Cryo-ZSSR: multiple-image super-resolution based on deep internal learning

Single-particle cryo-electron microscopy (cryo-EM) is an emerging imaging modality capable of visualizing proteins and macro-molecular complexes at near-atomic resolution. The low electron-doses used to prevent sample radiation damage, result in images where the power of the noise is 100 times greater than the power of the signal. To overcome the low-SNRs, hundreds of thousands of particle projections acquired over several days of data collection are averaged in 3D to determine the structure of interest. Meanwhile, recent image super-resolution (SR) techniques based on neural networks have shown state of the art performance on natural images. Building on these advances, we present a multiple-image SR algorithm based on deep internal learning designed specifically to work under low-SNR conditions. Our approach leverages the internal image statistics of cryo-EM movies and does not require training on ground-truth data. When applied to a single-particle dataset of apoferritin, we show that the resolution of 3D structures obtained from SR micrographs can surpass the limits imposed by the imaging system. Our results indicate that the combination of low magnification imaging with image SR has the potential to accelerate cryo-EM data collection without sacrificing resolution.

Unsupervised particle sorting for high-resolution single-particle cryo-EM

Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and data processing, have significantly lowered the barrier for non-expert users to successfully execute the structure determination workflow. Many critical data processing steps, however, still require expert user intervention in order to converge to the correct high-resolution structure. In particular, strategies to identify homogeneous populations of particles rely heavily on subjective criteria that are not always consistent or reproducible among different users. Here, we explore the use of unsupervised strategies for particle sorting that are compatible with the autonomous operation of the image processing pipeline. More specifically, we show that particles can be successfully sorted based on a simple statistical model for the distribution of scores assigned during refinement. This represents an important step towards the development of automated workflows for protein structure determination using single-particle cryo-EM.

Fundamental Limits in Multi-image Alignment

The performance of multi-image alignment, bringing different images into one coordinate system, is critical in many applications with varied signal-to-noise ratio (SNR) conditions. A great amount of effort is being invested into developing methods to solve this problem. Several important questions thus arise, including: Which are the fundamental limits in multi-image alignment performance? Does having access to more images improve the alignment? Theoretical bounds provide a fundamental benchmark to compare methods and can help establish whether improvements can be made. In this work, we tackle the problem of finding the performance limits in image registration when multiple shifted and noisy observations are available. We derive and analyze the Cram\'er-Rao and Ziv-Zakai lower bounds under different statistical models for the underlying image. The accuracy of the derived bounds is experimentally assessed through a comparison to the maximum likelihood estimator. We show the existence of different behavior zones depending on the difficulty level of the problem, given by the SNR conditions of the input images. We find that increasing the number of images is only useful below a certain SNR threshold, above which the pairwise MLE estimation proves to be optimal. The analysis we present here brings further insight into the fundamental limitations of the multi-image alignment problem.