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…
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48 results for “microscopy”
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…
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…
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.
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.
Estimation of Z-Thickness and XY-Anisotropy of Electron Microscopy Images using Gaussian Processeseess.IV
Serial section electron microscopy (ssEM) is a widely used technique for obtaining volumetric information of biological tissues at nanometer scale. However, accurate 3D reconstructions of identified cellular structures and volumetric quantifications require precise estimates of section thickness and anisotropy (or stre…
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.
AI enhances pollen recognition in veterinary imaging using holographic microscopy.
problem Challenges in recognizing pollen in holographic images due to speckle noise and artifacts.
method Training YOLOv8s and MobileNetV3L on dual-modality dataset, employing WGAN-SN for synthetic data augmentation.
result GAN-based augmentation improves object detection and classification in holographic images, closing the performance gap.
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…
The need for labour intensive pixel-wise annotation is a major limitation of many fully supervised learning methods for segmenting bioimages that can contain numerous object instances with thin separations. In this paper, we introduce a deep convolutional neural network for microscopy image segmentation. Annotation iss…
Develops statistical guarantees for image-to-image regression models.
problem Current image-to-image regression models lack statistical guarantees for model mistakes and hallucinations.
method Uncertainty quantification techniques with rigorous statistical guarantees for image-to-image regression problems.
result Derives uncertainty intervals around each pixel with formal mathematical guarantees.
Visualizing the details of different cellular structures is of great importance to elucidate cellular functions. However, it is challenging to obtain high quality images of different structures directly due to complex cellular environments. Fluorescence staining is a popular technique to label different structures but …
New method separates objects from images using deep neural networks trained to inpaint.
problem Fully self-supervised instance separation of occluded objects in images.
method Maximizes independence of two image regions given a fully self-supervised inpainting network.
result Method achieves similar segmentation performance to fully supervised methods on microscopy image datasets.
Algorithm aligns 3D density maps using Wasserstein distance.
problem Aligning 3D density maps in cryogenic electron microscopy.
method Minimizing 1-Wasserstein distance after rigid transformation using Bayesian optimization.
result Improved accuracy and efficiency in protein molecule alignment.
This research uses Siamese networks to identify partial mouse brain images from the Allen atlas.
problem Identifying precise mouse brain microscopy images from the Allen atlas.
method Siamese Networks with contrastive learning to find corresponding atlas plates for partial images.
result Siamese CNNs achieved 25% TOP-1 and 100% TOP-5 accuracy in identifying brain slices from the Allen atlas.
Few-shot cell segmentation from diverse sources to target domain.
problem Efficient cell segmentation from limited annotated images.
method Meta-learning combining cross-domain tasks and invariant representation.
result Promising results from 1-10-shot learning on public databases.
Local minimax analysis for Poisson deconvolution of discrete signals.
problem Estimating a discrete uniform signal from Poisson convolutions.
method Local minimax risk analysis of a broad class of kernels.
result Sharp estimation rates as a function of signal clustering.
With super-resolution optical microscopy, it is now possible to observe molecular interactions in living cells. The obtained images have a very high spatial precision but their overall quality can vary a lot depending on the structure of interest and the imaging parameters. Moreover, evaluating this quality is often di…
Single-molecule localization fluorescence microscopy constructs super-resolution images by sequential imaging and computational localization of sparsely activated fluorophores. Accurate and efficient fluorophore localization algorithms are key to the success of this computational microscopy method. We present a novel l…
Four-dimensional scanning transmission electron microscopy (4D-STEM) of local atomic diffraction patterns is emerging as a powerful technique for probing intricate details of atomic structure and atomic electric fields. However, efficient processing and interpretation of large volumes of data remain challenging, especi…
This paper studies a new Bayesian algorithm for the joint reconstruction and classification of reflectance confocal microscopy (RCM) images, with application to the identification of human skin lentigo. The proposed Bayesian approach takes advantage of the distribution of the multiplicative speckle noise affecting the …
A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing electron microscopy (EM) techniques possess required resolution in the lateral p…
Improved self-supervised denoising for Poisson-Gaussian noise.
problem Handling Poisson-Gaussian noise in self-supervised denoising.
method Extended blindspot model, improved training scheme without hyperparameters.
result Improved denoising performance on microscope image benchmarks.
Pseudo links have two crossing types: classical crossings and indeterminate crossings. They were first introduced by Ryo Hanaki as a possible tool for analyzing images produced by electron microscopy of DNA. A normalized bracket polynomial is defined for pseudo links and then used to construct and obstruction to cosmet…
Maps of brain microarchitecture are important for understanding neurological function and behavior, including alterations caused by chronic conditions such as neurodegenerative disease. Techniques such as knife-edge scanning microscopy (KESM) provide the potential for whole organ imaging at sub-cellular resolution. How…
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.
Divergence Phase Index: A Riesz-Transform Framework for Multidimensional Phase Difference Analysisstat.ML
DPI quantifies phase differences in 1D and multidimensional signals using Riesz transform.
problem Quantifying phase differences in signals of varying dimensions.
method Riesz transform framework for harmonic analysis.
result DPI detects hypersynchronization and subtle changes in images and artworks.
Compressed Sensing of Scanning Transmission Electron Microscopy (STEM) on Non-Rectangular Scansphysics.ins-det
Scanning Transmission Electron Microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In the last several years, attention was attracted by potential of STEM to explore b…
Super-resolution fluorescence microscopy, with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods stil…
Malaria is a serious infectious disease that is responsible for over half million deaths yearly worldwide. The major cause of these mortalities is late or inaccurate diagnosis. Manual microscopy is currently considered as the dominant diagnostic method for malaria. However, it is time consuming and prone to human error…
Bayesian calibration for BCP self-assembly models using image data and measure transport.
problem Calibrating models of BCP self-assembly from image data with aleatory uncertainty.
method Likelihood-free inference via measure transport and summary statistics.
result Expected information gains can be computed efficiently for model calibration.
Data driven segmentation is an important initial step of shape prior-based segmentation methods since it is assumed that the data term brings a curve to a plausible level so that shape and data terms can then work together to produce better segmentations. When purely data driven segmentation produces poor results, the …
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.
Determining the localization of specific protein in human cells is important for understanding cellular functions and biological processes of underlying diseases. Among imaging techniques, high-throughput fluorescence microscopy imaging is an efficient biotechnology to stain the protein of interest in a cell. In this w…
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for a probabilistic interpretation of cell and nuclear morphology and structure loca…
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…