[Nexus] Extending NeXus for pixelated scanning transmission electron microscopy

[Dieter Weber]

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
https://github.com/LiberTEM/LiberTEM/blob/master/fileformat/STEM%20application%20definition%20hierarchy.txt


* Minimum set of information that would be required for pixelated STEM:
https://github.com/LiberTEM/LiberTEM/blob/master/fileformat/basic%20pixelated%20STEM.txt

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:
https://github.com/LiberTEM/LiberTEM/issues/15

What would be the next steps?

As a reference, a bit more information on STEM:

A diagram of a STEM instrument:
https://en.wikipedia.org/wiki/File:STEM_fig.tif

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,
Dieter

--
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


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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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