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14 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2 [Next/Last]

Instruments / Technical Area	Publication Details	Published
VMXi-Versatile Macromolecular Crystallography in situ	CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments Oliver N. F. King , Karl E. Levik , James Sandy , Mark Basham Acta Crystallographica Section D Structural Biology 80, 744 - 764 DOI: 10.1107/S2059798324009276 Open Access Show Abstract ▼ Abstract: A group of three deep-learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The first tool, a classification network, assigns images into categories relating to experimental outcomes. The other two tools are networks that perform both object detection and instance segmentation, resulting in masks of individual crystals in the first case and masks of crystallization droplets in addition to crystals in the second case, allowing the positions and sizes of these entities to be recorded. The creation of these tools used transfer learning, where weights from a pre-trained deep-learning network were used as a starting point and repurposed by further training on a relatively small set of data. Two of the tools are now integrated at the VMXi macromolecular crystallography beamline at DLS, where they have the potential to absolve the need for any user input, both for monitoring crystallization experiments and for triggering in situ data collections. The third is being integrated into the XChem fragment-based drug-discovery screening platform, also at DLS, to allow the automatic targeting of acoustic compound dispensing into crystallization droplets.	Oct 2024
I11-High Resolution Powder Diffraction	Project M: investigating the effect of additives on calcium carbonate crystallisation through a school citizen science program Claire A. Murray , Project M Scientists , Laura Holland , Rebecca O'Brien , Alice Richards , Annabelle Baker , Mark Basham , David Bond , Leigh D. Connor , Sarah J. Day , Jacob Filik , Stuart Fisher , Peter Holloway , Karl Levik , Ronaldo Mercado , Jonathan Potter , Chiu C. Tang , Stephen P. Thompson , Julia E. Parker Crystengcomm 50 DOI: 10.1039/D3CE01173A Diamond Proposal Number(s): [15723] Open Access Show Abstract ▼ Abstract: Calcite and vaterite crystallisation is strongly influenced by the presence of additives during the reaction process, as demonstrated by organic molecules in biogenic calcium carbonate formation. The effect of additives on the lattice parameters of calcite and vaterite in syntheses are frequently reported, but only as discrete studies discussing a single polymorph. The intertwined nature of these polymorphs, due to their shared reaction pathway, is rarely discussed. In this work we report the results of a large scale citizen science project to explore the influence of amino acids and related additives on both polymorphs, highlighting their differences and commonalities in terms of the effect on the lattice parameters and polymorph selectivity.	Jan 2024
Data acquisition Detectors	Data analysis infrastructure for Diamond Light Source macromolecular & chemical crystallography and beyond M. Gerstel , A. W. Ashton , R. J. Gildea , K. E. Levik , G. Winter ICALEPCS2019 DOI: 10.18429/JACoW-ICALEPCS2019-WEMPR001 Open Access Show Abstract ▼ Abstract: The Diamond Light Source data analysis infrastructure, Zocalo, is built on a messaging framework. Analysis tasks are processed by a scalable pool of workers running on cluster nodes. Results can be written to a common file system, sent to another worker for further downstream processing and/or streamed to a LIMS. Zocalo allows increased parallelization of computationally expensive tasks and makes the use of computational resources more efficient. The infrastructure is low-latency, fault-tolerant, and allows for highly dynamic data processing. Moving away from static workflows expressed in shell scripts we can easily re-trigger processing tasks in the event that an issue is found. It allows users to re-run tasks with additional input and ensures that automatically and manually triggered processing results are treated equally. Zocalo was originally conceived to cope with the additional demand on infrastructure by the introduction of Eiger detectors with up to 18 Mpixels and running at up to 560 Hz framerate on single crystal diffraction beamlines. We are now adapting Zocalo to manage processing tasks for ptychography, tomography, cryo-EM, and serial crystallography workloads.	Oct 2019
Data acquisition	Treatment of x-ray diffraction data at diamond light source James Parkhurst , Graeme Winter , Richard Gildea , Markus Gerstel , Karl Levik , Irakli Sikharulidze , Dave Hall , Katherine Mcauley , Gwyndaf Evans , Alun Ashton Twenty-Fourth Congress and General Assembly of the International Union of Crystallography Show Abstract ▼ Abstract: In any experimental discipline, raw data represents the source from which all discoveries are derived. A more strict interpretation in X-ray diffraction experiments may refer to this as primary data since any pixel counts will have been manipulated (e.g. analogue to digital conversion, dark current correction, interpolation of pixels etc.); however the fundamental idea remains: this is the closest it is possible to get to the original experimental measurements. At Diamond Light Source, the principle of secure recording and storage of the primary data was embedded in the data acquisition system from the outset. The general user does not have permission to alter or delete the raw experimental data, and the acquisition system GDA is designed to prevent over-writing of the images.	Aug 2017
	Monitoring and cataloguing the progress of synchrotron experiments, data reduction, and data analysis at Diamond Light Source from a user's perspective Jun Aishima , Alun Ashton , Stuart Fisher , Karl Levik , Graeme Winter ICALEPCS2015 Open Access Show Abstract ▼ Abstract: The high data rates produced by the latest generation of detectors, more efficient sample handling hardware and ever more remote users of the beamlines at Diamond Light Source require advanced data reduction and data analysis tools to maximize the potential benefit to scientists. Here we describe some of our experiment data reduction and analysis steps, including real time image analysis with DIALS, our Fast DP and xia2-based data reduction pipelines, and Fast EP phasing and DIMPLE difference map calculation pipelines that aim to rapidly provide feedback about the recently completed measurements. SynchWeb, an interface to an open source laboratory information management system called ISPyB (co-developed at Diamond and the ESRF), provides a modern, flexible framework for managing samples and visualizing the data from all of these experiments and analyses, including plots, images, and tables of the analysed and reduced data, as well as showing experimental metadata, sample information.	Oct 2015
Data acquisition	SynchWeb: a modern interface for ISPyB Stuart Fisher , Karl Levik , Mark Williams , Alun Ashton , Katherine Mcauley Journal Of Applied Crystallography 48, 927 - 932 DOI: 10.1107/S1600576715004847 PMID: 26089766 Open Access Show Abstract ▼ Abstract: SynchWeb is a modern interface to the ISPyB database. It significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography. It adds a variety of new features including project management, an integrated diffraction image viewer, and a map and model viewer, as well as displaying results from automated analysis pipelines. Virtually all aspects of an experiment can be monitored through the web browser and the success of each experiment can be evaluated.	Jun 2015
I06-Nanoscience (XPEEM)	Data Analysis WorkbeNch (DAWN) Mark Basham , Jacob Filik , Michael Wharmby , Peter Chang , Baha El Kassaby , Matt Gerring , Jun Aishima , Karl Levik , Bill Pulford , Irakli Sikharulidze , Duncan Sneddon , Matthew Webber , Sarnjeet Dhesi , Francesco Maccherozzi , Olof Svensson , Sandor Brockhauser , Gabor Náray , Alun Ashton Journal Of Synchrotron Radiation 22, 828-838 DOI: 10.1107/S1600577515002283 PMID: 25931106 Open Access Show Abstract ▼ Abstract: Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single-crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientifc area.	May 2015
Data acquisition	SynchLink: an iOS app for ISPyB Helen Mary Ginn , Ghita Kouadri Mostefaoui , Karl Erik Levik , Jonathan Mark Grimes , Martin Austin Walsh , Alun William Ashton , David Ian Stuart Journal Of Applied Crystallography 47 (5), 1781 - 1783 DOI: 10.1107/S1600576714017531 PMID: 25294981 Open Access Show Abstract ▼ Abstract: The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.	Oct 2014
NONE-No attached Diamond beamline	Remote access to Diamond Light Source - Adding flexibility to MX experiments Dave Hall , Pierre Aller , Alun Ashton , Danny Axford , Alice Douangamath , Richard Fearn , Paul Hathaway , Karl Levik , Katherine Mcauley , Mark Williams Show Abstract ▼ Abstract: Diamond Light Source (DLS) provides a suite of world-leading beamlines for macromolecular crystallography (MX) experiments which are used by scientists from all over the world. Key to their success is an integrated approach to automating the hardware and software environments such that it is only necessary to enter the beamline hutch to change large batches of samples for the robotic sample changers. Alongside investing in automation, all beamlines are also equipped with Pilatus 6M-F detectors (25 – 100 Hz) resulting in fast data collections and high turnover of samples. Rapid downstream processing of the resulting data has been developed since this is essential to drive experimental decisions. The feedback from these pipelines needs to be made readily available to users in a timely manner and a number of tools are available for both local and remote visualization of results. Remote access to these facilities was a design requirement from the outset. Several tools have been integrated and developed to streamline the process of remote access yet give the same software environment remotely as would be experienced if the experimenter was present at the beamline. The advent of remote access for cryogenically frozen samples has led to the implementation of new shift patterns for the user programme, enabling frequent short shifts for the many groups who use DLS. Remote access to MX beamlines is also a prerequisite of many industrial clients of DLS. For the future we are moving forward with the development of remote access for insitu data collection from crystallization plates following on from the success of this method for screening and collecting data by users at the beamlines. The implementation and impact of remote access at DLS will be presented here.	Aug 2014
	ISPyB: an information management system for synchrotron macromolecular crystallography S. Delageniere , P. Brenchereau , L. Launer , Alun Ashton , R. Leal , S. Veyrier , J. Gabadinho , E. J. Gordon , S. D. Jones , K. E. Levik , S. M. Mcsweeney , S. Monaco , M. Nanao , D. Spruce , O. Svensson , M. A. Walsh , G. A. Leonard Bioinformatics 27 (22) DOI: 10.1093/bioinformatics/btr535 Show Abstract ▼ Abstract: Motivation: Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management.Results: ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.	Sep 2011

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