Making Ptychography a real-time microscopy technique

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1 Math. Und Naturwissenschafte, Physik, Institut für Strukturphysik, Strukturphysik kondensierter Materie Making Ptychography a real-time microscopy technique Dresden, 27.May.2006 Robert Hoppe PhD Student Tel:

2 Experimental Setups PETRA III., DESY TU Dresden LCSL, SLAC, USA Collaborations Code Users ID 13, ESRF, Fr KIT, Karslruhe FU Berlin NTNU, Norway

3 Nanoprobe Endstation at P06

4

5 Refractive X-Ray Lenses first realized in 1996 (Snigirev et al.) a variety of refractive lenses have been developed since applied in full-field imaging and scanning microscopy most important to achieve optimal performance: parabolic lens shape nanofocusing lenses Lengeler, RWTH 100 µm

6 Compound Refractive Lenses (CRL) 50µm 500µm 1500µm radius of curvature single lenses made of Be Bruno Lengeler RWTH Aachen Gernamy parabo cylind 8

7 Nanofocusing Lenses (NFLs) single lens Made at IHM at TU Dresden together with SAW Components NFLs on wafer! about single lenses! optical axis APL 82, 1485 (2003)

8 Nanofocusing Lenses (NFLs) vertical lens synchrotron radiation beam horizontal lens slits ESRF ID13 point focus sample & scanner

9 Beam size (FWHM) [nm] Lens Alignment Optimize Lens Position & Do it again Beam Direction [mm]

10 Ptychography Indirect Light Microscopy Technique Ta Kα fluorescence 500 nm 50 nm lines and spaces

11 Lens Alignment Record ptychogram at expected focus position Reconstructed wave front propagate wave front astigmatism QuickTime and a None decompressor are needed to see this picture. 500 nm (-1 mm to 1 mm)

12 Lens Alignment After alignment of nanofocusing lenses with high-resolution camera: Record ptychogram at expected focus position Reconstructed wave front Caustic: vertical horizontal 500 nm -1 mm 1 mm -1 mm 1 mm

13 Lens Alignment vertical horizontal 340 µm before ptychographic plane 200 µm behind ptychographic plane vertical lens 540 µm upstream

14 Lens Alignment Focus after lens alignment: -1 mm 1 mm -1 mm 1 mm

15 LCLS Experiment at MEC reconstructed illumination Im Re z intensity Schropp et al. Scientific Reports, Vol. 3 (2013), 1-5

16 Scanning Coherent X-Ray Diffraction Imaging: Ptychography sample far-field diffraction pattern J. Rodenburg, H. Faulkner. Appl. Phys. Lett. 85, 4795 (2004), P. Thibault, et al., Science 321, 379 (2008), A. Schropp, et al., Appl. Phys. Lett. 96, (2010), Y. Takahashi, et al., PRB 83, (2011).

17 Ptychographic Microscopy Experiment at P06: detector: Pilatus 300k (172µm pixel size) sample-detector distance: 2080 mm QuickTime and a None decompressor are needed to see this picture. exposure time: 1.5 s per point Sample: NTT AT test pattern SEM image (I. Snigireva)

18 Scanning Microscopy: Fluorescence Imaging Ta Kα fluorescence 500 nm E = kev 50 x 50 steps of 40 x 40 nm 2 2 x 2 µm 2 FOV exposure: 1.5 s per point

19 Scanning Microscopy: Ptychography illumination im re A. Schropp, et al., APL 96, (2010), S. Hönig, et al., Opt. Exp. 19, (2011). 500 nm E = kev 50 x 50 steps of 40 x 40 nm 2 2 x 2 µm 2 FOV exposure: 1.5 s per point detected fluence: ph/nm 2

20 Scanning Microscopy: Ptychography illumination 78 x 81 nm nm E = kev 50 x 50 steps of 40 x 40 nm 2 2 x 2 µm 2 FOV exposure: 1.5 s per point detected fluence: ph/nm 2

21 Scanning Microscopy: Ptychography pixel size: 3.84 nm 2 Different features have different resolution!! nm A. Schropp, et al., APL 100, (2012)

22 Ptychography: Reconstruction Algorithm generate transmitted wavefield propagate O cycle many times P update amplitudes update object & illumination backpropagate Maiden & Rodenburg, Ultramicroscopy 109, 1256 (2009)

23 Key Requirements of Ptychography Matrix Handling - Large number of far-field pattern matrices Nx(UxV) - Optional input matrix (UxV) - Object matrix (XxY) - Illumination matrix (UxV) -Math Update functions matrix (UxV) - Additional functions matrix (UxV) -Complex number calculations -Fast Fourier transformation -Low quality random Porting done number by W.Hoenig, calculation 2010 Portierung einer Ptychographie-Anwendung auf das CUDA GPU-Modell

24 GPU Porting Strategy Matrix Handling - All data is stored in Global GPU RAM - Matrix calculations: 1 Thread per Pixel Math functions -Float2 and self written operators -cufft -curand Porting done by W.Hoenig, 2010 Portierung einer Ptychographie-Anwendung auf das CUDA GPU-Modell

25 Original porting by W. Hönig

26 GPU Porting Numbers Test Example (176 Patterns, 256x256 px ) Reference(enhanced) CPU- implementation: 1.8s /iteration GPU- implementation: s /iteration

27 GPU Porting Numbers Real Usage (504 Patterns, 256x256 px each, 1000 iterations ) Reference CPU- implementation: ~2 h GPU- implementation: ~8 min QuickTime and a MPEG-4 Video decompressor are needed to see this picture. 100 nm Phase of Au Nanoparticles

28 GPU Porting Numbers Tomography (91 projection up to Patterns, 256x256 px each ) Reference CPU- implementation: 10 s /iteration 1 1/2 month GPU- implementation: ~0.5 s /iteration ~ 2 days

29

30 S. Hönig, V. Meier, J. Patommel, S. Ritter, D. Samberg, F. Seiboth, T. M. Scholz, A. Schropp, S. Stephan, C. G. Schroer Inst. of Structural Physics, TU Dresden, Dresden, Germany G. Wellreuther, P. Bhargava, T. Claußen, U. Bösenberg, G. Falkenberg P06, PETRA III., Dresden, Germany Hae Ja Lee, B. Nagler, E. C. Galtier, B. Arnold, U. Zastrau, J. B. Hastings LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA D. Nilsson, F. Uhlén, U. Vogt, H. M. Hertz Biomedical & X-Ray Physics, KTH-AlbaNova, Stockholm, Sweden B. Lengeler II. Phys. Institut, RWTH Aachen, Aachen, Germany M. Burghammer, S. Schröder ESRF, Grenoble, France

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