Related papers: cryoSPHERE: Single-particle heterogeneous reconstr…
Learning robust representations of 3D shapes from voxelized data is essential for advancing AI methods in biomedical imaging. However, most contemporary 3D computer vision approaches operate on point clouds, meshes, or octrees, while…
Particle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As…
Classifying structural variability in noisy projections of biological macromolecules is a central problem in Cryo-EM. In this work, we build on a previous method for estimating the covariance matrix of the three-dimensional structure…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Cryo-electron tomography (cryo-ET) provides direct 3D visualization of macromolecules inside the cell, enabling analysis of their in situ morphology. This morphology can be regarded as an SE(3)-invariant, denoised volumetric representation…
The 3D characterization of microstructures is crucial for understanding and designing functional materials. However, the scanning electron microscope (SEM), widely used in scientific research, captures only 2D electron intensity…
Single-shot wide-angle diffraction imaging is a widely used method to investigate the structure of non-crystallizing objects such as nanoclusters, large proteins or even viruses. Its main advantage is that information about the…
Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET…
In this paper we study the formal algebraic structure underlying the intrinsic classification algorithm, recently introduced by Hadani, Shkolnisky, Singer and Zhao, for classifying noisy projection images of similar viewing directions in…
Integrated Computational Materials Engineering (ICME) aims to accelerate optimal design of complex material systems by integrating material science and design automation. For tractable ICME, it is required that (1) a structural feature…
The single-particle cryo-EM field faces the persistent challenge of preferred orientation, lacking general computational solutions. We introduce cryoPROS, an AI-based approach designed to address the above issue. By generating the auxiliary…
Curvilinear structures frequently appear in microscopy imaging as the object of interest. Crystallographic defects, i.e., dislocations, are one of the curvilinear structures that have been repeatedly investigated under transmission electron…
Principal component analysis (PCA) plays an important role in the analysis of cryo-EM images for various tasks such as classification, denoising, compression, and ab-initio modeling. We introduce a fast method for estimating a compressed…
The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include `phase flipping', which corrects only for the Fourier phases but…
Speden is a computer program that reconstructs the electron density of single particles from their x-ray diffraction patterns, using a single-particle adaptation of the Holographic Method in crystallography. (Szoke, A., Szoke, H., and…
X-ray single particle imaging involves the measurement of a large number of noisy diffraction patterns of isolated objects in random orientations. The missing information about these patterns is then computationally recovered in order to…
We revisit the topic of common lines between projection images in single particle cryo-electron microscopy (cryo-EM). We derive a novel low-rank constraint on a certain $2n \times n$ matrix storing properly-scaled basis vectors for the…
Protein function and activity are a consequence of its three-dimensional structure. Single particle analysis of cryogenic electron micrographs has radically changed structural biology allowing atomic reconstruction of almost any type of…
Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics and molecular nanotechnology. In particular, revealing the distinct conformations of…
This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron…