16-19 October 2016
Copenhagen University
Europe/Copenhagen timezone

Data analysis platform in support of a Cryo-Electron Microscopy facility

17 Oct 2016, 17:00
1h 30m
Marble Hall (Copenhagen University)

Marble Hall

Copenhagen University

Thorvaldsensvej 40
Board: 26
Poster Posters


Mr. Kevin Savage (Diamond Light Source)


eBIC (electron Bio-Imaging Centre, http://diamond.ac.uk/Science/Integrated-facilities/eBIC.html) at Diamond Light Source provides scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for single particle analysis and cryo-tomography. Currently two powerful cryo-electron microscopes allow users to investigate the structure of individual cells and to visualise single bio-molecules, exploiting techniques that are rarely available at home laboratories. We are integrating and automating pipelines to help users perform both on-the-fly tomography and single particle analysis. The raw data is typically large, producing gigabytes of data for both tomography tilt series and single particle analysis each hour. On top of this, because radiation dose rates often have to be kept low, the data is very noisy and requires a lot of processing to produce high resolution 3d reconstructions of the original samples. Tomography data is being processed using custom automation around the IMOD (http://bio3d.colorado.edu/imod/) software. Single particle analysis automation will be based on the Scipion framework (http://scipion.cnb.csic.es/) using a variety of underlying tools. The software will run on our in house cluster, utilising our parallel file system and high performance network. We are also integrating with our ISPyB database and plan to add data input from Scipion later this year. This means we can expose results though the SynchWeb interface which will allow users to browse and search through their results as processing steps complete as well as track the full sample lifecycle including sample shipping and data collection.

Primary author

Mr. Kevin Savage (Diamond Light Source)


Dr. Alun Ashton (Diamond Light Source) Dr. Corey Hecksel (Diamond Light Source) Dr. Daniel Clare (Diamond Light Source) Prof. David Stewart (Diamond Light Source/STRUBI) Dr. Martyn Winn (STFC) Dr. Siebert Alistair (Diamond Light Source) Dr. Tom Burnley (STFC)

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