Published July 1, 2021 | Version 0.1.0
Software Open

Ptychography 4.0: 0.1.0

Creators

  • 1. Jülich Research Centre
  • 2. FZ Jülich
  • 3. HZM, TU Munich
  • 4. HZDR
  • 5. HZB
  • 6. HZM

Contributors

  • 1. Jülich Research Centre
  • 2. HU Berlin
  • 3. FZ Jülich

Description

Homepage: https://ptychography-4-0.github.io/ptychography/
GitHub repository: https://github.com/Ptychography-4-0/ptychography/
PyPI: https://pypi.org/project/ptychography40/

This repository collects implementations for ptychography that result from the work of the Ptychography 4.0 project.

Installation

The short version:

$ virtualenv -p python3.9 ~/ptychography-venv/
$ source ~/ptychography-venv/bin/activate
(ptychography-venv) $ pip install ptychography40

Please see our documentation for details!

Applications

  • Scalable, parallel implementation of the Single Side Band method that is suitable for live data processing.

Please see the algorithms section of our documentation for details!

Ptychography 4.0 is evolving rapidly and prioritizes features following user demand and contributions. In the future we'd like to implement live acquisition, and more analysis methods for all applications of pixelated STEM and other large-scale detector data. If you like to influence the direction this project is taking, or if you'd like to contribute, please contact us in the GitHub Issue tracker.

License

Ptychography 4.0 is licensed under GPLv3.

Notes

We gratefully acknowledge funding from the Information & Data Science Pilot Project 'Ptychography 4.0' of the Helmholtz Association. We gratefully acknowledge funding from the Initiative and Network Fund of the Helmholtz Association within the Helmholtz Young Investigator Group moreSTEM under Contract No. VH-NG-1317 at Forschungszentrum Jülich in Germany.

Files

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Additional details

Cites
10.1364/ao.51.005698 (DOI)
10.5281/zenodo.4543704 (DOI)
10.1038/srep26348 (DOI)
10.1016/j.ultramic.2016.03.006 (DOI)
10.1088/1742-6596/644/1/012032 (DOI)
10.1016/s0304-3991(79)80021-2 (DOI)
10.1107/s0567739469001045 (DOI)
10.1002/bbpc.19700741112 (DOI)
10.1038/374630a0 (DOI)
10.1364/josaa.10.000231 (DOI)
10.1088/0022-3727/25/2/003 (DOI)
10.1038/s41586-018-0298-5 (DOI)
10.1016/j.ultramic.2014.09.013 (DOI)
10.1016/j.ultramic.2014.10.013 (DOI)
arXiv:1805.04957 (arXiv)
10.5281/zenodo.1478763 (DOI)
10.1103/physrevlett.121.243902 (DOI)
10.1142/11389 (DOI)
10.1017/s1431927619000497 (DOI)

Funding

European Commission
ESTEEM3 - Enabling Science and Technology through European Electron Microscopy 823717

References

  • [Bon2012] Pierre Bon and Serge Monneret and Benoit Wattellier (2012): Noniterative boundary-artifact-free wavefront reconstruction from its derivatives. The Optical Society. 10.1364/ao.51.005698
  • [Clausen2018] Clausen, Alexander and Weber, Dieter and Ruzaeva, Karina and Migunov, Vadim and Baburajan, Anand and Bahuleyan, Abijith and Caron, Jan and Chandra, Rahul and Dey, Shankhadeep and Halder, Sayandip and Katz, Daniel S. and Levin, Barnaby D.A. and Nord, Magnus and Ophus, Colin and Peter, Simon and Schyndel van, Jay and Shin, Jaeweon and Sunku, Sai and Müller-Caspary, Knut and Dunin-Borkowski, Rafal E. (2021): LiberTEM/LiberTEM: 0.6.0. Zenodo. 10.5281/zenodo.4543704
  • [Jesse2016] S. Jesse and M. Chi and A. Belianinov and C. Beekman and S. V. Kalinin and A. Y. Borisevich and A. R. Lupini (2016): Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography. Springer Nature. 10.1038/srep26348
  • [Krajnak2016] Matus Krajnak and Damien McGrouther and Dzmitry Maneuski and Val O{\textquotesingle} Shea and Stephen McVitie (2016): Pixelated detectors and improved efficiency for magnetic imaging in {STEM} differential phase contrast. Elsevier {BV}. 10.1016/j.ultramic.2016.03.006
  • [Yang2015] H Yang and L Jones and H Ryll and M Simson and H Soltau and Y Kondo and R Sagawa and H Banba and I MacLaren and P D Nellist (2015): 4D {STEM}: High efficiency phase contrast imaging using a fast pixelated detector. {IOP} Publishing. 10.1088/1742-6596/644/1/012032
  • [Cowley1979] J.M. Cowley (1979): Coherent interference in convergent-beam electron diffraction and shadow imaging. Elsevier {BV}. 10.1016/s0304-3991(79)80021-2
  • [Hoppe1969] W. Hoppe (1969): Beugung im inhomogenen Primärstrahlwellenfeld. I. Prinzip einer Phasenmessung von Elektronenbeungungsinterferenzen. International Union of Crystallography ({IUCr}). 10.1107/s0567739469001045
  • [Hegerl1970] R. Hegerl and W. Hoppe (1970): Dynamische Theorie der Kristallstrukturanalyse durch Elektronenbeugung im inhomogenen Primärstrahlwellenfeld. Wiley. 10.1002/bbpc.19700741112
  • [Nellist1995] P. D. Nellist and B. C. McCallum and J. M. Rodenburg (1995): Resolution beyond the {\textquotesingle}information limit{\textquotesingle} in transmission electron microscopy. Springer Nature. 10.1038/374630a0
  • [McCallum1993] B. C. McCallum and J. M. Rodenburg (1993): Simultaneous reconstruction of object and aperture functions from multiple far-field intensity measurements. The Optical Society. 10.1364/josaa.10.000231
  • [Friedman1992] S L Friedman and J M Rodenburg (1992): Optical demonstration of a new principle of far-field microscopy. {IOP} Publishing. 10.1088/0022-3727/25/2/003
  • [Jiang2018] Yi Jiang and Zhen Chen and Yimo Han and Pratiti Deb and Hui Gao and Saien Xie and Prafull Purohit and Mark W. Tate and Jiwoong Park and Sol M. Gruner and Veit Elser and David A. Muller (2018): Electron ptychography of 2D materials to deep sub-{\aa}ngström resolution. Springer Nature. 10.1038/s41586-018-0298-5
  • [Pennycook2015] Timothy J. Pennycook and Andrew R. Lupini and Hao Yang and Matthew F. Murfitt and Lewys Jones and Peter D. Nellist (2015): Efficient phase contrast imaging in {STEM} using a pixelated detector. Part 1: Experimental demonstration at atomic resolution. Elsevier {BV}. 10.1016/j.ultramic.2014.09.013
  • [Yang2015a] Hao Yang and Timothy J. Pennycook and Peter D. Nellist (2015): Efficient phase contrast imaging in {STEM} using a pixelated detector. Part {II}: Optimisation of imaging conditions. Elsevier {BV}. 10.1016/j.ultramic.2014.10.013
  • [Li:2018ngp] Li, Xin and Dyck, Ondrej and Kalinin, Sergei V. and Jesse, Stephen (2018): Compressed Sensing of Scanning Transmission Electron Microscopy {(STEM)} on Non-Rectangular Scans. 1805.04957
  • [Clausen2018a] Clausen, Alexander and Weber, Dieter and {Probonopd} and Caron, Jan and Nord, Magnus and Müller-Caspary, Knut and Ophus, Colin and Dunin-Borkowski, Rafal (2018): Libertem/Libertem: 0.1.0. Zenodo. 10.5281/zenodo.1478763
  • [Goy2018] Alexandre Goy and Kwabena Arthur and Shuai Li and George Barbastathis (2018): Low Photon Count Phase Retrieval Using Deep Learning. American Physical Society ({APS}). 10.1103/physrevlett.121.243902
  • [Weber2020] Weber, Dieter and Clausen, Alexander and Dunin-Borkowski, Rafal (2020): Handbook on {Big} {Data} and machine learning in the physical sciences. World Scientific. 10.1142/11389
  • [Ophus_2019] Colin Ophus (2019): Four-Dimensional Scanning Transmission Electron Microscopy (4D-{STEM}): From Scanning Nanodiffraction to Ptychography and Beyond. Cambridge University Press ({CUP}). 10.1017/s1431927619000497