Maryam Farmand, Chunjoong Kim, Yijin Liu, Clare P Grey, Fiona C Strobridge, Tolek Tyliszczak, Rich Celestre, Peter Denes, John Joseph, Harinarayan Krishnan, Filipe RNC Maia, AL David Kilcoyne, Stefano Marchesini, Talita Perciano Costa Leite, Tony Warwick, Howard Padmore, Jordi Cabana, David A Shapiro

Dataflow at the COSMIC Beamline-Stream Processing and Supercomputing [TAG-None]

Microscopy and Microanalysis 24 (S2), 58-59 (2018)

Bjoern Enders, Kasra Nowrouzi, Harinarayan Krishnan, Stefano Marchesini, Jungjin Park, Young-Sang Yu, David A Shapiro

The COSMIC Imaging Beamline at the Advanced Light Source: a new facility for spectro microscopy of nano-materials [TAG-None]

Microscopy and Microanalysis 24 (S2), 8-11 (2018)

David A Shapiro, Richard Celestre, Bjoern Enders, John Joseph, Harinarayan Krishnan, Matthew A Marcus, Kasra Nowrouzi, Howard Padmore, Jungjin Park, Anthony Warwick, Young-Sang Yu

Nanosurveyor 2: A Compact Instrument for Nano-Ptychography at the Advanced Light Source [TAG-None]

Proceeedings MEDSI, DOI: 10.18429/JACoW-MEDSI2018-THPH07 (2018)

Richard Celestre, Kasra Nowrouzi, Howard Padmore, David Shapiro

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses [TAG-1]

Phys. Rev. Letters, 119, 158102, 2017 

Ruslan P.  Kurta, Jeffrey J. Donatelli, Chun Hong Yoon, Peter Berntsen, Johan Bielecki, Benedikt J. Daurer, Hasan DeMirci, Petra Fromme, Max Felix Hantke, Filipe R.N.C. Maia, Anna Munke, Carl Ne?elblad, Kanupriya Pande, Hemanth K.N. Reddy, Jonas A. Sellberg, Raymond G. Sierra, Martin Svenda, Gijs van der Schot, Ivan A. Vartanyants, Garth J.  Williams, P. Lourdu Xavier, Andrew Aquila, Peter H. Zwart, and Adrian P. Mancuso

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase [TAG-1]

Proc. National Acad. Sciences, 114(28), 7222-7227, 2017

Jeffrey J. Donatelli, James A. Sethian and Peter H. Zwart 

Structural enzymology using X-ray free electron lasers [TAG-1]

Structural Dynamics, 4, 044003

Christopher Kupitz, Jose L. Olmos Jr., Mark Holl, Lee Tremblay, Kanupriya Pande, Suraj Pandey, Dominik Oberthr, Mark Hunter, Mengning Liang, Andrew Aquila, Jason Tenboer, George Calvey, Andrea Katz, Yujie Chen, Max O. Wiedorn, Juraj Knoska, Alke Meents, Valerio Majriani, Tyler Norwood, Ishwor Poudyal, Thomas Grant, Mitchell D. Miller, Weijun Xu, Aleksandra Tolstikova, Andrew Morgan, Markus Metz, Jose M. Martin- Garcia, James D. Zook, Shatabdi Roy-Chowdhury, Jesse Coe, Nirupa Nagaratnam, Domingo Meza, Raimund Fromme, Shibom Basu, Matthias Frank, Tomas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry N. Chapman, Nadia Zatsepin, Garrett Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George N. Phillips Jr., and Marius Schmidt

Highly efficient photocatalytic water splitting over edge-modified phosphorene nanoribbons   [TAG-2]

J. Amer. Chem.  Soc. 139, 15429, 2017

W. Hu, L.  Lin, R. Zhang, C. Yang and J. Yang  

Interpolative separable density fitting decomposition for accelerating hybrid density functional calculations with applications to defects in silicon   [TAG-2]

J. Chem. Theory Comput. 13, 5420, 2017  

W. Hu, L. Lin and C. Yang

Projected Commutator DIIS Method for Accelerating Hybrid Functional Electronic Structure Calculations  [TAG-2]

J. Chem. Theory Comput.  13, 5458, 2017

W. Hu, L. Lin and C. Yang  

Accelerating selected columns of the density matrix computations via approximate column selection  [TAG-2]

SIAM J. Sci. Comput. 39, 1178, 2017

A.  Damle, L. Lin and L. Ying

Robust Determination of the Chemical Potential in the Pole Expansion and Selected Inversion Method for Solving Kohn-Sham density functional theory   [TAG-2]

J. Chem. Phys. 147, 144107, 2017

W. Jia and L. Lin

A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions, Part II: Eigenvalue problems   [TAG-2]

Math. Model. Numer. Anal. 51, 1733, 2017 L. Lin and B. Stamm

Localized spectrum slicing    [TAG-2]

Math. Comp. 86, 2345, 2017

L. Lin

Randomized estimation of spectral densities of large matrices made accurate   [TAG-2]

Numer. Math. 136, 183, 2017  

L. Lin

Adaptively compressed polarizability operator for accelerating large scale ab initio phonon calculations  [TAG-2]

Multiscale Model. Simul. 15, 29, 2017  

W.  Hu, L. Lin, A. Banerjee, E. Vecharynski and C. Yang

SCDM-k: Localized orbitals for solids via selected columns of the density matrix    [TAG-2]

J. Comput. Phys. 334, 1, 2017

A. Damle, L. Lin and L. Ying

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations    [TAG-2]

J. Comput. Phys. 335, 426 2017

G. Zhang, L. Lin,W. Hu, C. Yang and J.E. Pask

The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials    [TAG-12]

Journal of the American Chemical Society 139,5547-5557, 2017

M. Witman, S.  Ling, S. Jawahery, P. Boyd, M. Haranczyk, B. Slater, B. Smit

Accurate Characterization of the Pore Volume in Microporous Crystalline Materials    [TAG-12]

Langmuir 33, 14529-14538, 2017

D. Ongari, P. Boyd, S. Barthel, M. Witman, M. Haranczyk, B. Smit  

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages   [TAG-12]

ACS Central Science 3, 734-742, 2017

A. Slater, P. Reiss, A. Pulido, M. Little, D. Holden, L. Chen, Linjiang, S. Chong, B. Alston, R. Clowes, M. Haranczyk, M. Briggs, T. Hasell, G. Day, A. Cooper

Scanning electron microscopy as a source of morphological data on nanoparticles: image representativeness    [TAG-12]

Journal of Microscopy 265, 34-50, 2017

K. Odziomek, D. Ushizima, P. Oberbek, K.  Kurzydlowski, T. Puzyn, M. Haranczyk  

Machine learning for micro-tomography    [TAG-3,TAG-6,TAG-7]

Dev. X-Ray Tomogr. XI 18 (2017).

Parkinson, D. Y., Ushizima, D. M., Perciano, T., Krishnan, H., Barnard, H. S., MacDowell, A. A., Pelt, D., Sethian, J.A.

Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics  [TAG-3,TAG-6]

Journal of Synchrotron Radiation, 24(5): 1065-1077, Sept. 2017 

T. Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N. M. Larson, Daniel M. Pelt and F. W. Zok 

Maximal clique enumeration with data-parallel primitives  [TAG-6]

IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV), Phoenix, AZ, 2017, pp. 16-25, 2017 

B. Lessley, T. Perciano, M. Mathai, H. Childs and E. W. Bethel 

Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer  [TAG-3]

Computational Optical Sensing and Imaging CW2B, 2, 2017

Chen, M., Parkinson, D., Venkatakrishnan, S., Marchesini, S. & Waller, L 

Nearest-Neighbour Nanocrystal Bonding Dictates Framework Stability or Collapse in Colloidal Nanocrystal Frameworks [TAG-6]

Chemical Communications, Royal Society of Chemistry, 2017. 

Williams, Ushizima, Zhu, Anders, Milliron, Helms 

Machine learning for micro-tomography  [TAG-3,TAG-7]

Dev. X-Ray Tomogr. XI 18, 2017 

Parkinson, D. Y.; Ushizima, D. M.; Perciano, T.; Krishnan, H.; Barnard, H. S.; MacDowell, A. A.; Pelt, D.; Sethian, J. A 

Detection and Classification of Cervical Cells [TAG-6]

The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences, Kitzes, J., Turek, D., & Deniz, F. (Eds.), Oakland, CA: Univ. Calif. Press 2017. [book chapter] 

Ushizima, D.M.

Detection and Classification of Cervical Cells [TAG-6]

The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences, Kitzes, J., Turek, D., & Deniz, F. (Eds.), Oakland, CA: Univ. Calif. Press 2017. [book chapter] 

Ushizima, D.M.

Automating Cell Detection and Classification in Human Brain Fluorescent Microscopy Images Using Dictionary Learning and Sparse Coding [TAG-6]

Journal of Neuroscience Methods, 2017. 

Alegro, Theolas, Nguy, Castruita, Seeley, Ushizima, Grinberg

Convolutional Neural Networks with Tensor Flow: theory and practice [TAG-6, TAG-7]

Brazilian Society of Computation Press 2017. [book chapter] 

Araujo, Carneiro, Silva, Medeiros, Ushizima 

Computer Vision in python with libraries scikit-image and scikit-learn [TAG-6]

Brazilian Society of Computation Press 2017. [book chapter] 

Silva, Lopes, Araujo, Medeiros, Ushizima 

A multi-objective approach for calibration and detection of cells nuclei  [TAG-6] 

IEEE Congress on Evolutionary Computation, 2017.  

Oliveira, P., Moreira,  G., Ushizima, D.M., , C.M. Carneiro, F.M. Medeiros, F. Arujo, R. Silva, A Bianchi

Portable Learning Environments for Hands-On Computational Instruction Using Container- and Cloud- Based Technology to Teach Data Science [TAG-5, TAG-6]  

Practice and Experience in Advanced Research Computing Conference, PEARC’17. 

Holdgraf,  C.,  Culich,  A., Rokem, A.,  Deniz, F., Alegro,  M., Ushizima , D.M. 

Distributed Memory Parallel Markov Random Fields using Graph Partitioning [TAG-6]  

Fourth International Workshop on High Performance Big Graph Data Management, Analysis, and Mining (BigGraphs 2017):  IEEE BigData 2017

C. Heinemann, T. Perciano, D. Ushizima, and E. Wes Bethel 

Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics  [TAG-4] 

Journal of Synchrotron Radiation, 24(5): 1065-1077, September 2017 

T.  Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N.  M. Larson, Daniel M. Pelt and F. W. Zok 

On-the-Fly data assessment for high throughput X-ray diffraction measurement     [TAG-5] 

ICS Comb. Sci. 19, 377-385, 2017 

Ren, F., Pandolfi R., Van Campen, D., Hexemer, A., and Mehta, A. 

Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer    [TAG-4] 

Imaging and Applied Optics, 2017

Michael Chen, Dilworth Parkinson, Singanallur Venkatakrishnan, Stefano Marchesini, and Laura Waller

Nanometer-resolved spectroscopic study reveals the conversion mechanism at an elevated temperature  [TAG-4]

Crystal Growth & Design, 17,8, 2017

Guoqing Geng, Jiaqi Li, Young-Sang Yu, David A. Shapiro, David A. L. Kilcoyne, and Paulo J. M. Monteiro

Ptychographic imaging of nano-materials at the Advanced Light Source with the Nanosurveyor Instrument      [TAG-4] 

IOP Conference Series: Journal of Physics 849 012028, 2017

D.A. Shapiro, R. Celestre, Peter Denes, Maryam Farmand, John Joseph, A.L.D. Kilcoyne, Stefano Marchesini, Howard Padmore, Singanallur V.  Venkatakrishnan, Tony Warwick and Young-Sang Yuet 

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge   [TAG-4]

Scientific Reports, 7, 4757 (2017) 

Marcus Gallagher-Jones, Carlos Sato Baraldi Dias, Alan Pryor Jr, Karim Bouchmella, Lingrong Zhao, Yuan Hung Lo, Mateus Borba Cardoso, David Shapiro, Jose Rodriguez, and Jianwei Miao 

Near-edge X-ray refraction fine structure microscopy     [TAG-4]  

Appl. Phys. Lett. 110, 063101, 2017

Maryam Farmand, Richard Celestre, Peter Denes, A. L. David Kilcoyne, Stefano Marchesini, Howard Padmore, Tolek Tyliszczak, Tony Warwick, Xiaowen Shi, James Lee2,  Young-Sang Yu, Jordi Cabana, John Joseph, Harinarayan Krishnan, Talita Perciano, Filipe R. N. C. Maia, and David A. Shapiro 

Nanosurveyor: a framework for real-time data processing  [TAG-4, TAG-5]

Advanced Structural and Chemical Imaging 20173:7,  2017

B.J. Daurer, H. Krishnan, T. Perciano, F. R.N.C. Maia, D.A. Shapiro, J.A. Sethian, and Stefano Marchesini

Scanning electron microscopy image representativeness: morphological data on nanoparticles  [TAG-6]

Jour. of Microscopy, 265(1), 2017

Odziomek, K., , Ushizima, D., Oberbek, P., Kurzydlowski, K., Puzyn, T., and Haranczyk, M

Chebyshev polynomial filtered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations      [TAG-2]

J. Chem. Phys. 145, 154101, 2016 

A. S. Banerjee, L.  Lin, W. Hu, C. Yang, J. E. Pask 

PSelInv: A distributed memory parallel algorithm for selected inversion: the symmetric case      [TAG-2, TAG-8]

ACM Trans. Math. Software 43, 21, 2016 

M. Jacquelin, L. Lin and C. Yang 

Adaptively compressed exchange operators      [TAG-2]

J.  Chem. Theory Comput. 12, 2242, 2016 

L. Lin

Low rank approximation in G0W0 calculations      [TAG-2]

Sci. China Math., 59 1593, 2016

M.  Shao, L. Lin, C. Yang, F. Liu, F. Jornada, J. Deslippe and S. G. Louie 

Decay estimates of discretized Green’s functions for Schrodinger type operators     [TAG-2]

China Math., 59, 1561, 2016 

L. Lin and J. Lu

Approximating spectral densities of large matrices     [TAG-2]

SIAM Rev. 58, 34, 2016 

L.  Lin, Y. Saad and C. Yang 

Edge-modified phosphorene nanoflake heterojunctions as highly efficient solar cells     [TAG-2]

Nano Letters 16 1675, 2016 

W. Hu, L. Lin, C. Yang, J. Dai and J. Yang 

Enhancing the scalability and load balancing of the parallel selected inversion algorithm via tree-based asynchronous communication    [TAG-2]

IEEE IPDPS, 192, 2016 

M. Jacquelin, L. Lin, N. Wichmann and C. Yang

A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions. Part I: Second order linear PDE   [TAG-2]

Math.  Model. Numer. Anal. (M2AN) 50, 1193, 2016 

L. Lin and B. Stamm

Large-scale ab initio simulations based on systematically improvable atomic basis   [TAG-2]

Mater. Sci. 112 503, 2016

P. Li, X. Liu, M. Chen, P. Lin, X. Ren, L. Lin, C. Yang and L. He

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein [TAG-1]

Science, 352(6286), 725-729, 2016

Kanupriya Pande, Christopher D. M. Hutchison, Gerrit Groenhof, Andy Aquila, Josef S. Robinson, Jason Tenboer, Shibom Basu, Sbastien Boutet, Daniel P. DePonte, Mengning Liang, Thomas A. White, Nadia A. Zatsepin, Oleksandr Yefanov, Dmitry Morozov, Dominik Oberthuer, Cornelius Gati, Ganesh Subramanian, Daniel James, Yun Zhao, Jake Koralek, Jennifer Brayshaw, Christopher Kupitz, Chelsie Conrad, Shatabdi Roy-Chowdhury, Jesse D. Coe, Markus Metz, Paulraj Lourdu Xavier, Thomas D. Grant, Jason E. Koglin, Gihan Ketawala, Raimund Fromme, Vukica rajer, Robert Henning, John C. H. Spence, Abbas Ourmazd, Peter Schwander, Uwe Weierstall, Ma?hias Frank, Petra Fromme, Anton Barty, Henry N. Chapman, Keith Moffat, Jasper J. van Thor, Marius Schmidt

Metal-Organic Framework with Optimal Adsorption, Separation, and Selectivity towards Xenon  [TAG-12]

Nature Communications 7, 2016

D. Banerjee, A.M. Plonka, C.M. Simon, R.K. Motkuri, J. Liu, X.  Chen, B.Smit, J.B. Parise, M. Haranczyk, P.K. Thallapally

A multi-slice simulation algorithm for grazing-incidence small-angle X-ray scattering  [TAG-8,TAG-10]

J. Applied Crystallography, Vol.49, Part 6, December 2016.

Singanallur Venkatakrishnan, Jeffrey Donatelli, Dinesh Kumar, Abhinav Sarje, Sunil K. Sinha, Xiaoye S.  Li, Alexander Hexemer

Improved tomographic reconstruction of large-scale real-world data by filter optimization  [TAG-3]

Advanced Structural and Chemical Imaging, 2:17,  2016

D. M. Pelt and V. De Andrade

Robust model-based phase ptycho-tomography [TAG-3, TAG-4]

IEEE Signal Processing Letters, Vol. 23, no. 7, pp. 944-948, 2016

S. V. Venkatakrishnan, M. Farmand, Y.S.  Yu, H. Majidi, K. Van Benthem, S.  Marchesini, D. Shapiro, and A. Hexemer

Ammonia gas sensor based on the frequency-dependent impedance characteristics of ultrathin polyaniline films  [TAG-6]

Sensors and Actuators A: Physical, 2016

Santos, M.C.,   Bianchi, A., Ushizima, D., Pavinatto, F.J.,  Bianchi, R.F., 

Evaluation of Three Algorithms for the Segmentation of Overlapping Cervical Cells  [TAG-6]

IEEE Journal of Biomedical and Health Informatics, 99, pp. 2168-2194, 2016. 

Lu, Z.,  Carneiro, G.,  Bradley,  A., and Ushizima, D.M.