Tomas Ekeberg

Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules

Bellisario, Alfredo; Ekeberg, Tomas

Part of Machine Learning, 2024

• DOI for Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules
• Download full text (pdf) of Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules

Observation of a single protein by ultrafast X-ray diffraction

Ekeberg, Tomas; Assalauova, Dameli; Bielecki, Johan; Boll, Rebecca et al.

Part of Light, 2024

• DOI for Observation of a single protein by ultrafast X-ray diffraction
• Download full text (pdf) of Observation of a single protein by ultrafast X-ray diffraction

Coherent X-ray Diffraction Imaging of Single Particles: Background Impact on 3D Reconstruction

Wollter, August; Ekeberg, Tomas

Part of Journal of applied crystallography, p. 1384-1391, 2024

• DOI for Coherent X-ray Diffraction Imaging of Single Particles: Background Impact on 3D Reconstruction
• Download full text (pdf) of Coherent X-ray Diffraction Imaging of Single Particles: Background Impact on 3D Reconstruction

Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging

Wollter, August; De Santis, Emiliano; Ekeberg, Tomas; Marklund, Erik G. et al.

Part of Journal of Chemical Physics, 2024

• DOI for Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging
• Download full text (pdf) of Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging

Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Shen, Zhou; Xavier, Paul Lourdu; Bean, Richard; Bielecki, Johan et al.

Part of ACS Nano, p. 15576-15589, 2024

• DOI for Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles
• Download full text (pdf) of Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules

Bellisario, Alfredo; Ekeberg, Tomas

Part of Machine Learning, 2024

• DOI for Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules
• Download full text (pdf) of Deep learning phase retrieval in x-ray single-particle imaging for biological macromolecules

Observation of a single protein by ultrafast X-ray diffraction

Ekeberg, Tomas; Assalauova, Dameli; Bielecki, Johan; Boll, Rebecca et al.

Part of Light, 2024

• DOI for Observation of a single protein by ultrafast X-ray diffraction
• Download full text (pdf) of Observation of a single protein by ultrafast X-ray diffraction

Coherent X-ray Diffraction Imaging of Single Particles: Background Impact on 3D Reconstruction

Wollter, August; Ekeberg, Tomas

Part of Journal of applied crystallography, p. 1384-1391, 2024

• DOI for Coherent X-ray Diffraction Imaging of Single Particles: Background Impact on 3D Reconstruction
• Download full text (pdf) of Coherent X-ray Diffraction Imaging of Single Particles: Background Impact on 3D Reconstruction

Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging

Wollter, August; De Santis, Emiliano; Ekeberg, Tomas; Marklund, Erik G. et al.

Part of Journal of Chemical Physics, 2024

• DOI for Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging
• Download full text (pdf) of Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging

Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Shen, Zhou; Xavier, Paul Lourdu; Bean, Richard; Bielecki, Johan et al.

Part of ACS Nano, p. 15576-15589, 2024

• DOI for Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles
• Download full text (pdf) of Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Introduction to the virtual collection of papers on Artificial neural networks: applications in X-ray photon science and crystallography

Ekeberg, Tomas

Part of Journal of applied crystallography, p. 1-2, 2024

• DOI for Introduction to the virtual collection of papers on Artificial neural networks: applications in X-ray photon science and crystallography
• Download full text (pdf) of Introduction to the virtual collection of papers on Artificial neural networks: applications in X-ray photon science and crystallography

3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers

Konold, Patrick E.; You, Tong; Bielecki, Johan; Valerio, Joana et al.

Part of IUCrJ, p. 662-670, 2023

• DOI for 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers
• Download full text (pdf) of 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers

Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging

Zhuang, Yulong; Awel, Salah; Barty, Anton; Bean, Richard et al.

Part of IUCrJ, p. 204-214, 2022

• DOI for Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging
• Download full text (pdf) of Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging

Noise reduction and mask removal neural network for X-ray single-particle imaging

Bellisario, Alfredo; Maia, Filipe; Ekeberg, Tomas

Part of Journal of applied crystallography, p. 122-132, 2022

• DOI for Noise reduction and mask removal neural network for X-ray single-particle imaging
• Download full text (pdf) of Noise reduction and mask removal neural network for X-ray single-particle imaging

Ptychographic wavefront characterization for single-particle imaging at x-ray lasers

Daurer, Benedikt J.; Sala, Simone; Hantke, Max; Reddy, Hemanth K.N. et al.

Part of Optica, p. 551-562, 2021

• DOI for Ptychographic wavefront characterization for single-particle imaging at x-ray lasers
• Download full text (pdf) of Ptychographic wavefront characterization for single-particle imaging at x-ray lasers

3D diffractive imaging of nanoparticle ensembles using an x-ray laser

Ayyer, Kartik; Xavier, P. Lourdu; Bielecki, Johan; Shen, Zhou et al.

Part of Optica, p. 15-23, 2021

• DOI for 3D diffractive imaging of nanoparticle ensembles using an x-ray laser
• Download full text (pdf) of 3D diffractive imaging of nanoparticle ensembles using an x-ray laser

Megahertz single-particle imaging at the European XFEL

Sobolev, Egor; Zolotarev, Serguey; Giewekemeyer, Klaus; Bielecki, Johan et al.

Part of Communications Physics, 2020

• DOI for Megahertz single-particle imaging at the European XFEL
• Download full text (pdf) of Megahertz single-particle imaging at the European XFEL

Ab initio phasing of the diffraction of crystals with translational disorder

Morgan, Andrew J.; Ayyer, Kartik; Barty, Anton; Chen, Joe P. J. et al.

Part of Acta Crystallographica Section A, p. 25-40, 2019

• DOI for Ab initio phasing of the diffraction of crystals with translational disorder
• Download full text (pdf) of Ab initio phasing of the diffraction of crystals with translational disorder

Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

Gorkhover, Tais; Ulmer, Anatoli; Ferguson, Ken; Bucher, Max et al.

Part of Nature Photonics, p. 150-153, 2018

• DOI for Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging

Lundholm, Ida V.; Sellberg, Jonas A.; Ekeberg, Tomas; Hantke, Max F. et al.

Part of IUCrJ, p. 531-541, 2018

• DOI for Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging

Coherent diffraction of single Rice Dwarf Virus particles using soft X-rays at the Linac Coherent Light Source

Munke, Anna; van der Schot, Gijs; Maia, Filipe; Ekeberg, Tomas et al.

Part of Nature Scientific Data, 2018

Reproducibility of Single Protein Explosions Induced by X-ray Lasers

Östlin, Christofer; Timneanu, Nicusor; Jönsson, H. Olof; Ekeberg, Tomas et al.

Part of Physical Chemistry, Chemical Physics - PCCP, p. 12381-12389, 2018

• DOI for Reproducibility of Single Protein Explosions Induced by X-ray Lasers

Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source

Reddy, Hemanth K. N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah et al.

Part of Scientific Data, 2017

• DOI for Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source

Open data set of live cyanobacterial cells imaged using an X-ray laser

van der Schot, Gijs; Svenda, Martin; Maia, Filipe R.N.C.; Hantke, Max F. et al.

Part of Scientific Data, 2016

• DOI for Open data set of live cyanobacterial cells imaged using an X-ray laser
• Download full text (pdf) of Open data set of live cyanobacterial cells imaged using an X-ray laser

A data set from flash X-ray imaging of carboxysomes

Hantke, Max F.; Hasse, Dirk; Ekeberg, Tomas; John, Katja et al.

Part of Scientific Data, 2016

• DOI for A data set from flash X-ray imaging of carboxysomes
• Download full text (pdf) of A data set from flash X-ray imaging of carboxysomes

Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Ekeberg, Tomas; Svenda, Martin; Seibert, M. Marvin; Abergel, Chantal et al.

Part of Scientific Data, 2016

• DOI for Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
• Download full text (pdf) of Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser

Ekeberg, Tomas; Svenda, Martin; Abergel, Chantal; Maia, Filipe R. N. C. et al.

Part of Physical Review Letters, 2015

• DOI for Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser
• Download full text (pdf) of Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser

Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Ekeberg, Tomas; Engblom, Stefan; Liu, Jing

Part of The international journal of high performance computing applications, p. 233-243, 2015

• DOI for Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters
• Download full text (pdf) of Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Imaging single cells in a beam of live cyanobacteria with an X-ray laser

van der Schot, Gijs; Svenda, Martin; Maia, Filipe R. N. C.; Hantke, Max et al.

Part of Nature Communications, 2015

• DOI for Imaging single cells in a beam of live cyanobacteria with an X-ray laser

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 laser

Rath, Asawari D.; Timneanu, Nicusor; Maia, Filipe R. N. C.; Bielecki, Johan et al.

Part of Optics Express, p. 28914-28925, 2014

• DOI for 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 laser

Automated identification and classification of single particle serial femtosecond X-ray diffraction data

Andreasson, Jakob; Martin, Andrew V.; Liang, Meng; Timneanu, Nicusor et al.

Part of Optics Express, p. 2497-2510, 2014

• DOI for Automated identification and classification of single particle serial femtosecond X-ray diffraction data
• Download full text (pdf) of Automated identification and classification of single particle serial femtosecond X-ray diffraction data

High-throughput imaging of heterogeneous cell organelles with an X-ray laser

Hantke, Max F.; Hasse, Dirk; Maia, Filipe R. N. C.; Ekeberg, Tomas et al.

Part of Nature Photonics, p. 943-949, 2014

• DOI for High-throughput imaging of heterogeneous cell organelles with an X-ray laser

The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern

Martin, A. V.; Morgan, A. J.; Ekeberg, Tomas; Loh, N. D. et al.

Part of Optics Express, p. 15102-15112, 2013

• DOI for The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern

Sensing the wavefront of x-ray free-electron lasers using aerosol spheres

Loh, N. Duane; Starodub, Dmitri; Lomb, Lukas; Hampton, Christina Y. et al.

Part of Optics Express, p. 12385-12394, 2013

• DOI for Sensing the wavefront of x-ray free-electron lasers using aerosol spheres

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers

Park, Hyung Joo; Loh, N. Duane; Sierra, Raymond G.; Hampton, Christina Y. et al.

Part of Optics Express, p. 28729-28742, 2013

• DOI for Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers

Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging

Pedersoli, E.; Loh, N. D.; Capotondi, F.; Hampton, C. Y. et al.

Part of Journal of Physics B, p. 164033, 2013

• DOI for Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging

In vivo protein crystallization opens new routes in structural biology

Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol et al.

Part of Nature Methods, p. 259-262, 2012

• DOI for In vivo protein crystallization opens new routes in structural biology

Lipidic phase membrane protein serial femtosecond crystallography

Johansson, Linda C; Arnlund, David; White, Thomas A; Katona, Gergely et al.

Part of Nature Methods, p. 263-265, 2012

• DOI for Lipidic phase membrane protein serial femtosecond crystallography

Noise-robust coherent diffractive imaging with a single diffraction pattern

Martin, A. V.; Wang, F.; Loh, N. D.; Ekeberg, Tomas et al.

Part of Optics Express, p. 16650-16661, 2012

Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

Barty, Anton; Caleman, Carl; Aquila, Andrew; Timneanu, Nicusor et al.

Part of Nature Photonics, p. 35-40, 2012

• DOI for Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

Loh, N. D.; Hampton, C. Y.; Martin, A. V.; Starodub, D. et al.

Part of Nature, p. 513-517, 2012

• DOI for Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering

Yoon, Chun Hong; Schwander, Peter; Abergel, Chantal; Andersson, Inger et al.

Part of Optics Express, p. 16542-16549, 2011

• DOI for Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering

Single mimivirus particles intercepted and imaged with an X-ray laser

Seibert, M. Marvin; Ekeberg, Tomas; Maia, Filipe R. N. C.; Svenda, Martin et al.

Part of Nature, p. 78-81, 2011

• DOI for Single mimivirus particles intercepted and imaged with an X-ray laser

Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser

Lomb, Lukas; Barends, Thomas R. M.; Kassemeyer, Stephan; Aquila, Andrew et al.

Part of Physical Review B. Condensed Matter and Materials Physics, 2011

• DOI for Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser

Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns

Loh, N. D.; Bogan, M. J.; Elser, V.; Barty, A. et al.

Part of Physical Review Letters, 2010

• DOI for Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns

Hawk: the image reconstruction package for coherent X-ray diffractive imaging

Maia, Filipe R. N. C.; Ekeberg, Tomas; van der Spoel, David; Hajdu, Janos

Part of Journal of applied crystallography, p. 1535-1539, 2010

• DOI for Hawk: the image reconstruction package for coherent X-ray diffractive imaging

Femtosecond diffractive imaging of biological cells

Seibert, M. Marvin; Boutet, Sebastien; Svenda, Martin; Ekeberg, Tomas et al.

Part of Journal of Physics B, p. 194015, 2010

• DOI for Femtosecond diffractive imaging of biological cells

Structural variability and the incoherent addition of scattered intensities in single-particle diffraction

Maia, Filipe R. N. C.; Ekeberg, Tomas; Timneanu, Nicusor; van der Spoel, David et al.

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2009

• DOI for Structural variability and the incoherent addition of scattered intensities in single-particle diffraction

Condor: a simulation tool for flash X-ray imaging

Hantke, Max F.; Ekeberg, Tomas; Maia, Filipe R. N. C.

Part of Journal of applied crystallography, p. 1356-1362, 2016

• DOI for Condor: a simulation tool for flash X-ray imaging
• Download full text (pdf) of Condor: a simulation tool for flash X-ray imaging

Flash Diffractive Imaging in Three Dimensions

Ekeberg, Tomas

2012

• Download full text (pdf) of Flash Diffractive Imaging in Three Dimensions

Ptychographic imaging for the characterization of X-ray free-electron laser beams

Sala, S.; Daurer, B. J.; Hantke, M. F.; Ekeberg, Tomas et al.

Part of X-RAY MICROSCOPY CONFERENCE 2016 (XRM 2016), 2017

• DOI for Ptychographic imaging for the characterization of X-ray free-electron laser beams
• Download full text (pdf) of Ptychographic imaging for the characterization of X-ray free-electron laser beams

Three-dimensional structure determination with an X-ray laser

Ekeberg, Tomas; Svenda, Martin; Abergel, Chantal; Maia, Filipe et al.

Data requirements for single-particle diffractive imaging

Ekeberg, Tomas; Maia, Filipe

Enhanced EMC Recovers Biased Orientations with Realistic Distribution

Wollter, August; Ekeberg, Tomas