<div dir='auto'><div>Dear Tobias,</div><div dir="auto"><br></div><div dir="auto">thank you for your help! I can work on building such a file next week. We've been tied up with other issues in the last weeks, that's why this had to wait a bit. </div><div dir="auto"><br></div><div dir="auto">Best regards,</div><div dir="auto">Dieter<br><br><div data-smartmail="gmail_signature" dir="auto">-- <br>Dr. Dieter WEBER <br><br>Peter Grünberg Institute PGI-5 for Microstructure Research <br>Ernst Ruska-Centre ER-C for Microscopy and Spectroscopy with Electrons <br>Research Centre Jülich <br>D-52425 Jülich, Germany <br><br>Email: d.weber@fz-juelich.de <br>Phone: +49 2461 61 85118 <br></div><div class="gmail_extra" dir="auto"><br><div class="gmail_quote">On Apr 3, 2018 17:54, Tobias Richter <Tobias.Richter@esss.se> wrote:<br type="attribution"><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Dear Dieter et al,</p>
<p dir="ltr">We very much agree on the goals in your drafts. <br>
It looks like we need to get to the technical detail pretty soon.<br>
In order to understand what data you have to deal with an example file would go a long way.<br>
Could you maybe produce something in HDF5 that roughly follows your proposed structure?<br>
Then it's a less abstract problem and we can follow up with more informed comments and questions.</p>
<p dir="ltr">To keep the community here in the loop, I would prefer to keep the discussion on this list for the time being. </p>
<p dir="ltr">Best wishes,<br>
Tobias<br></p>
<p dir="ltr">On 15/03/2018, 15:36, "NeXus on behalf of Dieter Weber" <nexus-bounces@shadow.nd.rl.ac.uk on behalf of d.weber@fz-juelich.de> wrote:</p>
<p dir="ltr"> Dear all,<br>
<br>
with the LiberTEM project we are working towards an open software<br>
platform for pixelated scanning transmission electron microscopy (STEM).<br>
A widely supported file format for data exchange is perhaps the most<br>
important item on our agenda.<br>
<br>
The NeXus format seems ideally suited as a next-generation standardized<br>
file format for EM, and we'd like to extend it with the necessary base<br>
classes and application definitions for STEM data.<br>
<br>
This Tuesday, my colleague Alex and I joined the regular teleconference.<br>
Thank you for your support and the friendly reception! As a follow-up I<br>
am now sending this e-mail as you suggested.<br>
<br>
On GitHub I've created two very basic drafts:<br>
* Class hierarchy for STEM data<br>
https://github.com/LiberTEM/LiberTEM/blob/master/fileformat/STEM%20application%20definition%20hierarchy.txt<br>
<br>
<br>
* Minimum set of information that would be required for pixelated STEM:<br>
https://github.com/LiberTEM/LiberTEM/blob/master/fileformat/basic%20pixelated%20STEM.txt<br>
<br>
Now I'd kindly ask for your help and advice on how to implement this in<br>
NeXus. I've created a GitHub issue for discussions:<br>
https://github.com/LiberTEM/LiberTEM/issues/15<br>
<br>
What would be the next steps?<br>
<br>
As a reference, a bit more information on STEM:<br>
<br>
A diagram of a STEM instrument:<br>
https://en.wikipedia.org/wiki/File:STEM_fig.tif<br>
<br>
An electron beam is focused through a number of electron lenses and<br>
optionally an aberration corrector into a very finely focused probe.<br>
This probe is scanned pixel by across the sample. The transmitted beam<br>
is projected on a fluorescent screen, camera or detectors. The following<br>
signals can be collected to gain information on the sample at each pixel:<br>
<br>
* Transmitted and scattered beam, integrated over larger detector areas:<br>
Traditional brightfield or darkfield STEM<br>
* Image of transmitted and scattered beam as detector frame: pixelated<br>
STEM or scanning diffraction, depending on beam settings. This is an<br>
emerging technique enabled by fast direct-detection sensors<br>
* X-ray fluorescence: EDX/EDS<br>
* Electron energy loss spectroscopy: EELS<br>
* Cathodoluminescence, electron beam induced currents and so on: Less<br>
important for the beginning.<br>
<br>
In general, for the future we'd like to extend NeXus with all necessary<br>
base classes and application definitions for all common TEM and STEM<br>
methods. For now, our focus is on pixelated STEM as a pilot application.<br>
<br>
Many thanks in advance for your help!<br>
<br>
With best regards,<br>
Dieter<br>
<br>
--<br>
Dr. Dieter WEBER<br>
<br>
Peter Grünberg Institute, Microstructure Research (PGI-5)<br>
Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C)<br>
Forschungszentrum Jülich<br>
52425 Jülich, Germany<br>
<br>
Email: d.weber@fz-juelich.de<br>
Phone: +49 2461 61 85118<br>
<br>
<br>
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</blockquote></div><br></div></div></div>