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The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…

Cryo-electron tomography (cryo-ET) is uniquely suited to precisely localize macromolecular complexes in situ, that is in a close-to-native state within their cellular compartments, in three-dimensions at high resolution. Point pattern…

Cryogenic electron microscopy (cryo-EM) is an invaluable technique for determining high-resolution three-dimensional structures of biological macromolecules using transmission particle images. The inherent symmetry in these macromolecules…

A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps that exploits common…

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural variability has spurred the development of heterogeneous…

Multislice electron ptychography (MEP) is an inverse imaging technique that computationally reconstructs the highest-resolution images of atomic crystal structures from diffraction patterns. Available algorithms often solve this inverse…

Microplastics (MPs) are ubiquitous pollutants with demonstrated potential to impact ecosystems and human health. Their microscopic size complicates detection, classification, and removal, especially in biological and environmental samples.…

In this paper a deterministic preprocessing algorithm is presented, whose output can be given as input to most state-of-the-art epipolar geometry estimation algorithms, improving their results considerably. They are now able to succeed on…

Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the systemic study of shape, abundance, and distribution of macromolecular structures in single cells in near-atomic resolution. However, the systematic and efficient…

We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…

Cryo-Electron Microscopy (cryo-EM) has become an extremely powerful method for resolving structural details of large biomolecular complexes. However, challenging problems in single-particle methods remain open because of (1) the low…

Medical Informatics and the application of modern signal processing in the assistance of the diagnostic process in medical imaging is one of the more recent and active research areas today. This thesis addresses a variety of issues related…

Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable…

Characterizing crystal structures and interfaces down to the atomic level is an important step for designing advanced materials. Modern electron microscopy routinely achieves atomic resolution and is capable to resolve complex arrangements…

Identifying complex neural circuitry from electron microscopic (EM) images may help unlock the mysteries of the brain. However, identifying this circuitry requires time-consuming, manual tracing (proofreading) due to the size and intricacy…

With the growing amount of astronomical data, there is an increasing need for automated data processing pipelines, which can extract scientific information from observation data without human interventions. A critical aspect of these…

Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and…

Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…

This paper describes AutoFocus, an efficient multi-scale inference algorithm for deep-learning based object detectors. Instead of processing an entire image pyramid, AutoFocus adopts a coarse to fine approach and only processes regions…

The number of noisy images required for molecular reconstruction in single-particle cryo-electron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly-oriented, noisy projection images. In this work, we…