Cryo-electron microscopy (cryo-EM) is an emerging experimental method to characterize the structure of large biomolecular assemblies. Single particle cryo-EM records 2D images (so-called micrographs) of projections of the three-dimensional particle, which need to be processed to obtain the three-dimensional reconstruct…
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48 results for “cryo-electron microscopy”
New method for analyzing complex data spaces.
problem Dimensionality reduction and learning data representations for continuous spaces.
method Manifold factorization based on spectral graph methods.
result Recovering factors yields meaningful lower-dimensional representations.
Orthogonalization of data via Gromov-Wasserstein type feedback for clustering and visualizationstat.ML
Adaptive orthogonalization of data for clustering and visualization.
problem Clustering and visualization of data with high specificity.
method Adaptive orthogonalization process using Gromov-Wasserstein feedback.
result Method refines orthogonality of data to achieve high specificity clustering.
Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D images of biomolecules at near-atomic resolution. As such, it represents one of the most promising imaging techniques in structural biology. However, raw cryo-EM images are only highly corrupted - noisy and band-pass filtered - 2D projections o…
Geometric framework for inverse problems using foliations and dual connections.
problem Reconstruction problems in inverse problems.
method Vaisman foliations and Atiyah--Molino sequences to induce transverse foliations and dual connections.
result Unique, path-independent reconstruction with vanishing torsion and curvature duality.
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographsq-bio.QM
Cryo-electron microscopy (cryoEM) is an increasingly popular method for protein structure determination. However, identifying a sufficient number of particles for analysis (often >100,000) can take months of manual effort. Current computational approaches are limited by high false positive rates and require significant…
Confirmation bias leads to biased estimates in noisy data analysis.
problem Confirmation bias affects scientific conclusions in noisy data environments.
method Investigation of confirmation bias in Gaussian mixture models using K-means and EM algorithms.
result Estimates from algorithms are biased and resemble initial hypotheses, not the noise.
We introduce multi-frequency vector diffusion maps (MFVDM), a new framework for organizing and analyzing high dimensional datasets. The new method is a mathematical and algorithmic generalization of vector diffusion maps (VDM) and other non-linear dimensionality reduction methods. MFVDM combines different nonlinear emb…
We introduce a novel co-learning paradigm for manifolds naturally equipped with a group action, motivated by recent developments on learning a manifold from attached fibre bundle structures. We utilize a representation theoretic mechanism that canonically associates multiple independent vector bundles over a common bas…
We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of multiple objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and ca…
K-means fails in high dimensions with noise and few samples.
problem Clustering in high-dimensional data with noise and limited samples.
method Simple Gaussian Mixture Model (GMM) analysis.
result Almost every partition becomes a fixed point of k-means in high dimensions.
Data augmentation is a widely used trick when training deep neural networks: in addition to the original data, properly transformed data are also added to the training set. However, to the best of our knowledge, a clear mathematical framework to explain the performance benefits of data augmentation is not available. In…
Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing directions. One of the main challenges in cryo-EM is the typically…
Geometric shape matching for recovering protein conformations from single-particle Cryo-EM dataq-bio.BM
Researchers use shape analysis to recover protein structures from Cryo-EM data.
problem Recovering the three-dimensional backbone structure of single polypeptide proteins from noisy tomographic projections.
method Shape analysis and matrix Lie group actions to deform point clouds to match 2D tomography data.
result Optimal deformations are computed to recover the three-dimensional backbone structure of proteins.
Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural biologists to perform 6D translation-rotation searching, which is extremely comput…
A tensor network is a diagram that specifies a way to "multiply" a collection of tensors together to produce another tensor (or matrix). Many existing algorithms for tensor problems (such as tensor decomposition and tensor PCA), although they are not presented this way, can be viewed as spectral methods on matrices bui…
A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate s…
Cryo-em images are found to be low-dimensional.
problem Understanding the geometric structure of cryo-em data.
method Applied manifold learning techniques to CryoSBI representations.
result Cryo-em data inherently populate low-dimensional manifolds.
Study on estimating signals from shifted and noisy copies in high dimensions, revealing a phase transition.
problem Estimating a signal in high-dimensional space from its circularly-shifted and noisy copies.
method Analysis of sample complexity in the high-dimensional regime, focusing on the parameter α.
result A phase transition phenomenon governed by α, with different sample complexities based on α values.
Motivated by the task of 2-D classification in single particle reconstruction by cryo-electron microscopy (cryo-EM), we consider the problem of heterogeneous multireference alignment of images. In this problem, the goal is to estimate a (typically small) set of target images from a (typically large) collection of obser…
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from noisy and randomly orien…
Various alignment problems arising in cryo-electron microscopy, community detection, time synchronization, computer vision, and other fields fall into a common framework of synchronization problems over compact groups such as Z/L, U(1), or SO(3). The goal of such problems is to estimate an unknown vector of group eleme…
Fluorescence microscopy has enabled a dramatic development in modern biology. Due to its inherently weak signal, fluorescence microscopy is not only much noisier than photography, but also presented with Poisson-Gaussian noise where Poisson noise, or shot noise, is the dominating noise source. To get clean fluorescence…
SOLVAR efficiently analyzes cryo-EM data's structural variability.
problem Analyzing continuous heterogeneity in cryo-EM data.
method Low-rank assumption on covariance matrix for tractable estimation.
result Accurately captures dominant components of structural variability.
Method recovers particle orientations from cryo-EM projections.
problem Unknown orientations in cryo-EM images.
method Two-step process: estimating distances and recovering orientations.
result Accurate orientation recovery from noisy projections.
Deep learning improves 3D microscopy resolution without matched target images.
problem Anisotropic resolution in volumetric fluorescence microscopy.
method Cycle-consistent generative adversarial network trained on unpaired 2D images.
result Enhanced axial resolution and restored details between imaging planes.
Convolutional neural networks (CNN) have achieved state of the art performance on both classification and segmentation tasks. Applying CNNs to microscopy images is challenging due to the lack of datasets labeled at the single cell level. We extend the application of CNNs to microscopy image classification and segmentat…
A new diffusion model improves cryo-EM structure sampling.
problem Gaussian prior in VAE fails to match approximate posterior in cryo-EM data.
method Train a diffusion model as an expressive, learnable prior in cryoDRGN framework.
result Samples accurately follow the data distribution, not the VAE prior.
Automatic post-picking using MAPPOS improves particle image detection from Cryo-EM micrographsstat.ML
Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are…
Estimation of Z-Thickness and XY-Anisotropy of Electron Microscopy Images using Gaussian Processeseess.IV
Method estimates section thickness and XY anisotropy in ssEM images.
problem Accurate 3D reconstructions require precise section thickness and XY anisotropy estimates.
method Non-parametric Bayesian regression of image statistics.
result Method has lower estimation error compared to existing methods.
We discuss recently emerging applications of the state-of-art deep learning methods on optical microscopy and microscopic image reconstruction, which enable new transformations among different modes and modalities of microscopic imaging, driven entirely by image data. We believe that deep learning will fundamentally ch…
Paper addresses group synchronization with incomplete measurements and proves linear convergence of GPM.
problem Orthogonal group synchronization with incomplete measurements and additive noise.
method Generalized power method (GPM) with local error bound analysis.
result Linear convergence of GPM to a global maximizer under general additive noise model.
Machine learning classifies colorectal tissue using photoacoustic microscopy.
problem Traditional diagnostic methods for colorectal cancer are limited in detail and painful.
method Machine learning applied to acoustic resolution photoacoustic microscopy.
result Machine learning accurately classified benign and malignant tissue.
Cryo-EM reconstruction is reformulated as a stochastic inverse problem to handle structural heterogeneity.
problem Handling structural heterogeneity in cryo-EM 3D reconstruction.
method Formulated as a stochastic inverse problem over probability measures, using variational discrepancy and Wasserstein gradient flow.
result Validated approach using synthetic examples, demonstrating recovery of continuous structural distributions.
DISPR uses diffusion models to predict 3D cell shapes from 2D images.
problem Predicting 3D cell shapes from 2D microscopy images.
method Diffusion model trained to predict 3D shapes from 2D microscopy images as a prior.
result Adding DISPR predictions to minority cell classes improves classification accuracy.
Machine learning speeds up FLIM analysis in biomedical research.
problem Complex, slow, and computationally expensive FLIM analysis.
method Machine learning techniques for faster and smarter FLIM data extraction and interpretation.
result Higher accuracy in classifying and segmenting FLIM images compared to conventional methods.
Deconvolution microscopy has been extensively used to improve the resolution of the widefield fluorescent microscopy. Conventional approaches, which usually require the point spread function (PSF) measurement or blind estimation, are however computationally expensive. Recently, CNN based approaches have been explored a…
Multi-StyleGAN simulates live cell microscopy imagery.
problem Costly and complex live cell experiments.
method Generative adversarial network (GAN) synthesizing multi-domain time-lapse images.
result Captures biophysical factors and time dependencies in cell imagery.
Novel higher-order group synchronization for noisy local measurements on hypergraphs.
problem Synchronizing higher-order local measurements on hyperedges to global estimates on nodes.
method Message passing algorithm for global synchronization of higher-order measurements.
result Higher-order method outperforms standard pairwise synchronization methods in certain applications.
Malaria is a life-threatening disease affecting millions. Microscopy-based assessment of thin blood films is a standard method to (i) determine malaria species and (ii) quantitate high-parasitemia infections. Full automation of malaria microscopy by machine learning (ML) is a challenging task because field-prepared sli…
New method extracts biological concepts from cell microscopy images.
problem Extracting meaningful concepts from vision foundation models trained on cell microscopy images.
method Sparse dictionary learning (DL) combined with PCA whitening pre-processing.
result Successfully retrieved biologically meaningful concepts like cell types and genetic perturbations.
Study improves pollen detection in optical and holographic images using deep learning.
problem Improving pollen detection accuracy in holographic microscopy images.
method Used YOLOv8s for detection and MobileNetV3L for classification, addressing performance gaps through dataset expansion and automated labeling.
result Significant improvement in detection and classification performance on holographic images.
Prototype for adaptive electron microscopy scans reduces dose and time.
problem Reduce electron microscopy scan time and dose with minimal loss.
method Adaptive partial scanning with reinforcement learning.
result Reinforcement learning trained neural network optimizes scan paths.
UDVD uses deep learning to denoise videos without supervision.
problem Lack of clean video data for training deep learning models.
method UDVD is a CNN trained solely on noisy video data, adapting to local motion.
result UDVD performs as well as supervised methods, even with limited training data.
A novel method detects multiple mitosis events and mitigates annotation gaps in phase-contrast microscopy.
problem Detecting multiple mitosis events and handling annotation gaps in closely placed cells.
method Estimating a spatiotemporal likelihood map via 3DCNN to detect multiple mitosis events and mitigate annotation gaps.
result Our method outperformed compared methods in terms of F1-score using a challenging dataset.
An image dataset of 10 different size molecules, where each molecule has 2,000 structural variants, is generated from the 2D cross-sectional projection of Molecular Dynamics trajectories. The purpose of this dataset is to provide a benchmark dataset for the increasing need of machine learning, deep learning and image p…
Deep learning methods are becoming widely used for restoration of defects associated with fluorescence microscopy imaging. One of the major challenges in application of such methods is the availability of training data. In this work, we propose a unified method for reconstruction of multi-defect fluorescence microscopy…
Improves spline quality and accuracy in computational microscopy.
problem Detecting slender, overlapping structures in microscopy images.
method Differentiable rendering approach for spline refinement.
result Achieves high reliability and sub-pixel accuracy.