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van Driel TB, Nelson S, Armenta R, Blaj G, Boo S, Boutet S, Doering D, Dragone A, Hart P, Haller G, Kenney C, Kwaitowski M, Manger L, McKelvey M, Nakahara K, Oriunno M, Sato T, Weaver M. The ePix10k 2-megapixel hard X-ray detector at LCLS. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:608-615. [PMID: 32381760 PMCID: PMC7206547 DOI: 10.1107/s1600577520004257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/27/2020] [Indexed: 05/25/2023]
Abstract
The ePix10ka2M (ePix10k) is a new large area detector specifically developed for X-ray free-electron laser (XFEL) applications. The hybrid pixel detector was developed at SLAC to provide a hard X-ray area detector with a high dynamic range, running at the 120 Hz repetition rate of the Linac Coherent Light Source (LCLS). The ePix10k consists of 16 modules, each with 352 × 384 pixels of 100 µm × 100 µm distributed on four ASICs, resulting in a 2.16 megapixel detector, with a 16.5 cm × 16.5 cm active area and ∼80% coverage. The high dynamic range is achieved with three distinct gain settings (low, medium, high) as well as two auto-ranging modes (high-to-low and medium-to-low). Here the three fixed gain modes are evaluated. The resulting dynamic range (from single photon counting to 10000 photons pixel-1 pulse-1 at 8 keV) makes it suitable for a large number of different XFEL experiments. The ePix10k replaces the large CSPAD in operation since 2011. The dimensions of the two detectors are similar, making the upgrade from CSPAD to ePix10k straightforward for most setups, with the ePix10k improving on experimental performance. The SLAC-developed ePix cameras all utilize a similar platform, are tailored to target different experimental conditions and are designed to provide an upgrade path for future high-repetition-rate XFELs. Here the first measurements on this new ePix10k detector are presented and the performance under typical XFEL conditions evaluated during an LCLS X-ray diffuse scattering experiment measuring the 9.5 keV X-ray photons scattered from a thin liquid jet.
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Affiliation(s)
- Tim Brandt van Driel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Rebecca Armenta
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gabriel Blaj
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stephen Boo
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dionisio Doering
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Angelo Dragone
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Philip Hart
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gunther Haller
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Christopher Kenney
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Maciej Kwaitowski
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Leo Manger
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark McKelvey
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kaz Nakahara
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marco Oriunno
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Takahiro Sato
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matt Weaver
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Li X, Li C, Liu H. ClickX: a visualization-based program for preprocessing of serial crystallography data. J Appl Crystallogr 2019; 52:674-682. [PMID: 31236097 PMCID: PMC6557179 DOI: 10.1107/s1600576719005363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
A Python-based program for serial crystallography experimental data preprocessing is developed for both online and offline analysis. Enhanced features include a graphical user interface, batch job execution and fast parameter optimizations. Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.
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Affiliation(s)
- Xuanxuan Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, People's Republic of China.,Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, People's Republic of China
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, People's Republic of China
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White TA. Processing serial crystallography data with CrystFEL: a step-by-step guide. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:219-233. [PMID: 30821710 PMCID: PMC6400257 DOI: 10.1107/s205979831801238x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/31/2018] [Indexed: 11/11/2022]
Abstract
A step-by-step guide to processing serial crystallography data from X-ray free-electron lasers and synchrotron sources using CrystFEL is provided. This article provides a step-by-step guide to the use of the CrystFEL software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source. Whereas previous papers have described the theory and algorithms and their rationale, this paper describes the steps to be performed from a user perspective, including command-line examples.
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Affiliation(s)
- Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany
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Zohar S, Turner JJ. Multivariate analysis of x-ray scattering using a stochastic source. OPTICS LETTERS 2019; 44:243-246. [PMID: 30644871 DOI: 10.1364/ol.44.000243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The normalization of scattered intensity by incident flux is a crucial step in analyzing data from stochastic x-ray free electron laser sources and is complicated by non-linearities traditionally attributed to detector saturation. Here we show that such non-linearities can also arise when the sample spectra are non-uniform within the monochromator bandwidth. A method for modeling and removing this non-linearity using multivariate regression with shot-by-shot x-ray photon energy as an independent variable is presented. This approach demonstrates the benefit of event building and will allow for a reconsideration of data which has proven challenging to normalize.
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Veseli S, Schwarz N, Schmitz C. APS Data Management System. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1574-1580. [PMID: 30179199 PMCID: PMC6140395 DOI: 10.1107/s1600577518010056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/11/2018] [Indexed: 06/01/2023]
Abstract
As the capabilities of modern X-ray detectors and acquisition technologies increase, so do the data rates and volumes produced at synchrotron beamlines. This brings into focus a number of challenges related to managing data at such facilities, including data transfer, near real-time data processing, automated processing pipelines, data storage, handling metadata and remote user access to data. The Advanced Photon Source Data Management System software is designed to help beamlines deal with these issues. This paper presents the system architecture and describes its components and functionality; the system's current usage is discussed, examples of its use have been provided and future development plans are outlined.
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Affiliation(s)
- Siniša Veseli
- Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Nicholas Schwarz
- Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Collin Schmitz
- Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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Ke TW, Brewster AS, Yu SX, Ushizima D, Yang C, Sauter NK. A convolutional neural network-based screening tool for X-ray serial crystallography. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:655-670. [PMID: 29714177 PMCID: PMC5929353 DOI: 10.1107/s1600577518004873] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/26/2018] [Indexed: 05/24/2023]
Abstract
A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization.
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Affiliation(s)
- Tsung-Wei Ke
- International Computer Science Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella X. Yu
- International Computer Science Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Daniela Ushizima
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA 94704, USA
| | - Chao Yang
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Current Status of Single Particle Imaging with X-ray Lasers. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8010132] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Hutchison CDM, Cordon-Preciado V, Morgan RML, Nakane T, Ferreira J, Dorlhiac G, Sanchez-Gonzalez A, Johnson AS, Fitzpatrick A, Fare C, Marangos JP, Yoon CH, Hunter MS, DePonte DP, Boutet S, Owada S, Tanaka R, Tono K, Iwata S, van Thor JJ. X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature. Int J Mol Sci 2017; 18:E1918. [PMID: 28880248 PMCID: PMC5618567 DOI: 10.3390/ijms18091918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 01/03/2023] Open
Abstract
The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.
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Affiliation(s)
- Christopher D. M. Hutchison
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Violeta Cordon-Preciado
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Rhodri M. L. Morgan
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan;
| | - Josie Ferreira
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Gabriel Dorlhiac
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Alvaro Sanchez-Gonzalez
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Allan S. Johnson
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Ann Fitzpatrick
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK;
| | - Clyde Fare
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Jon P. Marangos
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Chun Hong Yoon
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Mark S. Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Daniel P. DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jasper J. van Thor
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
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Maia FRNC, White TA, Loh ND, Hajdu J. CCP-FEL: a collection of computer programs for free-electron laser research. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716011134] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The latest virtual special issue ofJournal of Applied Crystallography(http://journals.iucr.org/special_issues/2016/ccpfel) collects software for free-electron laser research and presents tools for a range of topics such as simulation of experiments, online monitoring of data collection, selection of hits, diagnostics of data quality, data management, data analysis and structure determination for both nanocrystallography and single-particle diffractive imaging. This article provides an introduction to the special issue.
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