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The Coherent X-ray Imaging Data Bank

Nature Methods volume 9, pages 854–855 (2012)Cite this article

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X-ray lasers produce pulses of X-rays 1 billion times brighter than those of synchrotrons; this capability creates extraordinary research opportunities in physics, chemistry and biology1,2. The high repetition rate of these machines leads to large volumes of data. For example, the Coherent X-ray Imaging beamline at the Linac Coherent Light Source (LCLS) produces three times more data per second than the ATLAS detector of the Large Hadron Collider. This data volume increase has created a need for tools to analyze and make efficient use of the new observations.

The lack of a common file format has been a significant barrier to the effective sharing of software tools and analysis techniques. As a solution, CXIDB is standardized on CXI files, which are based on the HDF5 format (http://hdfgroup.org/). In a CXI file, every measurement is represented by an entry that aims to contain all the required information for its measurement’s interpretation (Fig. 1d). The entries contain several defined standardized groups that store the data along with metadata such as experimental conditions and instruments. The dictionary of defined groups can be extended to accommodate new types of metadata, and additional data (such as notebooks) can be added to the corresponding CXIDB entry in auxiliary files. Data depositors are encouraged to list publications that can be used both to cite the data entry and to document how the data were collected and processed. CXIDB includes a catalog of publicly available software to provide newcomers with a list of useful resources. The availability of high-quality software will be crucial for the progress of coherent X-ray imaging, just as it was for X-ray crystallography. The Protein Data Bank is a remarkable manifestation of such a development.

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Figure 1: Sample images from the CXIDB, covering different light sources and experimental techniques, and their file structure.

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Acknowledgements

I thank D. Skinner and the data contributors for helping start this project and J. Hajdu for proofreading the manuscript and providing helpful suggestions. A majority of the work in this paper was supported by the Petascale Initiative in Computational Science at the National Energy Research Scientific Computing Center (NERSC), which is funded by the US Department of Energy, Office of Science. The computational sources were provided by NERSC, which is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231.

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  1. NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Filipe R N C Maia

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Correspondence to Filipe R N C Maia.

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Maia, F. The Coherent X-ray Imaging Data Bank. Nat Methods 9, 854–855 (2012). https://doi.org/10.1038/nmeth.2110

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