Scaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL

Chang, Hsing-Yin; Slaughter, Elliott; Mirchandaney, Seema; Donatelli, Jeffrey J.; Yoon, Chun Hong

doi:10.48550/arxiv.2109.05339

Cited by 2 publications

(2 citation statements)

References 15 publications

(7 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The protein structure was accurately recovered from noise-free diffraction images simulated on a PnCCD detector (Fig. 3), with a data set size comparable to what has previously been used to evaluate the MTIP algorithm (Chang et al, 2021). As expected, the addition of Poisson noise degraded the quality of the recovered structure (Donatelli et al, 2017), reducing the resolution from 15 to 20 A ˚.…”

Section: Type Origin Implementationmentioning

confidence: 72%

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

Peck¹,

Chang²,

Dujardin³

et al. 2022

J Appl Cryst

Self Cite

View full text Add to dashboard Cite

X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.

show abstract

Section: Type Origin Implementationmentioning

confidence: 72%

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

Peck¹,

Chang²,

Dujardin³

et al. 2022

J Appl Cryst

Self Cite

View full text Add to dashboard Cite

show abstract

“…Such scattering patterns are also referred to as 'speckles' due to their grainy appearance. A single particle of interest can then be reconstructed by algorithms, such as EMC (Loh & Elser, 2009;Ayyer et al, 2016) and M-TIP (Donatelli et al, 2017;Chang et al, 2021), from hundreds to tens of thousands of speckle patterns.…”

Section: Introductionmentioning

confidence: 99%

SpeckleNN: a unified embedding for real-time speckle pattern classification in X-ray single-particle imaging with limited labeled examples

Florin

Chang

Thayer

et al. 2023

Int Union Crystallogr J

View full text Add to dashboard Cite

With X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structure of noncrystalline nanoscale particles using X-ray single-particle imaging (SPI) techniques at room temperature. Classifying SPI scattering patterns, or `speckles', to extract single-hits that are needed for real-time vetoing and three-dimensional reconstruction poses a challenge for high-data-rate facilities like the European XFEL and LCLS-II-HE. Here, we introduce SpeckleNN, a unified embedding model for real-time speckle pattern classification with limited labeled examples that can scale linearly with dataset size. Trained with twin neural networks, SpeckleNN maps speckle patterns to a unified embedding vector space, where similarity is measured by Euclidean distance. We highlight its few-shot classification capability on new never-seen samples and its robust performance despite having only tens of labels per classification category even in the presence of substantial missing detector areas. Without the need for excessive manual labeling or even a full detector image, our classification method offers a great solution for real-time high-throughput SPI experiments.

show abstract

Scaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL

Cited by 2 publications

References 15 publications

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

SpeckleNN: a unified embedding for real-time speckle pattern classification in X-ray single-particle imaging with limited labeled examples

Contact Info

Product

Resources

About