Towards Integrated Facility-Wide Data Acquisition and Analysis at NSLS-II

Arkilic, Arman; Allan, Daniel; Caswell, Thomas A; Li, L.; Lauer, Kenneth; Abeykoon, Sameera K.

doi:10.1080/08940886.2017.1289810

Cited by 23 publications

(17 citation statements)

References 3 publications

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“…instrbuilder is part of a Python software suite that uses Bluesky (Arkilic et al, 2017) and associated modules created for x-ray science by a team at the NSLS-II (see https: //nsls-ii.github.io/). This combination generates an instrument and experiment control environment that facilitates reproducible experiments.…”

Section: Discussionmentioning

confidence: 99%

Instrbuilder: A Python package for electrical instrument control

Koerner¹

2019

JOSS

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Section: Discussionmentioning

confidence: 99%

Instrbuilder: A Python package for electrical instrument control

Koerner¹

2019

JOSS

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“…Higher-level automation is realized through Python routines based on the NSLS-II standard Ophyd hardware abstraction layer and Bluesky data collection suite (Arkilic et al, 2017;NSLS-II, 2019). The data collection graphical user interface Life Science Data Collection (LSDC) uses both Bluesky/Ophyd and dedicated Python libraries (Fig.…”

Section: Controls Systemsmentioning

confidence: 99%

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Schneider¹,

Shi²,

Andi³

et al. 2021

J Synchrotron Rad

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Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s−1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s−1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

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“…The Staubli robot is also under EPICS control through an IOC developed by EMBL. With all components under EPICS control, we developed our control code in Python using the Bluesky and Ophyd libraries developed at NSLS-II (Arkilic et al, 2017) to take advantage of capabilities such as logging and databroker access.…”

Section: Data Collectionmentioning

confidence: 99%

Solution scattering at the Life Science X-ray Scattering (LiX) beamline

et al. 2020

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This work reports the instrumentation and software implementation at the Life Science X-ray Scattering (LiX) beamline at NSLS-II in support of biomolecular solution scattering. For automated static measurements, samples are stored in PCR tubes and grouped in 18-position sample holders. Unattended operations are enabled using a six-axis robot that exchanges sample holders between a storage box and a sample handler, transporting samples from the PCR tubes to the X-ray beam for scattering measurements. The storage box has a capacity of 20 sample holders. At full capacity, the measurements on all samples last for ∼9 h. For in-line size-exclusion chromatography, the beamline-control software coordinates with a commercial high-performance liquid chromatography (HPLC) system to measure multiple samples in batch mode. The beamline can switch between static and HPLC measurements instantaneously. In all measurements, the scattering data span a wide q-range of typically 0.006–3.2 Å−1. Functionalities in the Python package py4xs have been developed to support automated data processing, including azimuthal averaging, merging data from multiple detectors, buffer scattering subtraction, data storage in HDF5 format and exporting the final data in a three-column text format that is acceptable by most data analysis tools. These functionalities have been integrated into graphical user interfaces that run in Jupyter notebooks, with hooks for external data analysis software.

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Towards Integrated Facility-Wide Data Acquisition and Analysis at NSLS-II

Cited by 23 publications

References 3 publications

Instrbuilder: A Python package for electrical instrument control

Instrbuilder: A Python package for electrical instrument control

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Solution scattering at the Life Science X-ray Scattering (LiX) beamline

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