[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,
Tobias
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
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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Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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