-
Notifications
You must be signed in to change notification settings - Fork 1
/
FilipeMaia.bib
2764 lines (2388 loc) · 174 KB
/
FilipeMaia.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@article{Quiney2005Iterative,
abstract = {Iterative algorithms that reconstruct images from far-field x-ray diffraction data are plagued with convergence difficulties. An iterative image reconstruction algorithm is described that ameliorates these convergence difficulties through the use of diffraction data obtained with illumination modulated in both intensity and phase.},
author = {Quiney, H. M. and Nugent, K. A. and Peele, A. G.},
citeulike-article-id = {6927036},
citeulike-linkout-0 = {http://dx.doi.org/10.1364/OL.30.001638},
citeulike-linkout-1 = {http://www.opticsinfobase.org/abstract.cfm?id=84467},
day = {1},
doi = {10.1364/OL.30.001638},
journal = {Opt. Lett.},
keywords = {fcdi},
month = {July},
number = {13},
pages = {1638--1640},
posted-at = {2010-03-29 16:34:08},
priority = {2},
publisher = {OSA},
title = {Iterative image reconstruction algorithms using wave-front intensity and phase variation},
url = {http://dx.doi.org/10.1364/OL.30.001638},
volume = {30},
year = {2005}
}
@article{Quiney2006Diffractive,
abstract = {The rapid development of new sources of coherent X-rays, such as third-generation synchrotrons, high-harmonic-generation lasers1 and X-ray free-electron lasers2, has led to the emergence of the new field of X-ray coherent science. The extension of coherent methods to the X-ray regime makes possible methods such as coherent diffraction, X-ray photon-correlation spectroscopy, speckle interferometry and ultrafast probing at atomic resolution and femtosecond timescales. Despite rapid improvements in the resolution that conventional X-ray optics can achieve, new methods for manipulating X-rays are required to push this to the atomic scale3. Here we demonstrate a coherent imaging technique that enables us to image the complex field at the focus of an X-ray zone plate without the need for conventional X-ray lenses. There are no fundamental limits on the resolution of this lensless imaging technique other than the wavelength of the X-rays themselves. The ability to characterize the beam with one measurement makes the method ideally suited to characterizing the fields generated by pulsed coherent X-ray sources.},
author = {Quiney, H. M. and Peele, A. G. and Cai, Z. and Paterson, D. and Nugent, K. A.},
citeulike-article-id = {6927031},
citeulike-linkout-0 = {http://dx.doi.org/10.1038/nphys218},
citeulike-linkout-1 = {http://dx.doi.org/10.1038/nphys218},
day = {29},
doi = {10.1038/nphys218},
issn = {1745-2473},
journal = {Nature Physics},
keywords = {fcdi},
month = {January},
number = {2},
pages = {101--104},
posted-at = {2010-03-29 16:31:30},
priority = {2},
publisher = {Nature Publishing Group},
title = {Diffractive imaging of highly focused X-ray fields},
url = {http://dx.doi.org/10.1038/nphys218},
volume = {2},
year = {2006}
}
@article{Thibault2009Probe,
abstract = {Ptychography is a coherent diffractive imaging method that uses multiple diffraction patterns obtained through the scan of a localized illumination on the specimen. Until recently, reconstruction algorithms for ptychographic datasets needed the a priori knowledge of the incident illumination. A new reconstruction procedure that retrieves both the specimen's image and the illumination profile was recently demonstrated with hard X-ray data. We present here the algorithm in greater details and illustrate its practical applicability with a visible light dataset. Improvements in the quality of the reconstruction are shown and compared to previous reconstruction techniques. Implications for future applications with other types of radiation are discussed.},
author = {Thibault, Pierre and Dierolf, Martin and Bunk, Oliver and Menzel, Andreas and Pfeiffer, Franz},
citeulike-article-id = {6927026},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ultramic.2008.12.011},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0304399108003458},
doi = {10.1016/j.ultramic.2008.12.011},
issn = {03043991},
journal = {Ultramicroscopy},
keywords = {ptychography},
month = {March},
number = {4},
pages = {338--343},
posted-at = {2010-03-29 16:29:28},
priority = {2},
title = {Probe retrieval in ptychographic coherent diffractive imaging},
url = {http://dx.doi.org/10.1016/j.ultramic.2008.12.011},
volume = {109},
year = {2009}
}
@article{Rodenburg2007Transmission,
abstract = {We demonstrate experimentally, for the first time, a new form of lensless microscopy. The image we obtain contains the entire wavefunction emanating from the sample. Large scale, quantitative phase information can be measured, unlike in conventional (Zernike) methods. For light optical experiments, we can dispense with expensive high-quality lenses and the very large working distances available would allow remote monitoring of e.g., environmental cells without compromising resolution. In short wavelength microscopy (X-rays and electrons), where lens components are of very limited numerical aperture, the technique has revolutionary implications: objects of any lateral size or shape can be used and, for transmission electron imaging, resolution down to the scale of the wavelength is likely to be limited only by the presence of atomic vibrations.},
author = {Rodenburg, J. and Hurst, A. and Cullis, A.},
citeulike-article-id = {6927018},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ultramic.2006.07.007},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0304399106001549},
doi = {10.1016/j.ultramic.2006.07.007},
issn = {03043991},
journal = {Ultramicroscopy},
keywords = {ptychography},
month = {February},
number = {2-3},
pages = {227--231},
posted-at = {2010-03-29 16:25:51},
priority = {2},
title = {Transmission microscopy without lenses for objects of unlimited size},
url = {http://dx.doi.org/10.1016/j.ultramic.2006.07.007},
volume = {107},
year = {2007}
}
@article{Eisebitt2004Lensless,
abstract = {Our knowledge of the structure of matter is largely based on X-ray diffraction studies of periodic structures and the successful transformation (inversion) of the diffraction patterns into real-space atomic maps. But the determination of non-periodic nanoscale structures by X-rays is much more difficult. Inversion of the measured diffuse X-ray intensity patterns suffers from the intrinsic loss of phase information1, 2, and direct imaging methods are limited in resolution by the available X-ray optics3. Here we demonstrate a versatile technique for imaging nanostructures, based on the use of resonantly tuned soft X-rays for scattering contrast and the direct Fourier inversion of a holographically formed interference pattern. Our implementation places the sample behind a lithographically manufactured mask with a micrometre-sized sample aperture and a nanometre-sized hole that defines a reference beam. As an example, we have used the resonant X-ray magnetic circular dichroism effect to image the random magnetic domain structure in a Co/Pt multilayer film with a spatial resolution of 50 nm. Our technique, which is a form of Fourier transform holography, is transferable to a wide variety of specimens, appears scalable to diffraction-limited resolution, and is well suited for ultrafast single-shot imaging with coherent X-ray free-electron laser sources4.},
author = {Eisebitt, S. and Luning, J. and Schlotter, W. F. and Lorgen, M. and Hellwig, O. and Eberhardt, W. and Stohr, J.},
citeulike-article-id = {3906},
citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature03139},
citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature03139},
day = {16},
doi = {10.1038/nature03139},
issn = {0028-0836},
journal = {Nature},
keywords = {fourier, holography},
month = {December},
number = {7019},
pages = {885--888},
posted-at = {2010-03-29 16:22:53},
priority = {2},
publisher = {Nature Publishing Group},
title = {Lensless imaging of magnetic nanostructures by X-ray spectro-holography},
url = {http://dx.doi.org/10.1038/nature03139},
volume = {432},
year = {2004}
}
@article{McNulty1992HighResolution,
abstract = {Fourier transform x-ray holography has been used to image gold test objects with submicrometer structure, resolving features as small as 60 nanometers. The hologram-recording instrument uses coherent 3.4-nanometer radiation from the soft x-ray undulator beamline X1A at the National Synchrotron Light Source. The specimen to be imaged is placed near the first-order focal spot produced by a Fresnel zone plate; the other orders, chiefly the zeroth, illuminate the specimen. The wave scattered by the specimen interferes with the spherical reference wave from the focal spot, forming a hologram with fringes of low spatial frequency. The hologram is recorded in digital form by a charge-coupled device camera, and the specimen image is obtained by numerical reconstruction. 10.1126/science.256.5059.1009},
author = {McNulty, Ian and Kirz, Janos and Jacobsen, Chris and Anderson, Erik H. and Howells, Malcolm R. and Kern, Dieter P.},
citeulike-article-id = {6927008},
citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.256.5059.1009},
citeulike-linkout-1 = {http://www.sciencemag.org/cgi/content/abstract/256/5059/1009},
citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17795006},
citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17795006},
day = {15},
doi = {10.1126/science.256.5059.1009},
journal = {Science},
month = {May},
number = {5059},
pages = {1009--1012},
posted-at = {2010-03-29 16:22:39},
priority = {2},
title = {High-Resolution Imaging by Fourier Transform X-ray Holography},
url = {http://dx.doi.org/10.1126/science.256.5059.1009},
volume = {256},
year = {1992}
}
@article{Whitehead2009Diffractive,
abstract = {The measured spatial coherence characteristics of the illumination used in a diffractive imaging experiment are incorporated in an algorithm that reconstructs the complex transmission function of an object from experimental x-ray diffraction data using 1.4 keV x rays. Conventional coherent diffractive imaging, which assumes full spatial coherence, is a limiting case of our approach. Even in cases in which the deviation from full spatial coherence is small, we demonstrate a significant improvement in the quality of wave field reconstructions. Our formulation is applicable to x-ray and electron diffraction imaging techniques provided that the spatial coherence properties of the illumination are known or can be measured.},
author = {Whitehead, L. W. and Williams, G. J. and Quiney, H. M. and Vine, D. J. and Dilanian, R. A. and Flewett, S. and Nugent, K. A. and Peele, A. G. and Balaur, E. and McNulty, I.},
citeulike-article-id = {6359097},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PRLTAO000103000024243902000001\&idtype=cvips\&gifs=yes},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRL/v103/e243902},
citeulike-linkout-2 = {http://dx.doi.org/10.1103/PhysRevLett.103.243902},
citeulike-linkout-3 = {http://link.aps.org/abstract/PRL/v103/i24/e243902},
citeulike-linkout-4 = {http://link.aps.org/pdf/PRL/v103/i24/e243902},
doi = {10.1103/PhysRevLett.103.243902},
journal = {Physical Review Letters},
month = {Dec},
number = {24},
pages = {243902+},
posted-at = {2010-03-29 15:50:00},
priority = {2},
publisher = {American Physical Society},
title = {Diffractive Imaging Using Partially Coherent X Rays},
url = {http://dx.doi.org/10.1103/PhysRevLett.103.243902},
volume = {103},
year = {2009}
}
@article{HauRiege2008Effect,
abstract = {The longitudinal coherence properties of self-amplified-spontaneous- emission x-ray free electron lasers limit the resolution of single-particle diffraction imaging. We found that for the Linac Coherent Light Source (LCLS) at a wavelength of 1.5 \r{A} the particles have to be smaller than 500 nm in diameter to achieve atomic-resolution imaging with a resolution length of less than 2 \r{A}, suggesting that the longitudinal coherence is sufficient for imaging most biomolecular samples of interest.},
author = {Hau-Riege, Stefan P.},
citeulike-article-id = {6900532},
citeulike-linkout-0 = {http://dx.doi.org/10.1364/OE.16.002840},
citeulike-linkout-1 = {http://www.opticsinfobase.org/abstract.cfm?id=154186},
day = {18},
doi = {10.1364/OE.16.002840},
journal = {Opt. Express},
month = {February},
number = {4},
pages = {2840--2844},
posted-at = {2010-03-24 13:30:31},
priority = {2},
publisher = {OSA},
title = {Effect of the coherence properties of self-amplified-spontaneous-emissionx-ray free electron lasers on single-particle diffractive imaging},
url = {http://dx.doi.org/10.1364/OE.16.002840},
volume = {16},
year = {2008}
}
@article{Elser2009Noise,
abstract = {An information theoretic criterion for the feasibility of reconstructing diffraction signals from noisy tomographs, when the positions of the tomographs within the signal are unknown, is derived. For shot-noise limited data, the number of detected photons per tomograph for successful reconstruction is much smaller than previously believed necessary, growing only logarithmically with the number of contrast elements of the diffracting object. Reconstruction up to the theoretic criterion is demonstrated on simulated data with an algorithm that combines the expectation-maximization (EM) principle with constraints arising from the bandlimited nature of the signal.},
address = {Piscataway, NJ, USA},
author = {Elser, Veit},
citeulike-article-id = {6897241},
citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=1669403},
citeulike-linkout-1 = {http://dx.doi.org/10.1109/TIT.2009.2027547},
doi = {10.1109/TIT.2009.2027547},
issn = {0018-9448},
journal = {IEEE Trans. Inf. Theor.},
number = {10},
pages = {4715--4722},
posted-at = {2010-03-23 21:19:56},
priority = {2},
publisher = {IEEE Press},
title = {Noise limits on reconstructing diffraction signals from random tomographs},
url = {http://dx.doi.org/10.1109/TIT.2009.2027547},
volume = {55},
year = {2009}
}
@book{Attwood2007Soft,
address = {The Edinburgh Building, Cambridge, CB2 2RU, UK},
author = {Attwood, D. T.},
citeulike-article-id = {6894113},
posted-at = {2010-03-23 10:31:43},
priority = {2},
publisher = {Cambridge University Press},
title = {Soft X-rays and extreme ultraviolet radiation: principles and applications},
year = {2007}
}
@book{2001International,
address = {Dordrecht/Boston/London},
citeulike-article-id = {6894036},
edition = {First},
editor = {Rossmann, M. G. and Arnold, E.},
posted-at = {2010-03-23 10:21:13},
priority = {2},
publisher = {Kluwer Academic Publishers},
title = {International Tables for Crystallography},
volume = {F},
year = {2001}
}
@article{Barty2008Threedimensional,
abstract = {Ultralow density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area, and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by x-ray diffractive imaging. Finite-element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion-limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.},
author = {Barty, A. and Marchesini, S. and Chapman, H. N. and Cui, C. and Howells, M. R. and Shapiro, D. A. and Minor, A. M. and Spence, J. C. and Weierstall, U. and Ilavsky, J. and Noy, A. and Hau-Riege, S. P. and Artyukhin, A. B. and Baumann, T. and Willey, T. and Stolken, J. and van Buuren, T. and Kinney, J. H.},
citeulike-article-id = {6891731},
citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/18764404},
citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=18764404},
day = {1},
issn = {0031-9007},
journal = {Physical review letters},
month = {August},
number = {5},
posted-at = {2010-03-22 17:50:16},
priority = {2},
title = {Three-dimensional coherent x-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms.},
url = {http://view.ncbi.nlm.nih.gov/pubmed/18764404},
volume = {101},
year = {2008}
}
@phdthesis{Thibault2007Algorithmic,
author = {Thibault, P.},
citeulike-article-id = {6891717},
month = {August},
posted-at = {2010-03-22 17:44:12},
priority = {2},
school = {Cornell University},
title = {Algorithmic methods in diffraction microscopy},
year = {2007}
}
@article{Levi1984Image,
abstract = {The method of projections onto convex sets can be used to solve many problems in image restoration, e.g., restoration from phase, spectral extrapolation, and signal recovery in computer-aided tomography. However, image-restoration problems involving nonconvex constraints cannot be handled by the method of projection onto convex sets in a fashion that ensures convergence. The restoration-from-magnitude (RFM) problem is such a case. To handle the RFM as well as other nonconvex constraints, we describe an algorithm known as generalized projections and discuss its properties. When sets are nonconvex, it is possible for the algorithm to exhibit pathological behavior that is never manifest in convex projections. We introduce an error criterion called the summed-distance error (SDE) and show under what circumstances the SDE is a monotonically decreasing function of the number of iterations. Near-optimum performance of the algorithm is achieved by relaxation parameters. Comparisons with other RFM methods are furnished for synthetic imagery.},
author = {Levi, Aharon and Stark, Henry},
citeulike-article-id = {6891713},
citeulike-linkout-0 = {http://dx.doi.org/10.1364/JOSAA.1.000932},
citeulike-linkout-1 = {http://www.opticsinfobase.org/abstract.cfm?id=1040},
day = {1},
doi = {10.1364/JOSAA.1.000932},
journal = {J. Opt. Soc. Am. A},
month = {September},
number = {9},
pages = {932--943},
posted-at = {2010-03-22 17:42:07},
priority = {2},
publisher = {OSA},
title = {Image restoration by the method of generalized projections with application to restoration from magnitude},
url = {http://dx.doi.org/10.1364/JOSAA.1.000932},
volume = {1},
year = {1984}
}
@article{Gerchberg1972Practical,
author = {Gerchberg, R. W. and Saxton, W. O.},
citeulike-article-id = {6891709},
journal = {Optik},
pages = {237--246},
posted-at = {2010-03-22 17:39:35},
priority = {2},
title = {A practical algorithm for the determination of the phase from image and diffraction plane pictures},
volume = {35},
year = {1972}
}
@article{Shannon1949Communication,
author = {Shannon, C. E.},
citeulike-article-id = {6891688},
citeulike-linkout-0 = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1697831},
issn = {0096-8390},
journal = {Proceedings of the IRE},
month = {January},
number = {1},
pages = {10--21},
posted-at = {2010-03-22 17:28:33},
priority = {2},
title = {Communication in the Presence of Noise},
url = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1697831},
volume = {37},
year = {1949}
}
@article{Corkum1993Plasma,
abstract = {During strong-field multiphoton ionization, a wave packet is formed each time the laser field passes its maximum value. Within the first laser period after ionization there is a significant probability that the electron will return to the vicinity of the ion with very high kinetic energy. High-harmonic generation, multiphoton two-electron ejection, and very high energy above-threshold-ionization electrons are all conssequences of this electron-ion interaction. One important parameter which determines the strength of these effects is the rate at which the wave packet spreads in the direction perpendicular to the laser electric field; another is the polarization of the laser. It will be essential for experimentalists to be aware of these crucial parameters in future experiments.},
author = {Corkum, P. B.},
citeulike-article-id = {1653472},
citeulike-linkout-0 = {http://dx.doi.org/10.1103/PhysRevLett.71.1994},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRL/v71/i13/p1994},
citeulike-linkout-2 = {http://link.aps.org/pdf/PRL/v71/i13/p1994},
day = {27},
doi = {10.1103/PhysRevLett.71.1994},
journal = {Physical Review Letters},
month = {Sep},
number = {13},
pages = {1994--1997},
posted-at = {2010-03-22 17:19:36},
priority = {2},
publisher = {American Physical Society},
title = {Plasma perspective on strong field multiphoton ionization},
url = {http://dx.doi.org/10.1103/PhysRevLett.71.1994},
volume = {71},
year = {1993}
}
@article{Lewenstein1994Theory,
abstract = {We present a simple, analytic, and fully quantum theory of high-harmonic generation by low-frequency laser fields. The theory recovers the classical interpretation of Kulander et al . in Proceedings of the SILAP III Works hop, edited by B. Piraux (Plenum, New York, 1993) and Corkum [Phys. Rev. Lett. 71 , 1994 (1993)] and clearly explains why the single-atom harmonic-generation spectra fall off at an energy approximately equal to the ionization energy plus about three times the oscillation energy of a free electron in the field. The theory is valid for arbitrary atomic potentials and can be generalized to describe laser fields of arbitrary ellipticity and spectrum. We discuss the role of atomic dipole matrix elements, electron rescattering processes, and of depletion of the ground state. We present the exact quantum-mechanical formula for the harmonic cutoff that differs from the phenomenological law I p +3.17 U p , where I p is the atomic ionization potential and U p is the ponderomotive energy, due to the account for quantum tunneling and diffusion effects.},
author = {Lewenstein, M. and Ph and Yu and L'Huillier, Anne and Corkum, P. B.},
citeulike-article-id = {1335251},
citeulike-linkout-0 = {http://dx.doi.org/10.1103/PhysRevA.49.2117},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRA/v49/i3/p2117},
citeulike-linkout-2 = {http://link.aps.org/pdf/PRA/v49/i3/p2117},
doi = {10.1103/PhysRevA.49.2117},
journal = {Physical Review A},
month = {Mar},
number = {3},
pages = {2117--2132},
posted-at = {2010-03-22 17:18:43},
priority = {2},
publisher = {American Physical Society},
title = {Theory of high-harmonic generation by low-frequency laser fields},
url = {http://dx.doi.org/10.1103/PhysRevA.49.2117},
volume = {49},
year = {1994}
}
@article{Smith1953Visible,
author = {Smith, S. J. and Purcell, E. M.},
citeulike-article-id = {4364974},
citeulike-linkout-0 = {http://dx.doi.org/10.1103/PhysRev.92.1069},
citeulike-linkout-1 = {http://link.aps.org/abstract/PR/v92/i4/p1069},
citeulike-linkout-2 = {http://link.aps.org/pdf/PR/v92/i4/p1069},
doi = {10.1103/PhysRev.92.1069},
journal = {Physical Review Online Archive (Prola)},
month = {Nov},
number = {4},
pages = {1069+},
posted-at = {2010-03-22 17:17:10},
priority = {2},
publisher = {American Physical Society},
title = {Visible Light from Localized Surface Charges Moving across a Grating},
url = {http://dx.doi.org/10.1103/PhysRev.92.1069},
volume = {92},
year = {1953}
}
@article{Adamo2009Light,
abstract = {The passage of a free-electron beam through a nanohole in a periodically layered metal-dielectric structure creates a new type of tunable, nanoscale radiation source—a ” light well”. In the reported demonstration, tunable light is generated at an intensity of ∼200 W/ cm 2 as electrons with energies in the 20–40 keV range are injected into gold-silica well structures with a lateral size of just a few hundred nanometers.},
author = {Adamo, G. and MacDonald, K. F. and Fu, Y. H. and Wang, C. M. and Tsai, D. P. and de Abajo, F. J. Garc'i{}a and Zheludev, N. I.},
citeulike-article-id = {5760868},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PRLTAO000103000011113901000001\&idtype=cvips\&gifs=yes},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRL/v103/e113901},
citeulike-linkout-2 = {http://dx.doi.org/10.1103/PhysRevLett.103.113901},
citeulike-linkout-3 = {http://link.aps.org/abstract/PRL/v103/i11/e113901},
citeulike-linkout-4 = {http://link.aps.org/pdf/PRL/v103/i11/e113901},
doi = {10.1103/PhysRevLett.103.113901},
journal = {Physical Review Letters},
month = {Sep},
number = {11},
pages = {113901+},
posted-at = {2010-03-22 17:15:21},
priority = {2},
publisher = {American Physical Society},
title = {Light Well: A Tunable Free-Electron Light Source on a Chip},
url = {http://dx.doi.org/10.1103/PhysRevLett.103.113901},
volume = {103},
year = {2009}
}
@book{Materlik2001TESLA,
address = {Hamburg, Germany},
author = {Materlik, G. and Tschentscher, T.},
chapter = {V},
citeulike-article-id = {6891665},
keywords = {tesla},
month = {March},
posted-at = {2010-03-22 17:13:06},
priority = {2},
publisher = {DESY},
title = {TESLA Technical Design Report},
year = {2001}
}
@article{Howells2009Assessment,
abstract = {X-ray diffraction microscopy (XDM) is a new form of X-ray imaging that is being practiced at several third-generation synchrotron-radiation X-ray facilities. Nine years have elapsed since the technique was first introduced and it has made rapid progress in demonstrating high-resolution three-dimensional imaging and promises few-nanometer resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available X-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called ” dose fractionation theorem” of Hegerl and Hoppe to calculate the dose needed to make an image of a single life-science sample by XDM with a given resolution. We find that the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered otherwise. The conclusion of this study is that, based on the natural contrast between protein and water and ” Rose-criterion” image quality, one should be able to image a frozen-hydrated biological sample using XDM at a resolution of about 10 nm.},
author = {Howells, M. R. and Beetz, T. and Chapman, H. N. and Cui, C. and Holton, J. M. and Jacobsen, C. J. and Kirz, J. and Lima, E. and Marchesini, S. and Miao, H.},
citeulike-article-id = {6891658},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.elspec.2008.10.008},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0368204808001424},
doi = {10.1016/j.elspec.2008.10.008},
issn = {03682048},
journal = {Journal of Electron Spectroscopy and Related Phenomena},
keywords = {damage},
month = {March},
number = {1-3},
pages = {4--12},
posted-at = {2010-03-22 17:05:49},
priority = {2},
title = {An assessment of the resolution limitation due to radiation-damage in X-ray diffraction microscopy},
url = {http://dx.doi.org/10.1016/j.elspec.2008.10.008},
volume = {170},
year = {2009}
}
@article{Walther1963Question,
abstract = {It is generally asserted that valuable phase information is irretrievably lost in the squaring operation required to obtain the intensity from the amplitude distribution in the image of a star formed by a lens. In this paper the phase reconstruction is studied under the constraint that the aperture of the lens be finite. It is shown that in some cases the phase reconstruction is unique; and that in other cases there is finite or denumerable infinite number of discrete solutions.Conversely, it is proved that every non-negative function that is integrable and band-limited can be realized as the intensity distribution in the image of a star formed by a lens.},
author = {Walther, Adriaan},
citeulike-article-id = {6806455},
citeulike-linkout-0 = {http://dx.doi.org/10.1080/713817747},
doi = {10.1080/713817747},
journal = {Optica Acta: International Journal of Optics},
keywords = {uniqueness},
number = {1},
pages = {41--49},
posted-at = {2010-03-11 14:47:28},
priority = {2},
publisher = {Taylor \& Francis},
title = {The Question of Phase Retrieval in Optics},
url = {http://dx.doi.org/10.1080/713817747},
volume = {10},
year = {1963}
}
@article{Wolf1962Complete,
abstract = {It is shown that the analytic properties of the temporal complex degree of coherence g(t) in the complex time plane (t complex) impose a relationship between|g(t)| and arg g(t) on the real time axis. This relationship involves, in general, the location of the zeros of the degree of coherence in the lower half of the complex t plane. It is suggested that the analytic continuation of the temporal degree of coherence of many spectral distributions has no zeros at all in this half plane. The spectral profiles of such distributions could be uniquely determined from measurements of|g(t)| alone. This possibility is of interest in connection with Michelson's well-known method of visibility curves. It is also of interest in connection with the recently proposed correlation and coincidence techniques (employing square-law detection) for determining narrow spectral profiles, such as those found in the output from an optical maser.},
author = {Wolf, E.},
citeulike-article-id = {515250},
citeulike-linkout-0 = {http://dx.doi.org/10.1088/0370-1328/80/6/307},
citeulike-linkout-1 = {http://stacks.iop.org/0370-1328/80/1269},
doi = {10.1088/0370-1328/80/6/307},
journal = {Proceedings of the Physical Society},
keywords = {uniqueness},
number = {6},
pages = {1269--1272},
posted-at = {2010-03-11 14:42:18},
priority = {2},
title = {Is a Complete Determination of the Energy Spectrum of Light Possible from Measurements of the Degree of Coherence?},
url = {http://dx.doi.org/10.1088/0370-1328/80/6/307},
volume = {80},
year = {1962}
}
@article{Bruck1979Ambiguity,
abstract = {The well-known problem of image reconstruction from its spectrum modulus has been studied for a discretely defined function. An approach has been developed, allowing for the study of two-dimensional brightness distributions. It is shown that the retrieval ambiguity represents a lesser problem in the two-dimensional case},
author = {Bruck, Y. and Sodin, L.},
citeulike-article-id = {902266},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/0030-4018(79)90358-4},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/0030-4018(79)90358-4},
citeulike-linkout-2 = {http://www.sciencedirect.com/science/article/B6TVF-4D5NYDD-9/2/c7925e54000ffd083db92693a87e5f8f},
doi = {10.1016/0030-4018(79)90358-4},
issn = {00304018},
journal = {Optics Communications},
keywords = {uniqueness},
month = {September},
number = {3},
pages = {304--308},
posted-at = {2010-03-11 14:28:01},
priority = {2},
title = {On the ambiguity of the image reconstruction problem},
url = {http://dx.doi.org/10.1016/0030-4018(79)90358-4},
volume = {30},
year = {1979}
}
@article{11298,
abstract = {We propose an iterative phase retrieval method that uses a series of diffraction patterns, measured only in intensity, to solve for both amplitude and phase of the image wave function over a wide field of view and at wavelength-limited resolution. The new technique requires an aperture that is scanned to two or more positions over the object wave function. A simple implementation of the method is modeled and demonstrated, showing how the algorithm uses overlapping data in real space to resolve ambiguities in the solution. The technique opens up the possibility of practical transmission lensless microscopy at subatomic resolution using electrons, x rays, or nuclear particles.},
author = {Faulkner, H. M. L. and Rodenburg, J. M.},
citeulike-article-id = {3886458},
citeulike-linkout-0 = {http://www.ncbi.nlm.nih.gov/pubmed/15323918},
journal = {Phys. Rev. Lett.},
keywords = {ptycography},
number = {2},
pages = {023903},
posted-at = {2010-02-16 17:34:56},
priority = {2},
title = {Movable aperture lensless transmission microscopy: a novel phase retrieval algorithm.},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15323918},
volume = {93},
year = {2004}
}
@article{Maiden2009Improved,
abstract = {The ptychographical iterative engine (or PIE) is a recently developed phase retrieval algorithm that employs a series of diffraction patterns recorded as a known illumination function is translated to a set of overlapping positions relative to a target sample. The technique has been demonstrated successfully at optical and X-ray wavelengths and has been shown to be robust to detector noise and to converge considerably faster than support-based phase retrieval methods. In this paper, the PIE is extended so that the requirement for an accurate model of the illumination function is removed.},
author = {Maiden, Andrew M. and Rodenburg, John M.},
citeulike-article-id = {5096630},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ultramic.2009.05.012},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0304399109001284},
day = {09},
doi = {10.1016/j.ultramic.2009.05.012},
issn = {03043991},
journal = {Ultramicroscopy},
keywords = {ptycography},
month = {September},
number = {10},
pages = {1256--1262},
posted-at = {2010-02-16 14:42:57},
priority = {2},
title = {An improved ptychographical phase retrieval algorithm for diffractive imaging},
url = {http://dx.doi.org/10.1016/j.ultramic.2009.05.012},
volume = {109},
year = {2009}
}
@article{Rodenburg2004Phase,
abstract = {We propose a method of iterative phase retrieval that uses measured intensities in the diffraction plane to solve the phase problem in a way that bypasses the problem of lens aberration, leading to greatly improved spatial resolution. This method is stable, easy to implement experimentally, and can be used to view a large area of the specimen when that is desired.},
author = {Rodenburg, J. M. and Faulkner, H. M. L.},
citeulike-article-id = {6670592},
citeulike-linkout-0 = {http://dx.doi.org/10.1063/1.1823034},
citeulike-linkout-1 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=APPLAB000085000020004795000001\&idtype=cvips\&gifs=yes},
citeulike-linkout-2 = {http://link.aip.org/link/?APL/85/4795},
doi = {10.1063/1.1823034},
journal = {Applied Physics Letters},
keywords = {ptycography},
number = {20},
pages = {4795--4797},
posted-at = {2010-02-16 14:21:50},
priority = {2},
publisher = {AIP},
title = {A phase retrieval algorithm for shifting illumination},
url = {http://dx.doi.org/10.1063/1.1823034},
volume = {85},
year = {2004}
}
@article{Rodenburg2007HardXRay,
abstract = {We demonstrate a hard-x-ray microscope that does not use a lens and is not limited to a small field of view or an object of finite size. The method does not suffer any of the physical constraints, convergence problems, or defocus ambiguities that often arise in conventional phase-retrieval diffractive imaging techniques. Calculation times are about a thousand times shorter than in current iterative algorithms. We need no a priori knowledge about the object, which can be a transmission function with both modulus and phase components. The technique has revolutionary implications for x-ray imaging of all classes of specimen.},
author = {Rodenburg, J. M. and Hurst, A. C. and Cullis, A. G. and Dobson, B. R. and Pfeiffer, F. and Bunk, O. and David, C. and Jefimovs, K. and Johnson, I.},
citeulike-article-id = {2563099},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PRLTAO000098000003034801000001\&idtype=cvips\&gifs=yes},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRL/v98/e034801},
citeulike-linkout-2 = {http://dx.doi.org/10.1103/PhysRevLett.98.034801},
citeulike-linkout-3 = {http://link.aps.org/abstract/PRL/v98/i3/e034801},
citeulike-linkout-4 = {http://link.aps.org/pdf/PRL/v98/i3/e034801},
doi = {10.1103/PhysRevLett.98.034801},
journal = {Physical Review Letters},
keywords = {ptycography},
month = {Jan},
number = {3},
pages = {034801+},
posted-at = {2010-02-16 14:20:56},
priority = {4},
publisher = {American Physical Society},
title = {Hard-X-Ray Lensless Imaging of Extended Objects},
url = {http://dx.doi.org/10.1103/PhysRevLett.98.034801},
volume = {98},
year = {2007}
}
@article{Beazley2003Automated,
abstract = {Scripting languages such as Python and Tcl are a powerful tool for the construction of flexible scientific software because they provide scientists with an interpreted problem solving environment and they provide a modular framework for controlling software components written in C, C++, and Fortran. However, a common problem faced by the developers of a scripted scientific application is that of integrating compiled code with an interpreter. To solve this problem, an extensible compiler, simplified wrapper and interface generator (SWIG), has been developed to automate the task of integrating compiled code with scripting language interpreters. SWIG requires no modifications to existing code and uses existing source to create bindings for nine different target languages including Python, Perl, Tcl, Ruby, Guile, and Java. By automating language integration, SWIG enables scientists to use scripting languages at all stages of software development and allows existing software to be more easily integrated into a scripting environment. Although SWIG has been in use for more than 6 years, little has been published on its design and the underlying mechanisms that make it work. Therefore, the primary goal of this paper is to cover these topics.},
address = {Amsterdam, The Netherlands, The Netherlands},
author = {Beazley, D.},
citeulike-article-id = {881608},
citeulike-linkout-0 = {http://portal.acm.org/citation.cfm?id=860018},
citeulike-linkout-1 = {http://dx.doi.org/10.1016/S0167-739X(02)00171-1},
citeulike-linkout-2 = {http://linkinghub.elsevier.com/retrieve/pii/S0167739X02001711},
citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6V06-48CFW80-2/2/2b6de06199938cbb00493821c0f78531},
doi = {10.1016/S0167-739X(02)00171-1},
issn = {0167739X},
journal = {Future Generation Computer Systems},
keywords = {swig},
month = {July},
number = {5},
pages = {599--609},
posted-at = {2010-02-10 14:57:28},
priority = {2},
publisher = {Elsevier Science Publishers B. V.},
title = {Automated scientific software scripting with SWIG},
url = {http://dx.doi.org/10.1016/S0167-739X(02)00171-1},
volume = {19},
year = {2003}
}
@article{Bauschke2006Strongly,
abstract = {A new iterative method for finding the projection onto the intersection of two closed convex sets in a Hilbert space is presented. It is a Haugazeau-like modification of a recently proposed averaged alternating reflections method which produces a strongly convergent sequence.},
author = {Bauschke, H. and Combettes, P. and Luke, D.},
citeulike-article-id = {6650805},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jat.2006.01.003},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021904506000049},
doi = {10.1016/j.jat.2006.01.003},
issn = {00219045},
journal = {Journal of Approximation Theory},
keywords = {algorithms, haar},
month = {July},
number = {1},
pages = {63--69},
posted-at = {2010-02-10 14:49:26},
priority = {2},
title = {A strongly convergent reflection method for finding the projection onto the intersection of two closed convex sets in a Hilbert space},
url = {http://dx.doi.org/10.1016/j.jat.2006.01.003},
volume = {141},
year = {2006}
}
@article{Elser2003Phase,
abstract = {Several strategies in phase retrieval are unified by an iterative \"difference map\" constructed from a pair of elementary projections and three real parameters. For the standard application in optics, where the two projections implement Fourier modulus and object support constraints, respectively, the difference map reproduces the \"hybrid\" form of Fienup's input\&\#150;output map when a particular choice is made for two of the parameters. The geometric construction of the difference map illuminates the distinction between its fixed points and the recovered object, as well as the mechanism whereby the form of stagnation encountered by alternating projection schemes is avoided. When support constraints are replaced by object histogram or atomicity constraints, the difference map lends itself to crystallographic phase retrieval. Numerical experiments with synthetic data suggest that structures with hundreds of atoms can be solved. \©2003 Optical Society of America},
author = {Elser, Veit},
citeulike-article-id = {526151},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=JOAOD6000020000001000040000001\&idtype=cvips\&gifs=yes},
journal = {Journal of the Optical Society of America A: Optics, Image Science, and Vision},
keywords = {algorithms, diff\_map},
number = {1},
pages = {40--55},
posted-at = {2010-02-10 14:11:05},
priority = {2},
publisher = {OSA},
title = {Phase retrieval by iterated projections},
url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=JOAOD6000020000001000040000001\&idtype=cvips\&gifs=yes},
volume = {20},
year = {2003}
}
@book{Schroeder2006Visualization,
author = {Schroeder, Will and Martin, Ken and Lorensen, Bill},
citeulike-article-id = {6650139},
edition = {4th},
keywords = {vtk},
month = {December},
posted-at = {2010-02-10 13:58:27},
priority = {2},
publisher = {Kitware},
title = {Visualization Toolkit: An Object-Oriented Approach to 3D Graphics},
year = {2006}
}
@inproceedings{Frigo2005Design,
abstract = {FFTW is an implementation of the discrete Fourier transform (DFT) that adapts to the hardware in order to maximize performance. This paper shows that such an approach can yield an implementation that is competitive with hand-optimized libraries, and describes the software structure that makes our current FFTW3 version flexible and adaptive. We further discuss a new algorithm for real-data DFTs of prime size, a new way of implementing DFTs by means of machine-specific single-instruction, multiple-data (SIMD) instructions, and how a special-purpose compiler can derive optimized implementations of the discrete cosine and sine transforms automatically from a DFT algorithm. Keywords—Adaptive software, cosine transform, fast Fourier transform (FFT), Fourier transform, Hartley transform, I/O tensor.},
author = {Frigo, Matteo and Steven and Johnson, G.},
booktitle = {Proceedings of the IEEE},
citeulike-article-id = {4165112},
citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.136.7045},
keywords = {fftw3},
pages = {216--231},
posted-at = {2010-02-10 13:47:51},
priority = {2},
title = {The design and implementation of FFTW3},
url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.136.7045},
volume = {93},
year = {2005}
}
@manual{Galassi2009GNU,
author = {Galassi, M.},
citeulike-article-id = {6650101},
isbn = {0954612078},
month = {January},
posted-at = {2010-02-10 13:46:17},
priority = {2},
title = {GNU Scientific Library Reference Manual - Third Edition},
year = {2009}
}
@inbook{Sayre1980Imaging,
author = {Sayre, D.},
booktitle = {Springer Lecture Notes in Physics},
citeulike-article-id = {6650081},
editor = {Schlenker, M.},
keywords = {oversampling},
location = {Berlin},
pages = {229--235},
posted-at = {2010-02-10 13:33:29},
priority = {2},
publisher = {Springer-Verlag},
title = {Imaging Processes and Coherence in Physics},
volume = {112},
year = {1980}
}
@article{Sayre1952Some,
author = {Sayre, D.},
citeulike-article-id = {6650054},
citeulike-linkout-0 = {http://dx.doi.org/10.1107/S0365110X52002276},
citeulike-linkout-1 = {http://scripts.iucr.org/cgi-bin/paper?S0365110X52002276},
doi = {10.1107/S0365110X52002276},
journal = {Acta Crystallographica},
keywords = {oversampling},
month = {Nov},
number = {6},
pages = {843+},
posted-at = {2010-02-10 13:22:21},
priority = {2},
title = {{Some implications of a theorem due to Shannon}},
url = {http://dx.doi.org/10.1107/S0365110X52002276},
volume = {5},
year = {1952}
}
@article{Shapiro2005Biological,
abstract = {We have used the method of x-ray diffraction microscopy to image the complex-valued exit wave of an intact and unstained yeast cell. The images of the freeze-dried cell, obtained by using 750-eV x-rays from different angular orientations, portray several of the cell's major internal components to 30-nm resolution. The good agreement among the independently recovered structures demonstrates the accuracy of the imaging technique. To obtain the best possible reconstructions, we have implemented procedures for handling noisy and incomplete diffraction data, and we propose a method for determining the reconstructed resolution. This work represents a previously uncharacterized application of x-ray diffraction microscopy to a specimen of this complexity and provides confidence in the feasibility of the ultimate goal of imaging biological specimens at 10-nm resolution in three dimensions.},
author = {Shapiro, David and Thibault, Pierre and Beetz, Tobias and Elser, Veit and Howells, Malcolm and Jacobsen, Chris and Kirz, Janos and Lima, Enju and Miao, Huijie and Neiman, Aaron M. and Sayre, David},
citeulike-article-id = {557078},
citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0503305102},
citeulike-linkout-1 = {http://www.pnas.org/content/102/43/15343.abstract},
citeulike-linkout-2 = {http://www.pnas.org/content/102/43/15343.full.pdf},
citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/102/43/15343},
citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/16219701},
citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=16219701},
day = {25},
doi = {10.1073/pnas.0503305102},
journal = {PNAS},
keywords = {cell},
month = {October},
number = {43},
pages = {15343--15346},
posted-at = {2010-02-10 13:00:14},
priority = {2},
title = {Biological imaging by soft x-ray diffraction microscopy},
url = {http://dx.doi.org/10.1073/pnas.0503305102},
volume = {102},
year = {2005}
}
@article{Oszlanyi2005It,
author = {Oszl{\'{a}}nyi, G{\'{a}}bor and S{\"{u}}to, Andr{\'{a}}s},
citeulike-article-id = {2351},
citeulike-linkout-0 = {http://dx.doi.org/10.1107/S0108767304027746},
citeulike-linkout-1 = {http://scripts.iucr.org/cgi-bin/paper?S0108767304027746},
doi = {10.1107/S0108767304027746},
journal = {Acta Crystallographica Section A},
keywords = {charge\_flip},
month = {Jan},
number = {1},
pages = {147--152},
posted-at = {2010-02-10 12:44:06},
priority = {0},
publisher = {International Union of Crystallography},
title = {{{\it Ab initio} structure solution by charge flipping. II. Use of weak reflections}},
url = {http://dx.doi.org/10.1107/S0108767304027746},
volume = {61},
year = {2005}
}
@article{Oszlanyi2004Ab,
abstract = {In this paper, an extremely simple structure solution method termed charge flipping is presented. It works ab initio on high-resolution X-ray diffraction data in the manner of Fourier recycling. The real-space modification simply changes the sign of charge density below a threshold, while in reciprocal space the moduli Fobs are retained resulting in an Fobs map without weighting. The algorithm is tested using synthetic data for a wide range of structures, the solution statistics are analysed and the quality of reconstruction is checked. Finally, mathematical aspects of the algorithm are considered in detail, and these show that in this chaotic iteration process the solution is a limit cycle and not a fixed point.},
author = {Oszlanyi, Gabor and Suto, Andras},
citeulike-article-id = {526142},
citeulike-linkout-0 = {http://www.blackwell-synergy.com/doi/abs/10.1107/S0108767303027569},
citeulike-linkout-1 = {http://dx.doi.org/10.1107/S0108767303027569},
doi = {10.1107/S0108767303027569},
journal = {Acta Crystallographica Section A},
keywords = {charge\_flip},
number = {2},
pages = {134--141},
posted-at = {2010-02-10 12:42:47},
priority = {2},
title = {Ab initio structure solution by charge flipping},
url = {http://dx.doi.org/10.1107/S0108767303027569},
volume = {60},
year = {2004}
}
@article{Luke2005Relaxed,
author = {Luke, D. Russell},
citeulike-article-id = {39745},
citeulike-linkout-0 = {http://dx.doi.org/10.1088/0266-5611/21/1/004},
citeulike-linkout-1 = {http://www.ingentaconnect.com/content/iop/ip/2005/00000021/00000001/art00004},
doi = {10.1088/0266-5611/21/1/004},
issn = {0266-5611},
journal = {Inverse Problems},
keywords = {raar},
number = {1},
pages = {37--50},
posted-at = {2010-02-10 12:40:23},
priority = {0},
publisher = {Institute of Physics Publishing},
title = {Relaxed averaged alternating reflections for diffraction imaging},
url = {http://dx.doi.org/10.1088/0266-5611/21/1/004},
volume = {21},
year = {2005}
}
@article{Miao1998Phase,
abstract = {It is suggested that, given the magnitude of Fourier transforms sampled at the Bragg density, the phase problem is underdetermined by a factor of 2 for 1D, 2D, and 3D objects. It is therefore unnecessary to oversample the magnitude of Fourier transforms by 2× in each dimension (i.e., oversampling by 4× for 2D and 8× for 3D) in retrieving the phase of 2D and 3D objects. Our computer phasing experiments accurately retrieved the phase from the magnitude of the Fourier transforms of 2D and 3D complex-valued objects by using positivity constraints on the imaginary part of the objects and loose supports, with the oversampling factor much less than 4 for 2D and 8 for 3D objects. Under the same conditions we also obtained reasonably good reconstructions of 2D and 3D complex-valued objects from the magnitude of their Fourier transforms with added noise and a central stop.},
author = {Miao, J. and Sayre, D. and Chapman, H. N.},
citeulike-article-id = {6649888},
citeulike-linkout-0 = {http://dx.doi.org/10.1364/JOSAA.15.001662},
citeulike-linkout-1 = {http://www.opticsinfobase.org/abstract.cfm?id=1528},
day = {1},
doi = {10.1364/JOSAA.15.001662},
journal = {J. Opt. Soc. Am. A},
month = {June},
number = {6},
pages = {1662--1669},
posted-at = {2010-02-10 12:39:05},
priority = {2},
publisher = {OSA},
title = {Phase retrieval from the magnitude of the Fourier transforms of nonperiodic objects},
url = {http://dx.doi.org/10.1364/JOSAA.15.001662},
volume = {15},
year = {1998}
}
@article{Fienup1978Reconstruction,
author = {Fienup, J. R.},
citeulike-article-id = {2460593},
citeulike-linkout-0 = {http://www.opticsinfobase.org/abstract.cfm?id=6754},
day = {1},
journal = {Opt. Lett.},
keywords = {hio},
month = {July},
number = {1},
pages = {27+},
posted-at = {2010-02-10 12:32:34},
priority = {2},
publisher = {OSA},
title = {Reconstruction of an object from the modulus of its Fourier transform},
url = {http://www.opticsinfobase.org/abstract.cfm?id=6754},
volume = {3},
year = {1978}
}
@article{Bauschke2003Hybrid,
abstract = {The phase-retrieval problem, fundamental in applied physics and engineering, addresses the question of how to determine the phase of a complex-valued function from modulus data and additional a priori information. Recently we identified two important methods for phase retrieval, namely, Fienup's basic input-output and hybrid input-output (HIO) algorithms, with classical convex projection methods and suggested that further connections between convex optimization and phase retrieval should be explored. Following up on this work, we introduce a new projection-based method, termed the hybrid projection-reflection (HPR) algorithm, for solving phase-retrieval problems featuring nonnegativity constraints in the object domain. Motivated by properties of the HPR algorithm for convex constraints, we recommend an error measure studied by Fienup more than 20 years ago. This error measure, which has received little attention in the literature, lends itself to an easily implementable stopping criterion. In numerical experiments we found the HPR algorithm to be a competitive alternative to the HIO algorithm and the stopping criterion to be reliable and robust.},
address = {Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1, Canada. [email protected]},
author = {Bauschke, H. H. and Combettes, P. L. and Luke, D. R.},
citeulike-article-id = {494343},
citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12801170},
citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12801170},
issn = {1084-7529},
journal = {J Opt Soc Am A Opt Image Sci Vis},
keywords = {hpr},
month = {June},
number = {6},
pages = {1025--1034},
posted-at = {2010-02-10 12:30:53},
priority = {2},
title = {Hybrid projection-reflection method for phase retrieval.},
url = {http://view.ncbi.nlm.nih.gov/pubmed/12801170},
volume = {20},
year = {2003}
}
@article{Ravasio2009SingleShot,
abstract = {Coherent x-ray diffractive imaging is a powerful method for studies on nonperiodic structures on the nanoscale. Access to femtosecond dynamics in major physical, chemical, and biological processes requires single-shot diffraction data. Up to now, this has been limited to intense coherent pulses from a free electron laser. Here we show that laser-driven ultrashort x-ray sources offer a comparatively inexpensive alternative. We present measurements of single-shot diffraction patterns from isolated nano-objects with a single 20\^{A} fs pulse from a table-top high-harmonic x-ray laser. Images were reconstructed with a resolution of 119\^{A} nm from the single shot and 62\^{A} nm from multiple shots.},
author = {Ravasio, A. and Gauthier, D. and Maia, F. R. N. C. and Billon, M. and Caumes, J. P. and Garzella, D. and G\'{e}l\'{e}oc, M. and Gobert, O. and Hergott, J. F. and Pena, A. M. and Perez, H. and Carr\'{e}, B. and Bourhis, E. and Gierak, J. and Madouri, A. and Mailly, D. and Schiedt, B. and Fajardo, M. and Gautier, J. and Zeitoun, P. and Bucksbaum, P. H. and Hajdu, J. and Merdji, H.},
citeulike-article-id = {5182800},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PRLTAO000103000002028104000001\&idtype=cvips\&gifs=yes},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRL/v103/e028104},
citeulike-linkout-2 = {http://dx.doi.org/10.1103/PhysRevLett.103.028104},
citeulike-linkout-3 = {http://link.aps.org/abstract/PRL/v103/i2/e028104},
citeulike-linkout-4 = {http://link.aps.org/pdf/PRL/v103/i2/e028104},
doi = {10.1103/PhysRevLett.103.028104},
journal = {Physical Review Letters},
keywords = {hhghamed, reconstruction},
month = {Jul},
number = {2},
pages = {028104+},
posted-at = {2010-01-19 20:09:24},
priority = {0},
publisher = {American Physical Society},
title = {Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source},
url = {http://dx.doi.org/10.1103/PhysRevLett.103.028104},
volume = {103},
year = {2009}
}
@article{Maia2009Structural,
abstract = {X-ray lasers may allow structural studies on single particles and biomolecules without crystalline periodicity in the samples. We examine here the effect of sample dynamics as a source of structural heterogeneity on the resolution of the reconstructed image of a small protein molecule. Structures from molecular-dynamics simulations of lysozyme were sampled and aligned. These structures were then used to calculate diffraction patterns corresponding to different dynamic states. The patterns were incoherently summed and the resulting data set was phased using the oversampling method. Reconstructed images of hydrated and dehydrated lysozyme gave resolutions of 3.7\^{a}€'\~{A}… and 7.6\^{a}€'\~{A}… , respectively. These are significantly worse than the root-mean-square deviation of the hydrated ( 2.7\^{a}€'\~{A}… for all atoms and 1.45\^{a}€'\~{A}… for C- \^{I}± positions) or dehydrated ( 3.7\^{a}€'\~{A}… for all atoms and 2.5\^{a}€'\~{A}… for C- \^{I}± positions) structures. The noise introduced by structural dynamics and incoherent addition of dissimilar structures restricts the maximum resolution to be expected from direct image reconstruction of dynamic systems. A way of potentially reducing this effect is by grouping dynamic structures into distinct structural substates and solving them separately.},
author = {Maia, Filipe R. N. C. and Ekeberg, Tomas and T\^{i}mneanu, Nicu\c{s}or and van der Spoel, David and Hajdu, Janos},
citeulike-article-id = {6563713},
citeulike-linkout-0 = {http://dx.doi.org/10.1103/PhysRevE.80.031905},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRE/v80/i3/e031905},
citeulike-linkout-2 = {http://link.aps.org/pdf/PRE/v80/i3/e031905},
doi = {10.1103/PhysRevE.80.031905},
journal = {Physical Review E},
keywords = {imaging, reconstruction, variability},
month = {Sep},
number = {3},
pages = {031905+},
posted-at = {2010-01-19 19:58:47},
priority = {0},
publisher = {American Physical Society},
title = {Structural variability and the incoherent addition of scattered intensities in single-particle diffraction},
url = {http://dx.doi.org/10.1103/PhysRevE.80.031905},
volume = {80},
year = {2009}
}
@article{NeTeDuaneLoh2009Reconstruction,
abstract = {We introduce the EMC algorithm for reconstructing a particle's three-dimensional (3D) diffraction intensity from very many photon shot-noise limited two-dimensional measurements, when the particle orientation in each measurement is unknown. The algorithm combines a maximization step (M) of the intensity's likelihood function, with expansion (E) and compression (C) steps that map the 3D intensity model to a redundant tomographic representation and back again. After a few iterations of the EMC update rule, the reconstructed intensity is given to the difference-map algorithm for reconstruction of the particle contrast. We demonstrate reconstructions with simulated data and investigate the effects of particle complexity, number of measurements, and the number of photons per measurement. The relatively transparent scaling behavior of our algorithm provides an estimate of the data processing resources required for future single-particle imaging experiments.},
author = {Ne Te Duane Loh and Elser, Veit},
citeulike-article-id = {5656376},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PLEEE8000080000002026705000001\&idtype=cvips\&gifs=yes},
citeulike-linkout-1 = {http://link.aps.org/abstract/PRE/v80/e026705},
citeulike-linkout-2 = {http://dx.doi.org/10.1103/PhysRevE.80.026705},
doi = {10.1103/PhysRevE.80.026705},
journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
keywords = {em, orientation},
number = {2},
pages = {026705+},