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  • 1.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Liang, Meng
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Wang, Fenglin
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Hartmann, Robert
    Erk, Benjamin
    Rudek, Benedikt
    Chapman, Henry N.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Automated identification and classification of single particle serial femtosecond X-ray diffraction data2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 3, p. 2497-2510Article in journal (Refereed)
    Abstract [en]

    The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of America

  • 2. Barty, Anton
    et al.
    Kirian, Richard A.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Yoon, Chun Hong
    White, Thomas A.
    Chapman, Henry
    Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data2014In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 47, p. 1118-1131Article in journal (Refereed)
    Abstract [en]

    The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.

  • 3.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gunn, Laura H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flueckiger, Leonie
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lundholm, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kulyk, Olena
    Higashiura, Akifumi
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Ne-Te Duane
    Wysong, Taylor E.
    Bostedt, Christoph
    Gorkhover, Tais
    Iwan, Bianca
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Osipov, Timur
    Walter, Peter
    Hart, Philip
    Bucher, Maximilian
    Ulmer, Anatoli
    Ray, Dipanwita
    Carini, Gabriella
    Ferguson, Ken R.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Electrospray sample injection for single-particle imaging with x-ray lasers2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed)
  • 4.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time2016In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1042-1047Article in journal (Refereed)
  • 5.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Benner, W. Henry
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tîmneanu, Nicuşor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Loh, N. Duane
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Awel, Salah
    Wiedorn, Max O.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastian
    Williams, Garth
    Koglin, Jason
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed)
  • 6. Duane Loh, N.
    et al.
    Starodub, D.
    Lomb, L.
    Hampton, C. Y.
    Martin, A. V.
    Sierra, R. G.
    Barty, A.
    Aquila, A.
    Schulz, J.
    Steinbrener, J.
    Shoeman, R. L.
    Kassemeyer, S.
    Bostedt, C.
    Bozek, J.
    Epp, S. W.
    Erk, B.
    Hartmann, R.
    Rolles, D.
    Rudenko, A.
    Rudek, B.
    Foucar, L.
    Kimmel, N.
    Weidenspointner, G.
    Hauser, G.
    Holl, P.
    Pedersoli, E.
    Liang, M.
    Hunter, M. S.
    Gumprecht, L.
    Coppola, N.
    Wunderer, C.
    Graafsma, H.
    Maia, F. R. N. C.
    Ekeberg, T.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, H.
    Hirsemann, H.
    Nass, K.
    White, T. A.
    Tobias, H. J.
    Farquar, G. R.
    Henry Benner, W.
    Hau-Riege, S.
    Reich, C.
    Hartmann, A.
    Soltau, H.
    Marchesini, S.
    Bajt, S.
    Barthelmess, M.
    Strueder, L.
    Ullrich, J.
    Bucksbaum, P.
    Hodgson, K. O.
    Frank, M.
    Schlichting, I.
    Chapman, H. N.
    Bogan, M. J.
    Profiling structured beams using injected aerosols2012In: Proceedings of SPIE: The International Society for Optical Engineering, 2012, p. 850403-Conference paper (Refereed)
    Abstract [en]

    Profiling structured beams produced by X-ray free-electron lasers (FELs) is crucial to both maximizing signal intensity for weakly scattering targets and interpreting their scattering patterns. Earlier ablative imprint studies describe how to infer the X-ray beam profile from the damage that an attenuated beam inflicts on a substrate. However, the beams in-situ profile is not directly accessible with imprint studies because the damage profile could be different from the actual beam profile. On the other hand, although a Shack-Hartmann sensor is capable of in-situ profiling, its lenses may be quickly damaged at the intense focus of hard X-ray FEL beams. We describe a new approach that probes the in-situ morphology of the intense FEL focus. By studying the translations in diffraction patterns from an ensemble of randomly injected sub-micron latex spheres, we were able to determine the non-Gaussian nature of the intense FEL beam at the Linac Coherent Light Source (SLAC National Laboratory) near the FEL focus. We discuss an experimental application of such a beam-profiling technique, and the limitations we need to overcome before it can be widely applied.

  • 7.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
  • 8. Gorkhover, Tais
    et al.
    Ulmer, Anatoli
    Ferguson, Ken
    Bucher, Max
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bruza, Petr
    Carron, Sebastian
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rupp, Daniela
    Sauppe, Mario
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N.
    Faigel, Gyula
    Möller, Thomas
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bostedt, Christoph
    Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles2018In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal (Refereed)
  • 9.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Uetrecht, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Bari, Sadia
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Epp, Sascha W.
    Chapman, Henry N.
    Barty, Anton
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A data set from flash X-ray imaging of carboxysomes2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed)
    Abstract [en]

    Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

  • 10.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gijs, van der Schot
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha
    Chapman, Henry N.
    Barty, Anton
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    High-throughput imaging of heterogeneous cell organelles with an X-ray laser2014In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 8, no 12, p. 943-949Article in journal (Refereed)
    Abstract [en]

    We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.

  • 11.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Coherent Diffractive Imaging with X-ray Lasers2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics.

    While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved  image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank.

    We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles.

    XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data.

    We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.

    List of papers
    1. High-throughput imaging of heterogeneous cell organelles with an X-ray laser
    Open this publication in new window or tab >>High-throughput imaging of heterogeneous cell organelles with an X-ray laser
    Show others...
    2014 (English)In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 8, no 12, p. 943-949Article in journal (Refereed) Published
    Abstract [en]

    We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.

    National Category
    Structural Biology
    Identifiers
    urn:nbn:se:uu:diva-237619 (URN)10.1038/nphoton.2014.270 (DOI)000345818600014 ()
    Available from: 2014-12-03 Created: 2014-12-03 Last updated: 2017-12-05Bibliographically approved
    2. A data set from flash X-ray imaging of carboxysomes
    Open this publication in new window or tab >>A data set from flash X-ray imaging of carboxysomes
    Show others...
    2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed) Published
    Abstract [en]

    Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-300202 (URN)10.1038/sdata.2016.61 (DOI)000390225400006 ()
    Note

    Data Descriptor

    Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
    3. Condor: a simulation tool for flash X-ray imaging
    Open this publication in new window or tab >>Condor: a simulation tool for flash X-ray imaging
    2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1356-1362Article, review/survey (Refereed) Published
    Abstract [en]

    Flash X-ray imaging has the potential to determine structures down to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces Condor, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data. Condor is designed to be easy to use and can be either installed as a Python package or used from its web interface (http://lmb.icm.uu.se/condor). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.

    Keywords
    femtosecond coherent diffractive imaging, X-ray free-electron lasers, simulation, single-particle imaging, computer programs
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-300211 (URN)10.1107/S1600576716009213 (DOI)000382755900027 ()
    Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
    4. Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
    Open this publication in new window or tab >>Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
    2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1042-1047Article in journal (Refereed) Published
    National Category
    Biophysics Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-287197 (URN)10.1107/S1600576716005926 (DOI)000377020600036 ()
    Projects
    eSSENCE
    Available from: 2016-04-18 Created: 2016-04-22 Last updated: 2018-01-10Bibliographically approved
    5. Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
    Open this publication in new window or tab >>Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
    Show others...
    2014 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 47, p. 1118-1131Article in journal (Refereed) Published
    Abstract [en]

    The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-228011 (URN)10.1107/S1600576714007626 (DOI)000336738500032 ()
    Available from: 2014-07-03 Created: 2014-07-02 Last updated: 2017-12-05Bibliographically approved
  • 12.
    Hantke, Max Felix
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Oxford, Dept Chem, Chem Res Lab, 12 Mansfield Rd, Oxford OX1 3TA, England.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Kulyk, Olena
    Acad Sci Czech Republ, Inst Phys, ELI Beamlines, Na Slovance 2, CZ-18221 Prague, Czech Republic.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K.N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Arizona State Univ, Dept Phys, 550 E Tyler Dr, Tempe, AZ 85287 USA.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Acad Sci Czech Republ, Inst Phys, ELI Beamlines, Na Slovance 2, CZ-18221 Prague, Czech Republic;Chalmers Univ Technol, Dept Phys, Condensed Matter Phys, Gothenburg, Sweden.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Acad Sci Czech Republ, Inst Phys, ELI Beamlines, Na Slovance 2, CZ-18221 Prague, Czech Republic.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Lawrence Berkeley Natl Lab, NERSC, Berkeley, CA USA.
    Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams2018In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 673-680Article in journal (Refereed)
    Abstract [en]

    Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70-2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the 'Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100-500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.

  • 13. Kurta, Ruslan P.
    et al.
    Donatelli, Jeffrey J.
    Yoon, Chun Hong
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Fromme, Petra
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Pande, Kanupriya
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sierra, Raymond G.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Aquila, Andrew
    Zwart, Peter H.
    Mancuso, Adrian P.
    Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses2017In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 119, no 15, p. 158102:1-7, article id 158102Article in journal (Refereed)
  • 14. Loh, N. D.
    et al.
    Hampton, C. Y.
    Martin, A. V.
    Starodub, D.
    Sierra, R. G.
    Barty, A.
    Aquila, A.
    Schulz, J.
    Lomb, L.
    Steinbrener, J.
    Shoeman, R. L.
    Kassemeyer, S.
    Bostedt, C.
    Bozek, J.
    Epp, S. W.
    Erk, B.
    Hartmann, R.
    Rolles, D.
    Rudenko, A.
    Rudek, B.
    Foucar, L.
    Kimmel, N.
    Weidenspointner, G.
    Hauser, G.
    Holl, P.
    Pedersoli, E.
    Liang, M.
    Hunter, M. M.
    Gumprecht, L.
    Coppola, N.
    Wunderer, C.
    Graafsma, H.
    Maia, F. R. N. C.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, H.
    Hirsemann, H.
    Nass, K.
    White, T. A.
    Tobias, H. J.
    Farquar, G. R.
    Benner, W. H.
    Hau-Riege, S. P.
    Reich, C.
    Hartmann, A.
    Soltau, H.
    Marchesini, S.
    Bajt, S.
    Barthelmess, M.
    Bucksbaum, P.
    Hodgson, K. O.
    Strueder, L.
    Ullrich, J.
    Frank, M.
    Schlichting, I.
    Chapman, H. N.
    Bogan, M. J.
    Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 486, no 7404, p. 513-517Article in journal (Refereed)
    Abstract [en]

    The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology(1) to climate science(2), yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate(3); visible light scattering provides insufficient resolution(4); and X-ray synchrotron studies have been limited to ensembles of particles(5). Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source(6) free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins(7), vibrational energy transfer by the hydrodynamic interaction of amino acids(8), and large-scale production of nanoscale structures by flame synthesis(9).

  • 15.
    Lundholm, Ida V.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bruza, Petr
    Bucher, Max
    Carron, Sebastian
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ferguson, Ken
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rupp, Daniela
    Sauppe, Mario
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ulmer, Anatoli
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Faigel, Gyula
    Chapman, Henry N.
    Möller, Thomas
    Bostedt, Christoph
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gorkhover, Tais
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging2018In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed)
  • 16. Martin, A. V.
    et al.
    Wang, F.
    Loh, N. D.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, F. R. N. C.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, C. Y.
    Sierra, R. G.
    Aquila, A.
    Bajt, S.
    Barthelmess, M.
    Bostedt, C.
    Bozek, J. D.
    Coppola, N.
    Epp, S. W.
    Erk, B.
    Fleckenstein, H.
    Foucar, L.
    Frank, M.
    Graafsma, H.
    Gumprecht, L.
    Hartmann, A.
    Hartmann, R.
    Hauser, G.
    Hirsemann, H.
    Holl, P.
    Kassemeyer, S.
    Kimmel, N.
    Liang, M.
    Lomb, L.
    Marchesini, S.
    Nass, K.
    Pedersoli, E.
    Reich, C.
    Rolles, D.
    Rudek, B.
    Rudenko, A.
    Schulz, J.
    Shoeman, R. L.
    Soltau, H.
    Starodub, D.
    Steinbrener, J.
    Stellato, F.
    Strueder, L.
    Ullrich, J.
    Weidenspointner, G.
    White, T. A.
    Wunderer, C. B.
    Barty, A.
    Schlichting, I.
    Bogan, M. J.
    Chapman, H. N.
    Noise-robust coherent diffractive imaging with a single diffraction pattern2012In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 15, p. 16650-16661Article in journal (Refereed)
    Abstract [en]

    The resolution of single-shot coherent diffractive imaging at X-ray free-electron laser facilities is limited by the low signal-to-noise level of diffraction data at high scattering angles. The iterative reconstruction methods, which phase a continuous diffraction pattern to produce an image, must be able to extract information from these weak signals to obtain the best quality images. Here we show how to modify iterative reconstruction methods to improve tolerance to noise. The method is demonstrated with the hybrid input-output method on both simulated data and single-shot diffraction patterns taken at the Linac Coherent Light Source. (C) 2012 Optical Society of America

  • 17.
    Munke, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Bean, Richard J.
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    Bucher, Maximilian
    Chapman, Henry N.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Elser, Veit
    Fromme, Petra
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Higashiura, Akifumi
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lan, Ti-Yen
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liu, Haiguang
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nakagawa, Atsushi
    Nam, Daewoong
    Nelson, Garrett
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ourmazd, Abbas
    Rose, Max
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schwander, Peter
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Sierra, Raymond G.
    Song, Changyong
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Vartanyants, Ivan A.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wiedorn, Max O.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Yoon, Chun Hong
    Zook, James
    Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed)
  • 18. Park, Hyung Joo
    et al.
    Loh, N. Duane
    Sierra, Raymond G.
    Hampton, Christina Y.
    Starodub, Dmitri
    Martin, Andrew V.
    Barty, Anton
    Aquila, Andrew
    Schulz, Joachim
    Steinbrener, Jan
    Shoeman, Robert L.
    Lomb, Lukas
    Kassemeyer, Stephan
    Bostedt, Christoph
    Bozek, John
    Epp, Sascha W.
    Erk, Benjamin
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Rudek, Benedikt
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Hauser, Guenter
    Holl, Peter
    Pedersoli, Emanuele
    Liang, Mengning
    Hunter, Mark S.
    Gumprecht, Lars
    Coppola, Nicola
    Wunderer, Cornelia
    Graafsma, Heinz
    Maia, Filipe R. N. C.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Hirsemann, Helmut
    Nass, Karol
    Tobias, Herbert J.
    Farquar, George R.
    Benner, W. Henry
    Hau-Riege, Stefan
    Reich, Christian
    Hartmann, Andreas
    Soltau, Heike
    Marchesini, Stefano
    Bajt, Sasa
    Barthelmess, Miriam
    Strueder, Lothar
    Ullrich, Joachim
    Bucksbaum, Philip
    Frank, Matthias
    Schlichting, Ilme
    Chapman, Henry N.
    Bogan, Michael J.
    Elser, Veit
    Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers2013In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, no 23, p. 28729-28742Article in journal (Refereed)
    Abstract [en]

    Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

  • 19. Pedersoli, E.
    et al.
    Loh, N. D.
    Capotondi, F.
    Hampton, C. Y.
    Sierra, R. G.
    Starodub, D.
    Bostedt, C.
    Bozek, J.
    Nelson, A. J.
    Aslam, M.
    Li, S.
    Dravid, V. P.
    Martin, A. V.
    Aquila, A.
    Barty, A.
    Fleckenstein, H.
    Gumprecht, L.
    Liang, M.
    Nass, K.
    Schulz, J.
    White, T. A.
    Coppola, N.
    Bajt, S.
    Barthelmess, M.
    Graafsma, H.
    Hirsemann, H.
    Wunderer, C.
    Epp, S. W.
    Erk, B.
    Rudek, B.
    Rudenko, A.
    Foucar, L.
    Kassemeyer, S.
    Lomb, L.
    Rolles, D.
    Shoeman, R. L.
    Steinbrener, J.
    Hartmann, R.
    Hartmann, A.
    Hauser, G.
    Holl, P.
    Kimmel, N.
    Reich, C.
    Soltau, H.
    Weidenspointner, G.
    Benner, W. H.
    Farquar, G. R.
    Hau-Riege, S. P.
    Hunter, M. S.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tobias, H. J.
    Marchesini, S.
    Frank, M.
    Strueder, L.
    Schlichting, I.
    Ullrich, J.
    Chapman, H. N.
    Bucksbaum, P. H.
    Kiskinova, M.
    Bogan, M. J.
    Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging2013In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 46, no 16 SI, p. 164033-Article in journal (Refereed)
    Abstract [en]

    Unraveling the complex morphology of functional materials like core-shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core-shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with similar to 10 nm core diameter and similar to 30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core-shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.

  • 20.
    Pietrini, Alberto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A statistical approach to detect protein complexes at X-ray free electron laser facilities2018In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed)
  • 21.
    Rath, Asawari D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    Kirian, Richard
    Bean, Richard
    Barty, Anton
    Galli, Lorenzo
    Nass, Karol
    Barthelmess, Miriam
    Aquila, Andrew
    Toleikis, Sven
    Treusch, Rolf
    Roling, Sebastian
    Wöstmann, Michael
    Zacharias, Helmut
    Chapman, Henry N.
    Bajt, Saša
    DePonte, Daniel
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 23, p. 28914-28925Article in journal (Refereed)
    Abstract [en]

    We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 1016 W/cm2 with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.

  • 22.
    Reddy, Hemanth K. N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Yoon, Chun Hong
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bobkov, Sergey
    Bucher, Maximilian
    Carini, Gabriella A.
    Carron, Sebastian
    Chapman, Henry
    Daurer, Benedikt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fromme, Petra
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hart, Philip
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Kurta, Ruslan P.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nam, Daewoong
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ourmazd, Abbas
    Rose, Max
    Schwander, Peter
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Song, Changyong
    Spence, John C. H.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed)
  • 23.
    van der Schot, Gijs
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DePonte, Daniel P.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Schulz, Joachim
    Kirian, Richard
    Liang, Mengning
    Stellato, Francesco
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Almeida, F. Nunes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Martin, Andrew V.
    Schorb, Sebastian
    Bostedt, Christoph
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha
    Foucar, Lutz
    Rudek, Benedikt
    Hartmann, Robert
    Kimmel, Nils
    Holl, Peter
    Englert, Lars
    Duane Loh, Ne-Te
    Chapman, Henry N.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Imaging single cells in a beam of live cyanobacteria with an X-ray laser2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 5704Article in journal (Refereed)
    Abstract [en]

    There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

  • 24.
    van der Schot, Gijs
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DePonte, Daniel P.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Schulz, Joachim
    Kirian, Richard A.
    Liang, Mengning
    Stellato, Francesco
    Bari, Sadia
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nunes de Almeida, Francisca
    Odić, Duško
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Martin, Andrew V.
    Schorb, Sebastian
    Bostedt, Christoph
    Bozek, John D.
    Carron, Sebastian
    Ferguson, Ken
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha W.
    Foucar, Lutz
    Rudek, Benedikt
    Erk, Benjamin
    Hartmann, Robert
    Kimmel, Nils
    Holl, Peter
    Englert, Lars
    Loh, N. Duane
    Chapman, Henry N.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Open data set of live cyanobacterial cells imaged using an X-ray laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160058Article in journal (Refereed)
    Abstract [en]

    Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

1 - 24 of 24
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