SR and FELs:  XNPIG2014,  FOM2014,  ISSRNS2014,  MMC2014,  SXNS13,  FEL2014,  IMC2014,  XTOP2014,  ICEM2014,  XRM2014, 
ISSC14,  MAX IV,  Bombannes2014,  AWSB2014,  RACIRI2014, 
CAS,  HERCULES,  GRK,  ZSC,  PSI,  Diamond,  UXSS2013,  BSR2013,  XRM2012,  ICXOM22, 
Nanoscience:  Grenoble-INP,  AS NanoScience,  ESONN,  Nanosmat,  iNanoSchool,  ISSON14, 

Presentations at conferences:
K. Stachnik, I. Mohacsi, A. Meents, High resolution ptychography using off-axis illuminated zone plates, 12th International School and Symposium on Synchrotron Radiation in Natural Science, 15 - 20 June 2014, Warsaw, Poland, (Slides, Proceedings).
K. Stachnik, I. Mohacsi, A. Meents, High resolution off-axis ptychography with zone plates, DESY Photon Science Users’ Meeting 2014, 30 - 31 January 2014, Hamburg, Germany, (Poster).
K. Stachnik, A. Meents, Scanning X-ray microscopy with a single photon counting 2D detector, XLVIII Zakopane School of Physics, 20 - 25 May 2013, Zakopane, Poland, (Slides, Proceedings).
K. Stachnik, A. Meents, A simulation tool for ptychography experiment, Ptycho2013 International workshop on the state and the future of ptychography, 4 - 7 May 2013, Hohenkammer, Germany, (Poster).

Attended courses:
K. Stachnik, International Summer School of Crystallography 2014, May 11th - 17th, 2014, DESY, Hamburg, Germany.
K. Stachnik, Science with Advanced Coherent Light Sources, GRK Fall School 2013, October 7th - 11th, Research Campus Bahrenfeld, Hamburg, Germany, (Poster).
K. Stachnik, HSC15: Synchrotron X-ray Imaging for Biology, September 16th - 20th, 2013, ESRF, Grenoble, France, (Poster).
K. Stachnik, Summer Student Programme 2012 at DESY, July 17th - September 6th, 2012, Hamburg, Germany, (Slides, Final Report).

Theses:
K. Stachnik, Ptychographical measurements of biological specimens, Master thesis, AGH UST, Krakow, 2014.
K. Stachnik, High resolution differential phase contrast scanning X-ray microscopy with a single photon counting 2D detector, Bachelor thesis, AGH UST, Krakow, 2013.

Erasmus   ESN   Erasmus@AGH   Prezentacja 18.04.2013  
Uni-Hamburg:   Degree programs   Erasmus@UH   Erste Schritte   UniExp   Fachbereich Physik   Veranstaltungen Suchen  
Studierendenwerk-Hamburg   Campus-Hamburg  
Erasmus Mundus Joint Doctorates  

PhotonScience@DESY:   Seminars   Research Course   Research   Students  
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MNiSW  NCN   NCBiR   OSF   Granty na badania   EuroDesk   ERC   Horizon 2020   EURAXESS  (PL)   BUWIWM  

DESY:   HASYLAB   DORIS   PETRA   FLASH   XFEL   CFEL  
Europe:   ESRF   Soleil   EuroFEL   HZB   Diamond   SLS@PSI   SwissFEL@PSI   DAFNE   Elletra   ALBA   ANKA  
Polska:   SOLARIS   PolFEL   PL-Grid  

USA:   ALS@LBL   NSLS@BNL   SSRL@SLAC   APS@ANL   SRC@Madison  
World:   Spring8   Canadian Light Source   Australian Synchrotron   PhotonFactory@KEK   NSRRC  

Research:   TUM   MPG-Heidelberg   Uni-Goettingen   Uni-Hamburg   CXS   CXRO   Stony Brook   U. of Rochester   Microscopy Resource Center  
Munich-Centre for Advanced Photonics   Ultimate Microscopy   MicroscopyU   CAMERA  
X-ray Optics   AttoWorld   Way for Light   BioStruct-X   BioXFEL  
COST  (MPNS Action MP1203)   microbeam.eu  

FFTW   NADIA   CXPhasing   CXIDB   xafs.org   saxsview   IFEFFIT   Tools@ESFR   X-ray Server   EXPGUI for GSAS   xForum   Debian SR Software  
openGDA   HDF   McXtrace   XRMC   PaNdata   Hawk   shadow3  
ImageMagick   GraphicsMagick   CImg Library   ImageScience   CBFlib   RosettaCode FFT   OKOTechnologies   OsiriX  
3ds Max   Maya   Amira   Fiji (ImageJ)  

X-Ray Data Booklet  
X-Ray optics calculator  
Fresnel zone plate calculator  
X-Ray attenuation & absorption calculator  
X-Ray Interactions with Matter - resources @CXRO  
Energy unit conversions  
International Tables for Crystallography  (Bilbao server)  

Overview:   NSF   Nano.gov   NNIN   UnderstandingNano   NanotechnologyNow   Nanotechweb.org   NanoNet   NanoTomorrows  
NanoProfessor  
Research:   BNL   PNL   MRSEC   Foresight   nanoHUB   Cambridge   Manchester   London-nano   Bristol   ETH   SNI   EMPA   NBI  
ACMiN   ZTMSiN   Nano@WFiIS  

Xradia   Rigaku   Dectris   Bruker   MicroWorks   Hamamatsu  
Nanosurf   Nanosight  

Books:
Soft X-rays and Extreme Ultraviolet Radiation, D. Attwood, Cambridge, 2007.
An Introduction to Synchrotron Radiation: Techniques and Applications, P. Willmott, Wiley, 2011.
The Physics of Synchrotron Radiation, A. Hofmann, CUP, 2004.  Cambridge Books Online
Magnetism and Synchrotron Radiation,  E. Beaurepaire, H. Bulou, F. Scheurer, Springer, 2010.
Elements of Modern X-ray Physics,  J. Als-Nielsen, D. McMorrow, Wiley, 2011.
Generalized Phase Contrast. Applications in Optics and Photonics,  J.Gluckstad, D. Palima, Springer, 2009.
Nanobeam X-Ray Scattering: Probing Matter at the Nanoscale,  J. Stangl, C. Mocuta, V. Chamard, D. Carbone, Wiley, 2014.
Neutron and X-ray Optics,  J.T. Cremer, Jr., Elsevier, 2013.

Mathematical Methods for Optical Sciences,  G. Gbur, Cambridge, 2011.
Introduction to Fourier Optics,  J. Goodman, McGraw Hill, 1996.
A Student's Guide to Fourier Transforms,  J.F. James, Cambridge, 2011.
Diffraction, Fourier Optics and Imaging,  O.K. Ersoy, Wiley, 2007.
Coherent X-Ray Optics,  D.M. Paganin, Oxford, 2006.
Computational Fourier Optics - A Matlab Tutorial,  D. Voelz, SPIE Press, 2011.
Fundamentals of the Physical Theory of Diffraction,  P.Ya. Ufimtsef, Wiley, 2007.
Fourier Methods in Imaging,  R.L. Easton, Wiley, 2010.
Image Processing,  A.M. Grigoryan and M.M. Grigoryan, CRC Press, 2013.
Mathematical Foundations of Imaging, Tomography and Wavefield Inversion,  A.J. Devaney, Cambridge, 2012.

Coherent Optics: Fundamentals and Applications,  W. Lauterborn, T. Kurz, Springer, 2003.
Handbook of Coherent-Domain Optical Methods,  V.V. Tuchin, Springer, 2013.
Handbook of Mathematical Methods in Imaging,  O. Scherzer (Ed.), Springer, 2011.
Digital Holographic Microscopy,  M.K. Kim, Springer, 2011.

Synchrotron Radiation,  H. Wiedemann, Springer, 2003.
Free Electron Lasers,  Edited by S. Varro, InTech, 2012.

Lectures:
Synchrotron Radiation for Materials Science Applications,  - lectures by Prof. D.T. Attwood, Berkeley, (video).
Coherent X-ray and their Applications,  - lectures from ESRF.
CERN Accelerator School,  - lectures from the previuos schools.
Introduction to X-ray Powder Diffraction,  - lectures by Prof. J. Connolly, Univ. of New Mexico.
Lectures on image processing,  - lectures by A. Peters.

Theses:
Scanning Transmission X-ray Microscopy with a Segmented Detector,  M. Feser, Ph.D. thesis, Stony Brook University, 2002.
Soft X-ray diffraction imaging with and without lenses and Radiation damage studies,  T. Beetz, Ph.D. thesis, Stony Brook University, 2004.
Experimental Phase Retrieval using Coherent X-Ray Diffraction,  A.P. Mancuso, Ph.D. thesis, University of Melbourne, 2005.
Phase Contrast Microscopy with Soft and Hard X-rays Using a Segmented Detector,  B. Hornberger, Ph.D. thesis, Stony Brook University, 2007.
Experimental Coherent X-Ray Diffractive Imaging: Capabilities and Limitations of the Technique,  A. Schropp, Ph.D. thesis, Universität Hamburg, 2008.
X-ray imaging with a grating interferometer,  M. Bech, Ph.D. thesis, University of Copenhagen, 2009.
Closing the Gap to the Diffraction Limit: Near Wavelength Limited Tabletop Soft X-Ray Coherent Diffractive Imaging,  R.L. Sandberg, Ph.D. thesis, University of Colorado, 2009.
X-ray Diffraction Microscopy: Computational Methods and Scanning-type Experiments,  J.F. Steinbrener, Ph.D. thesis, Stony Brook University, 2010.
Hard X-ray Phase Contrast Microscopy - Techniques and Applications,  C. Holzner, Ph.D. thesis, Stony Brook University, 2010.
Methods for coherent lensless imaging and x-ray wavefront measurement,  M. Guizar-Sicairos, Ph.D. thesis, University of Rochester, 2010.
Quantitative Studies of X-Ray Optical Coherence,  S. Flewett, Ph.D. thesis, University of Melbourne, 2010.
Lensless holography methods for soft X-ray resonant coherent imaging,  D. Zhu, Ph.D. thesis, Stanford University, 2010.
Studies of Phase Contrast X-ray Imaging of Biological Interfaces,  K.S. Morgan, Ph.D. thesis, Monash University, 2011.
Phase contrast in X-ray imaging,  A.W. Greaves, Ph.D. thesis, Swinburne University of Technology, 2011.
Soft X-ray coherence and coherent diffractive imaging,  R. Rick, Ph.D. thesis, Stanford University, 2011.
Coherence properties of third and fourth generation x-ray sources. Theory and experiment,  A. Singer, Ph.D. thesis, Universität Hamburg, 2012.

Algorithmic Methods in Diffraction Microscopy,  P. Thibault, Ph.D. thesis, Cornell University, 2007.
Development of a Lensless Microscopy Technique for Imaging Cellular Structures,  M. Dierolf, Diploma Thesis, Ulm University, 2007.
A study on new approaches in coherent x-ray microscopy of biological specimens,  K. Giewekemeyer, Ph.D. thesis, Gottingen University, 2011.
Advances in Ptychography,  T.B. Edo, Ph.D. Thesis, University of Sheffield, 2011.
Dichroic Coherent Diffractive Imaging,  A. Tripathi, Ph.D. Thesis, University of California, San Diego, 2012.
High-Resolution 3D Ptychography,  S. Stephan, Ph.D. Thesis, Technische Universität Dresden, 2013.
A generalised holographic approach to coherent diffractive imaging,  A.J. Morgan, Ph.D. Thesis, University of Melbourne, 2013.
Coherent Diffraction Imaging and Ptychography of Human Metaphase Chromosomes,  L. Shemilt, Ph.D. Thesis, University College London, 2014.

Articles:
Zernike phase contrast in scanning microscopy with X-rays,  Ch. Holzner et al., Nature Physics 6, 2010, Supplementary Information
Differential phase contrast with a segmented detector in a scanning X-ray microprobe,  B. Hornberger et al., J. Synchrotron Rad. 15 (2008) 355.
Quantitative amplitude and phase contrast imaging in a scanning transmission X-ray microscope,  B. Hornberger et al., Ultramicroscopy 107 (2007) 644.
Integrating Silicon detector with segmentation for scanning transmission X-ray microscopy,  M. Feser, B. Hornberger, C. Jacobsen, G. De Geronimo, P. Rehak, P. Holl, L. Struder, Nucl. Instr. Meth. A 565 (2006) 841.
Quantitative Phase Imaging with a Scanning Transmission X-Ray Microscope,  M.D. de Jonge et al., Phys. Rev. Lett. 100, 163902 (2008).
Coherent methods in X-ray sciences,  K.A. Nugent, Adv. Phys. 59 (2009) 1-99.
Diffractive Imaging Using Partially Coherent X Rays,  L.W. Whitehead, G.J. Williams, H.M. Quiney, D.J. Vine, R.A. Dilanian, S. Flewett, K.A. Nugent, A.G. Peele, E. Balaur, I. McNulty, Phys. Rev. Lett. 103, 243902 (2009).
Contrast mechanisms in scanning transmission X-ray microscopy,  P. Thibault, M. Dierolf, C.M. Kevish, A. Menzel, O. Bunk, Phys. Rev. A 80, 043813 (2009).
X-ray Diffraction Microscopy,  P. Thibault, V. Elser, Annu. Rev. Condens. Matter Phys. 1 (2010) 237-255.
Coherence measurements and coherent diffractive imaging at FLASH,  I.A. Vartanyants, A.P. Mancuso, A. Singer, O.M. Yefanov and J. Gulden, J. Phys. B: At. Mol. Opt. Phys. 43 194016 (2010).
Transmission and emission X-ray microscopy: operation modes, contrast mechanisms and applications,  B. Kaulich, P. Thibault, A. Gianoncelli, M. Kiskinova, J. Phys. Condens. Matter 23 083002 (2011).
New directions in X-ray microscopy,  R. Falcone, Ch. Jacobsen, J. Kirz, S. Marchesini, D. Shapiro, J. Spence, Contemporary Physics 52 (2011) 293-318.
Coherent X-ray Diffraction Imaging,  J. Miao, R.L. Sandberg and Ch. Song, IEEE J. of Selected Topics in Quantum electronics, vol. 18 no. 1 (2012) 399-410.
Differential phase-contrast microscopy at atomic resolution,  N. Shibata et al., Nature Phys. 8 (2012) 611.
Maximum-likelihood refinement for coherent diffractive imaging,  P. Thibault, M. Guizar-Sicairos, New J. Phys. 14, 063004 (2012).
Nanoscale Hard X-Ray Microscopy Methods for Material Studies,  M. Holt, R. Harder, R. Winarski, V. Rose, Annu. Rev. Mater. Res. 43 (2013).
Phase retrieval algorithms: a personal tour,  J.R. Fienup, Appl. Opt. 52, 45-56 (2013).

Hard-X-Ray Lensless Imaging of Extended Objects,  J.M. Rodenburg, A.C. Hurst, A.G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs and I. Johnson, Phys. Rev. Lett. 98, 034801 (2007).
Ptychography and Related Diffractive Imaging Methods,  J.M. Rodenburg, Advances in Imaging and Electron Physics, Vol. 150, 2008.
Ptychography & lensless X-ray imaging,  M. Dierolf, O. Bunk, S. Kynde, P. Thibault, I. Johnson, A. Menzel, K. Jefimovs, Ch. David, O. Marti, F. Pfeiffer, Europhysics News 39 (2008) 22-24.
High-resolution scanning x-ray diffraction microscopy,  P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, Science 321 (2008) 379-382.
Influence of the overlap parameter on the convergence of the ptychographical iterative engine,  O. Bunka, M. Dierolfa, S. Kyndea, I. Johnsona, O. Martib, F. Pfeiffera, Ultramicroscopy 108 (2008) 481–487.
An improved ptychographical phase retrieval algorithm for diffractive imaging,  A.M. Maiden, J.M. Rodenburg, Ultramicroscopy 109 (2009) 1256.
Ptychographic Fresnel coherent diffractive imaging,  D.J. Vine, G.J. Williams, B. Abbey, M.A. Pfeifer, J.N. Clark, M.D. de Jonge, I. McNulty, A.G. Peele, K.A. Nugent, Phys. Rev. A 80, 063823 (2009).
Quantitative biological imaging by ptychographic x-ray diffraction microscopy,  K. Giewekemeyer, P. Thibault, S. Kalbfleisch, A. Beerlink, C.M. Kewish, M. Dierolf, F. Pfeiffer, T. Salditt, PNAS vol. 107 no. 2 (2010) 529-534.
Ptychographic X-ray computed tomography at the nanoscale,  M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C.M. Kewish, R. Wepf, O. Bunk, F. Pfeiffer, Nature 467 (2010) 436.
Ptychographic coherent diffractive imaging of weakly scattering specimens,  M. Dierolf, P. Thibault, A. Menzel, C.M. Kewish, K. Jefimovs, I. Schlichting, K. von König, O. Bunk, F. Pfeiffer, New J. Phys. 12 035017 (2010).
Coherent diffractive imaging using short wavelength light sources,  H.M. Quiney, J. Mod. Optics 57 (2010) 1109-1149.
Superresolution imaging via ptychography,  A.M. Maiden, M.J. Humphry, F. Zhang, J.M. Rodenburg, J. Opt. Soc. Am. A 28 (2011) 604-612.
Towards high-resolution ptychographic x-ray diffraction microscopy,  Y. Takahashi, A. Suzuki, N. Zettsu, Y. Kohmura, Y. Senba, H. Ohashi, K. Yamauchi, T. Ishikawa, Phys. Rev. B 83, 214109 (2011).
Characterization of high-resolution diffractive X-ray optics by ptychographic coherent diffractive imaging,  J. Vila-Comamala, A. Diaz, M. Guizar-Sicairos, A. Mantion, C.M. Kewish, A. Menzel, O. Bunk, C. David, Optics Express 19, 21333-21344 (2011).
Hard X-ray imaging of bacterial cells: nano-diffraction and ptychographic reconstruction,  R.N. Wilke et al., Optics Express 20, 19232-19254, 2012.
Ptychographic transmission microscopy in three dimensions using a multi-slice approach,  A.M. Maiden, M.J. Humphry, J.M. Rodenburg, J. Opt. Soc. Am. A 29 (2012) 1606.
An annealing algorithm to correct positioning errors in ptychography,  A.M. Maiden et al., Ultramicroscopy 120 (2012) 64-72.
Soft X-ray spectromicroscopy using ptychography with randomly phased illumination,  A.M. Maiden, G.R. Morrison, B. Kaulich, A. Gianoncelli, J.M. Rodenburg, Nature Comm. 4 (2013) 1669.
Translation position determination in ptychographic coherent diffraction imaging,  F. Zhang, I. Peterson, J. Vila-Comamala, A. Diaz, F. Berenguer, R. Bean, B. Chen, A. Menzel, I.K. Robinson, J.M. Rodenburg, Optics Express 21, 13592-13606, 2013.
Reconstructing state mixtures from diffraction measurements,  P. Thibault, A. Menzel, Nature 494 (2013) 68-71.
Ptychographic Imaging at the Swiss Light Source,  A. Menzel, A. Diaz, M. Guizar-Sicairos, Synchrotron Rad. News 26 (2013) 26-31.
Sampling in X-ray ptychography,  T.B. Edo, D.J. Batey, A.M. Maiden, C. Rau, U. Wagner, Z.D. Pešić, T.A. Waigh, J.M. Rodenburg, Phys. Rev. A 87, 053850 (2013).
Augmented projections for ptychographic imaging,  S. Marchesini, A. Schirotzek, C. Yang, H. Wu, F. Maia, Inverse Problems 29 115009 (2013).
High-resolution and high-sensitivity phase-contrast imaging by focused hard x-ray ptychography with a spatial filter,  Y. Takahashi, A. Suzuki, S. Furutaku, K. Yamauchi, Y. Kohmura, T. Ishikawa, Appl. Phys. Lett. 102, 094102 (2013).
Semi-transparent central stop in high-resolution X-ray ptychography using Kirkpatrick–Baez focusing,  R.N. Wilke, M. Vassholz, T. Salditt, Acta Cryst. A69, 490-497 (2013).
High-resolution chemical imaging of gold nanoparticles using hard x-ray ptychography,  R. Hoppe, J. Reinhardt, G. Hofmann, J. Patommel, J.-D. Grunwaldt, C.D. Damsgaard, G. Wellenreuther, G. Falkenberg and C.G. Schroer, Appl. Phys. Lett. 102, 203104 (2013).
Single shot ptychographical iterative engine based on multi-beam illumination,  X. Pan, Ch. Liu, J. Zhu, Appl. Phys. Lett. 103, 171105 (2013).
Near-field ptychography: phase retrieval for inline holography using a structured illumination,  M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, P. Thibault, Scientific Reports 3, 1927 (2013).
Whole-cell phase contrast imaging at the nanoscale using Fresnel Coherent Diffractive Imaging Tomography,  M.W.M. Jones, G.A. van Riessen, B. Abbey, C.T. Putkunz, M.D. Junker, E. Balaur, D.J. Vine, I. McNulty, B. Chen, B.D. Arhatari, S. Frankland, K.A. Nugent, L. Tilley, A.G. Peele, Scientific Reports 3, 2288 (2013).
Ptychography – a label free, high-contrast imaging technique for live cells using quantitative phase information,  J. Marrison, L. Räty, P. Marriott, P. O'Toole, Scientific Reports 3, 2369 (2013).
Wide-field, high-resolution Fourier ptychographic microscopy,  G. Zheng, R. Horstmeyer, Ch. Yang, Nature Photonics 7, 739–745 (2013).
X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,  M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, O. Bunk, Scientific Reports 4, 3857 (2014).
High-Resolution Multislice X-Ray Ptychography of Extended Thick Objects,  A. Suzuki, S. Furutaku, K. Shimomura, K. Yamauchi, Y. Kohmura, T. Ishikawa and Y. Takahashi, Phys. Rev. Lett. 112, 053903 (2014).
High-dynamic-range coherent diffractive imaging: ptychography using the mixed-mode pixel array detector,  K. Giewekemeyer, H.T. Philipp, R.N. Wilke, A. Aquila, M. Osterhoff, M.W. Tate, K.S. Shanks, A.V. Zozulya, T. Salditt, S.M. Gruner, A.P. Mancuso, J. Synchrotron Rad. 21 (2014) 1167-1174.
Observations of artefacts in the x-ray ptychography method,  N. Burdet, G.R. Morrison, X. Huang, X. Shi, J.N. Clark, F. Zhang, M. Civita, R. Harder, I.K. Robinson, Optics Express 22, 10294-10303 (2014).
Dynamic Imaging Using Ptychography,  J.N. Clark, X.J.Huang, R.J. Harder, I.K. Robinson, Phys. Rev. Lett. 112, 113901 (2014).

Iterative algorithms for ptychographic phase retrieval,  C. Yang, J. Qian, A. Schirotzek, F. Maia, S. Marchesini, arXiv:1105.5628, 2011.
Optimization and Parallelization of a Ptychography Reconstruction Code,  T.L. Falch, J.B. Fløystad, A.C. Elster and D.W. Breiby, NIK, 2012. (source code)
Sparse ptychographical coherent diffractive imaging from noisy measurements,  W. Katkovnik, J. Astola, JOSA A 30, pp.367-379 (2013).
Compressive ptychographical coherent diffractive imaging based on Poissonian maximum likelihood and sparse approximations for phase and magnitude,  W. Katkovnik, J. Astola, to be published. (source code)
Computer-simulated Fresnel diffraction using the Fourier transform,  S. Trester, Computing in Science & Engineering, Vol. 1, 1999.

Manuals:
STXM User's Manual: version (pdf),  (html).
User information: P11@PETRAIII, 
PILATUS,  MEDIPIX,  LAMBDA, 

Personal homepages:
J. Rodenburg   P. Thibault   R. Winter  

Journals:   J. Synchrotron Rad.   Ultramicroscopy   Materials   Nanotechnology   J. of Nanoscience & Nanotechnology   Europhysics News  
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