DOI: 10.5281/zenodo.18241821
title: NanoMAX example dataset - ptychography on siemens stars - EH1

description: Example (single-beam single-slice) hard X-ray ptychographic dataset recorded at the Imaging Endstation (EH1) [1] of the NanoMAX beamline [2] at the MAX IV Laboratory [3]. 

The datasets were recorded on a siemens star sample at different photon energies. They are kept in the folder and file structure typical to the lab and beamline. The upload contains the raw data, the script used to reconstruct the raw data, the final reconstruction results and a jupyter notebook loading the reconstructions to create a figure of the reconstructed objects. 

Data setes were recorded at photon energies from 5 keV to 17 keV in 1 keV steps. A pair of KB-mirrors [4] was used to focus the probing X-ray beam. The sample was positioned 1500µm downstream of the focus postion and scanned in a Fermat-spiral scanning pattern [6] over a scan region of 6µm x 6µm with an average step size of 0.3µm. At each scan position a diffraction pattern was recorded with an Eiger2 X 4M detector (DECTRIS, Switzland) [7] and an exposure time of 0.5 seconds. The detector was positioned 7.180m downstream of the sample. All measurments were taken under vacuum conditions. There were no windows between the KB mirrors, the sample and the detector.

Reconstructions were performed using the ptypy-framework [8] using 1000 iterations of the difference-map (DM) algorithm [9], followed by 1000 iterations of the maximum likelihood (ML) algorithm [10] without position refinement and another 1000 iterations with positions refinement. All algorithms were implemented for GPUs using cupy [11].  

We acknowledge the MAX IV Laboratory for internal beamtime on the NanoMAX beamline. Research conducted at MAX IV, a Swedish national user facility, is supported by Vetenskapsrådet (Swedish Research Council, VR) under contract 2018-07152, Vinnova (Swedish Governmental Agency for Innovation Systems) under contract 2018-04969 and Formas under contract 2019-02496.



References:

[1] Maik Kahnt et al., "Current capabilities of the imaging endstation at the NanoMAX beamline", AIP Conf. Proc. 27 September 2023; 2990 (1): 040018. https://doi.org/10.1063/5.0169244 [2] Ulf Johansson et al., "NanoMAX: the hard X-ray nanoprobe beamline at the MAX IV Laboratory", J. Synchrotron Rad. 28, 1935-1947 (2023). https://doi.org/10.1107/S1600577521008213 [3] Aymeric Robert et al., "MAX IV Laboratory". Eur. Phys. J. Plus 138, 495 (2023). https://doi.org/10.1140/epjp/s13360-023-04018-w [4] Maik Kahnt et al., "Complete alignment of a KB-mirror system guided by ptychography," Opt. Express 30, 42308-42322 (2022) https://doi.org/10.1364/OE.470591[6] Xiaojing Huang et al., "Optimization of overlap uniformness for ptychography", Opt. Express 22, 12634-12644 (2014). https://doi.org/10.1364/OE.22.012634 [7] Tilman Donath et al., "EIGER2 hybrid-photon-counting X-ray detectors for advanced synchrotron diffraction experiments", J. Synchrotron Rad. 30, 723-738.(2023). https://doi.org/10.1107/S160057752300454X [8] Björn Enders et al.,  "Computational framework for ptychographic reconstructions", Proc. R. Soc. A.47220160640 (2016). http://doi.org/10.1098/rspa.2016.0640 [9] Pierre Thibault et al., “Probe retrieval in ptychographic coherent diffractive imaging,” Ultramicroscopy 109(4), 338–343 (2009). https://doi.org/10.1016/j.ultramic.2008.12.011[10] Pierre Thibault et al., "Maximum-likelihood refinement for coherent diffractive imaging," New J. Phys. 14 063004 (2012). https://doi.org/10.1088/1367-2630/14/6/063004 [11] Ryosuke Okuta et al. "Cupy: A numpy-compatible library for nvidia gpu calculations." Proceedings of workshop on machine learning systems (LearningSys) in the thirty-first annual conference on neural information processing systems (NIPS). Vol. 6. (2017).