[Nexus] Extending NeXus for pixelated scanning transmission electron microscopy

Tobias Richter Tobias.Richter at esss.se
Tue Apr 3 16:54:34 BST 2018

Dear Dieter et al,

We very much agree on the goals in your drafts. 
It looks like we need to get to the technical detail pretty soon.
In order to understand what data you have to deal with an example file would go a long way.
Could you maybe produce something in HDF5 that roughly follows your proposed structure?
Then it's a less abstract problem and we can follow up with more informed comments and questions.

To keep the community here in the loop, I would prefer to keep the discussion on this list for the time being. 

Best wishes,

On 15/03/2018, 15:36, "NeXus on behalf of Dieter Weber" <nexus-bounces at shadow.nd.rl.ac.uk on behalf of d.weber at fz-juelich.de> wrote:

    Dear all,
    with the LiberTEM project we are working towards an open software
    platform for pixelated scanning transmission electron microscopy (STEM).
    A widely supported file format for data exchange is perhaps the most
    important item on our agenda.
    The NeXus format seems ideally suited as a next-generation standardized
    file format for EM, and we'd like to extend it with the necessary base
    classes and application definitions for STEM data.
    This Tuesday, my colleague Alex and I joined the regular teleconference.
    Thank you for your support and the friendly reception! As a follow-up I
    am now sending this e-mail as you suggested.
    On GitHub I've created two very basic drafts:
    * Class hierarchy for STEM data
    * Minimum set of information that would be required for pixelated STEM:
    Now I'd kindly ask for your help and advice on how to implement this in
    NeXus. I've created a GitHub issue for discussions:
    What would be the next steps?
    As a reference, a bit more information on STEM:
    A diagram of a STEM instrument:
    An electron beam is focused through a number of electron lenses and
    optionally an aberration corrector into a very finely focused probe.
    This probe is scanned pixel by across the sample. The transmitted beam
    is projected on a fluorescent screen, camera or detectors. The following
    signals can be collected to gain information on the sample at each pixel:
    * Transmitted and scattered beam, integrated over larger detector areas:
    Traditional brightfield or darkfield STEM
    * Image of transmitted and scattered beam as detector frame: pixelated
    STEM or scanning diffraction, depending on beam settings. This is an
    emerging technique enabled by fast direct-detection sensors
    * X-ray fluorescence: EDX/EDS
    * Electron energy loss spectroscopy: EELS
    * Cathodoluminescence, electron beam induced currents and so on: Less
    important for the beginning.
    In general, for the future we'd like to extend NeXus with all necessary
    base classes and application definitions for all common TEM and STEM
    methods. For now, our focus is on pixelated STEM as a pilot application.
    Many thanks in advance for your help!
    With best regards,
    Dr. Dieter WEBER
    Peter Grünberg Institute, Microstructure Research (PGI-5)
    Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C)
    Forschungszentrum Jülich
    52425 Jülich, Germany
    Email: d.weber at fz-juelich.de
    Phone: +49 2461 61 85118
    Forschungszentrum Juelich GmbH
    52425 Juelich
    Sitz der Gesellschaft: Juelich
    Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
    Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
    Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
    Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
    Prof. Dr. Sebastian M. Schmidt
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