A new dataset for denoising real fluorescence microscopy images.
problem Noisy real fluorescence microscopy images.
method Constructed a dataset of 12,000 real fluorescence microscopy images with different noise levels.
result Deep learning methods perform best on the denoising of the FMD dataset.
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.
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.
A deep model learns to infer fluorescence labels from unlabeled microscopy images.
problem Challenges in obtaining high quality images of cellular structures due to complex environments and label staining limitations.
method Developed a novel deep model using global pixel transformer layers and dense blocks, incorporating multi-scale input strategy.
result Significantly outperforms state-of-the-art methods in fluorescence image prediction tasks.
DLBI uses deep learning and Bayesian inference to reconstruct super-resolution fluorescence microscopy images more accurately and faster.
problem Bottlenecks in existing super-resolution fluorescence microscopy methods, including long execution time and poor structure reconstruction.
method Combines deep learning for capturing local features and correlation along time-axis with statistical inference for refining and giving physical meaning to the reconstructed images.
result Provides more accurate and realistic reconstruction than state-of-the-art methods, DLBI is two orders of magnitude faster.
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.
Unified method for multi-defect microscopy image restoration with limited training data.
problem Challenges in applying deep learning methods due to limited training data for multi-defect microscopy images.
method Two-stage approach: data augmentation with GAN and conditional GAN training.
result Proposed method gives comparable or superior results to existing methods in image quality restoration.
GANs generate biological cell images capturing protein relationships.
problem Synthesize cells from fluorescence microscopy images.
method Adapted GANs with casual dependencies for multi-channel image generation.
result Demonstrated ability to predict temporal evolution from static images.
New CNN method improves deconvolution microscopy without PSF measurement.
problem Computational expense and blind estimation in conventional deconvolution microscopy.
method Cycle consistent CNN with explicit PSF modeling layers for blind deconvolution.
result Algorithm robustness and efficacy confirmed through experimental results.
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.
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…
Deep learning improves single-molecule localization for super-resolution microscopy.
problem Accurate and efficient localization of single molecules for super-resolution microscopy.
method A novel deep learning network architecture that uses temporal context to simultaneously detect and localize molecules.
result Achieves state-of-the-art performance on the SMLM2016 challenge, excels at high densities.
TUNet improves protein classification in cell images.
problem Classifying specific proteins in human cells using microscopy images.
method TUNet model incorporating segmentation maps for improved classification.
result TUNet achieves competitive performance in protein classification.
MarmoNet automates analysis of marmoset brain axonal projections.
problem Automatically detect and segment axonal tracer signals in noisy, cluttered images.
method Uses machine learning, specifically CNNs and image registration, to process and map axonal projections.
result Automated pipeline extracts and maps axonal projections robustly.
Deep learning enhances optical microscopy and image reconstruction.
problem Improving image data transformations in optical microscopy.
method Application of deep learning methods on optical microscopy and image reconstruction.
result Deep learning enables new transformations among different modes and modalities of microscopic imaging.
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…
Bayesian method detects neuron spike activities from noisy fluorescence data.
problem Detecting neuron spike activities from noisy fluorescence data.
method Random finite set (RFS) based Bayesian approach.
result Gains 12% extra detection accuracy compared to MLSpike method.
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.
A dataset of 10 molecule types for machine learning studies.
problem Lack of suitable datasets for machine learning in molecular imaging.
method Generated 2D cross-sectional projections of 10 molecule types from Molecular Dynamics trajectories.
result Benchmark dataset for machine learning, deep learning, and image processing in scattering, imaging, and microscopy.
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.
Automated malaria diagnosis from field slides achieves accurate results.
problem Challenges in analyzing field-prepared thin blood film microscopy images.
method Fully automated framework using machine learning, including CNNs trained on diverse field samples.
result Results are close to sufficient for drug resistance monitoring and clinical use-cases.
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.
Lazy labels enable deep learning for microscopy segmentation without full annotation.
problem Lack of pixel-wise annotations limits fully supervised learning for bioimage segmentation.
method Lazy labels combined with coarse labels for training a deep neural network.
result Model achieves accurate segmentation with minimal pixel-wise annotations.
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.
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.
New method optimizes protein design by sampling from realistic inputs.
problem Optimizing properties of interest in design problems, especially with black box predictive models.
method Conditioning by Adaptive Sampling, using model-based adaptive sampling to estimate conditional input distributions.
result Achieves state-of-the-art results on protein fluorescence problem.
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.
We present a sparse knowledge gradient (SpKG) algorithm for adaptively selecting the targeted regions within a large RNA molecule to identify which regions are most amenable to interactions with other molecules. Experimentally, such regions can be inferred from fluorescence measurements obtained by binding a complement…
New method classifies reticulocytes from red blood cells without labels.
problem Classifying reticulocytes from mature red blood cells without fluorescent labels.
method Unsupervised machine learning on morpho-rheological markers.
result Promising results in classifying reticulocytes from mature red blood cells.
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.
Deep neural network assesses quality of super-resolution images.
problem Evaluating the quality of super-resolution images from experts' scores.
method Deep neural network trained on expert scores to quantify image quality.
result Deep neural network's quality predictions correlate with human expert evaluations.
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…
Automated process links oral health to systemic conditions using machine learning.
problem Correlating oral health with systemic health conditions.
method Intraoral fluorescent biomarker imaging, machine learning segmentation, and clinical examination.
result Machine learning classifier achieved AUC of 0.677, indicating a learned association between disease signatures in images and periodontal disease.
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.
We consider factoring low-rank tensors in the presence of outlying slabs. This problem is important in practice, because data collected in many real-world applications, such as speech, fluorescence, and some social network data, fit this paradigm. Prior work tackles this problem by iteratively selecting a fixed number …
Deep learning reduces artifacts in limited angle X-ray microscopy.
problem Artifacts in image reconstruction from limited angle data in TXM.
method Training a U-Net deep neural network from synthetic data to reduce artifacts.
result Significant improvement in image quality and structural similarity.
A new method avoids noise amplification when subtracting or dividing stochastic signals.
problem Noise amplification when subtracting or dividing stochastic signals.
method Normalizing flows to approximate the distribution of the signal of interest.
result Normalizing flows can generate an approximation of the probability distribution over the signal of interest, avoiding subtraction or division.
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.
Novel co-learning method for manifolds with group actions using multiple fibre bundles.
problem Learning from manifolds with group actions without labeled data.
method Representation theory to associate multiple fibre bundles, leveraging group actions for unsupervised learning.
result Improved robust nearest neighbor search and community detection on cryo-electron microscopy images.
MuLANN tackles multi-domain learning with adversarial approach.
problem Automated microscopy data with domain bias.
method Semi-supervised multi-domain learning with MuLANN.
result Improves state of the art on image benchmarks and bioimage dataset.
Combines spatial context priors with data term for better dendritic spine segmentation.
problem Poor segmentation results due to overlapping pixel intensity distributions.
method Combines nonparametric context priors with learned-intensity data term and nonparametric shape priors.
result Significant improvements in dendritic spine segmentation.
Paper proposes CNN for diagnosing rare muscular dystrophies from images.
problem Challenges in diagnosing rare diseases due to lack of data.
method Uses a Convolutional Neural Network (CNN) for patch-based classification of confocal microscopy images.
result CNN system identifies problematic areas and provides global patient evaluation.