Tomas Ekeberg
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View article: Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules
Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules Open
Phase retrieval is an important optimization problem that occurs, for example, in the analysis of coherent diffraction patterns from isolated proteins. All iterative algorithms employed for phase retrieval in this context require some a pr…
View article: Coherent X-ray diffraction imaging of single particles: background impact on 3D reconstruction
Coherent X-ray diffraction imaging of single particles: background impact on 3D reconstruction Open
Coherent diffractive imaging with X-ray free-electron lasers could enable structural studies of macromolecules at room temperature. This type of experiment could provide a means to study structural dynamics on the femtosecond timescale. Ho…
View article: Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles
Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles Open
Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) creates opportunities for r…
View article: Enhanced EMC—Advantages of partially known orientations in x-ray single particle imaging
Enhanced EMC—Advantages of partially known orientations in x-ray single particle imaging Open
Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins’ or…
View article: Resolving non-equilibrium shape variations amongst millions of gold nanoparticles
Resolving non-equilibrium shape variations amongst millions of gold nanoparticles Open
Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented oppor…
View article: Introduction to the virtual collection of papers on <i>Artificial neural networks: applications in X-ray photon science and crystallography</i>
Introduction to the virtual collection of papers on <i>Artificial neural networks: applications in X-ray photon science and crystallography</i> Open
Artificial intelligence is more present than ever, both in our society in general and in science. At the center of this development has been the concept of deep learning, the use of artificial neural networks that are many layers deep and …
View article: Observation of a single protein by ultrafast X-ray diffraction
Observation of a single protein by ultrafast X-ray diffraction Open
* runs/ - The raw data from the pnCCD * histograms.h5 - Histogram of the values recorded by each pixel throughout the data acquisition. Used for pedestal and gain correction. * mask.h5 - Detector bad pixels mask. * 1SS8.pdb - PDB model of …
View article: 3D diffractive imaging of nanoparticle ensembles using an x-ray laser
3D diffractive imaging of nanoparticle ensembles using an x-ray laser Open
Please check the README.md file for more information about the dataset.
View article: 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers
3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers Open
X-ray free-electron lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit involves the delivery of samples to the X-ray interacti…
View article: 3D-Printed Sheet Jet for Stable Megahertz Liquid Sample Delivery at X-ray Free Electron Lasers
3D-Printed Sheet Jet for Stable Megahertz Liquid Sample Delivery at X-ray Free Electron Lasers Open
X-ray Free Electron Lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit is the delivery of samples to the X-ray interaction poi…
View article: Observation of a single protein by ultrafast X-ray diffraction
Observation of a single protein by ultrafast X-ray diffraction Open
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory 1 , the extremely inten…
View article: Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging
Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging Open
One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact tha…
View article: Megahertz single-particle imaging at the European XFEL
Megahertz single-particle imaging at the European XFEL Open
The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European X…
View article: Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging
Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging Open
One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even id…
View article: Ptychographic wavefront characterization for single-particle imaging at x-ray lasers
Ptychographic wavefront characterization for single-particle imaging at x-ray lasers Open
A well-characterized wavefront is important for many x-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual biomolecules randomly sample a nanometer region of highly focused femtosecond…
View article: Supplementary document for Ptychographic wavefront characterisation forsingle-particle imaging at X-ray lasers - 5130626.pdf
Supplementary document for Ptychographic wavefront characterisation forsingle-particle imaging at X-ray lasers - 5130626.pdf Open
Supplementary File
View article: Ptychographic wavefront characterisation for single-particle imaging at X-ray lasers
Ptychographic wavefront characterisation for single-particle imaging at X-ray lasers Open
A well-characterised wavefront is important for many X-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual bio-molecules randomly sample a nanometer-region of highly-focused femtosecon…
View article: 3D diffractive imaging of nanoparticle ensembles using an x-ray laser
3D diffractive imaging of nanoparticle ensembles using an x-ray laser Open
Single particle imaging at x-ray free electron lasers (XFELs) has the potential to determine the structure and dynamics of single biomolecules at room temperature. Two major hurdles have prevented this potential from being reached, namely,…
View article: Megahertz single-particle imaging at the European XFEL
Megahertz single-particle imaging at the European XFEL Open
The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European X…
View article: 3D diffractive imaging of nanoparticle ensembles using an X-ray laser
3D diffractive imaging of nanoparticle ensembles using an X-ray laser Open
We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 …
View article: Ptychographic wavefront characterisation for single-particle imaging at X-ray lasers
Ptychographic wavefront characterisation for single-particle imaging at X-ray lasers Open
A well-characterised wavefront is important for many X-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual bio-molecules randomly sample a nanometer-region of highly-focused femtosecon…
View article: Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. Corrigendum
Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. Corrigendum Open
Corrections to the article by Daurer et al. [ IUCrJ (2017). 4 , 251–262] are given.
View article: <i>Ab initio</i>phasing of the diffraction of crystals with translational disorder
<i>Ab initio</i>phasing of the diffraction of crystals with translational disorder Open
To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protei…
View article: Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging Open
Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the…
View article: Rapid sample delivery for megahertz serial crystallography at X-ray FELs
Rapid sample delivery for megahertz serial crystallography at X-ray FELs Open
Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the m…
View article: Controlling Protein Orientation in Vacuum Using Electric Fields
Controlling Protein Orientation in Vacuum Using Electric Fields Open
Single-particle imaging using X-ray free-electron lasers is an emerging technique that could provide high-resolution structures of macromolecules in the gas phase. One of the largest difficulties in realizing this goal is the unknown orien…
View article: Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source
Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source Open
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent so…