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A crucial step in single particle analysis (SPA) of cryogenic electron microscopy (Cryo-EM), 2D classification and alignment takes a collection of noisy particle images to infer orientations and group similar images together. Averaging…

A standard approach to approximate inference in state-space models isto apply a particle filter, e.g., the Condensation Algorithm.However, the performance of particle filters often varies significantlydue to their stochastic nature.We…

Beam damage is a major limitation in electron microscopy that becomes increasingly severe at higher resolution. One possible route to circumvent radiation damage, which forms the basis for single-particle electron microscopy and related…

Operando/in-situ liquid cell transmission electron microscopy (LCTEM) allows for real time imaging of dynamic nanoscale liquid-based processes. However, due to the thick liquid cell of traditional LCTEM holders and thus scattering of the…

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…

Implicit particle filtering is a sequential Monte Carlo method for data assim- ilation, designed to keep the number of particles manageable by focussing attention on regions of large probability. These regions are found by min- imizing, for…

We present a particle filter construction for a system that exhibits time-scale separation. The separation of time-scales allows two simplifications that we exploit: i) The use of the averaging principle for the dimensional reduction of the…

A major challenge facing existing sequential Monte-Carlo methods for parameter estimation in physics stems from the inability of existing approaches to robustly deal with experiments that have different mechanisms that yield the results…

Fluorescence microscopy is a widely used method among cell biologists for studying the localization and co-localization of fluorescent protein. For microbial cell biologists, these studies often include tedious and time-consuming manual…

Laser flash melting and revitrification experiments have recently improved the time resolution of cryo-electron microscopy (cryo-EM) to the microsecond timescale, making it fast enough to observe many of the protein motions that are…

Sequential Monte Carlo algorithms, or Particle Filters, are Bayesian filtering algorithms which propagate in time a discrete and random approximation of the a posteriori distribution of interest. Such algorithms are based on Importance…

The complex range of interactions between electrons and electromagnetic fields gave rise to countless scientific and technological advances. A prime example is photon-induced nearfield electron microscopy (PINEM), enabling the detection of…

Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…

Continuously comparing theory predictions to experimental data is a common task in analysis of particle physics such as fitting parton distribution functions (PDFs). However, typically, both the computation of scattering amplitudes and the…

Resampling is a key component of sample-based recursive state estimation in particle filters. Recent work explores differentiable particle filters for end-to-end learning. However, resampling remains a challenge in these works, as it is…

The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…

Splitting and merging are long standing issues in PIC codes. I propose a novel algorithm devoted to exact splitting for Particle-In-Cell (PIC) codes relying on Adaptive Mesh Refinement (AMR) grids. AMR grids have - by definition - a…

The problem of robotic lime picking is challenging; lime plants have dense foliage which makes it difficult for a robotic arm to grasp a lime without coming in contact with leaves. Existing approaches either do not consider leaves, or treat…

Particle filters provide Monte Carlo approximations of intractable quantities such as point-wise evaluations of the likelihood in state space models. In many scenarios, the interest lies in the comparison of these quantities as some…

Filtering is concerned with online estimation of the state of a dynamical system from partial and noisy observations. In applications where the state of the system is high dimensional, ensemble Kalman filters are often the method of choice.…