EEG recordings are inherently contaminated by artifacts such as ocular, muscular, and environmental noise, which obscure neural activity and complicate preprocessing. Artifact classification offers advantages in stability and transparency, providing a viable alternative to ICA-based methods that enable flexible use alongside human inspections and across various applications. However, artifact classification is limited by its training data as it requires extensive manual labeling, which cannot fully cover the diversity of real-world EEG. Semi-synthetic data (SSD) methods have been proposed to address this limitation, but prior approaches typically injected single artifact types using ICA components or required separately recorded artifact signals, reducing both the realism of the generated data and the applicability of the method. To overcome these issues, we introduce SSDLabeler, a framework that generates realistic, annotated SSDs by decomposing real EEG with ICA, epoch-level artifact verification using RMS and PSD criteria, and reinjecting multiple artifact types into clean data. When applied to train a multi-label artifact classifier, it improved accuracy on raw EEG across diverse conditions compared to prior SSD and raw EEG training, establishing a scalable foundation for artifact handling that captures the co-occurrence and complexity of real EEG.

Synthetic data provides a promising approach to address data scarcity for training machine learning models; however, adoption without proper quality assessments may introduce artifacts, distortions, and unrealistic features that compromise model performance and clinical utility. This work introduces a novel knowledge-based anomaly detection method for detecting network-induced shape artifacts in synthetic images. The introduced method utilizes a two-stage framework comprising (i) a novel feature extractor that constructs a specialized feature space by analyzing the per-image distribution of angle gradients along anatomical boundaries, and (ii) an isolation forest-based anomaly detector. We demonstrate the effectiveness of the method for identifying network-induced shape artifacts in two synthetic mammography datasets from models trained on CSAW-M and VinDr-Mammo patient datasets respectively. Quantitative evaluation shows that the method successfully concentrates artifacts in the most anomalous partition (1st percentile), with AUC values of 0.97 (CSAW-syn) and 0.91 (VMLO-syn). In addition, a reader study involving three imaging scientists confirmed that images identified by the method as containing network-induced shape artifacts were also flagged by human readers with mean agreement rates of 66% (CSAW-syn) and 68% (VMLO-syn) for the most anomalous partition, approximately 1.5-2 times higher than the least anomalous partition. Kendall-Tau correlations between algorithmic and human rankings were 0.45 and 0.43 for the two datasets, indicating reasonable agreement despite the challenging nature of subtle artifact detection. This method is a step forward in the responsible use of synthetic data, as it allows developers to evaluate synthetic images for known anatomic constraints and pinpoint and address specific issues to improve the overall quality of a synthetic dataset.

Electroencephalography (EEG) allows monitoring of brain activity, providing insights into the functional dynamics of various brain regions and their roles in cognitive processes. EEG is a cornerstone in sleep research, serving as the primary modality of polysomnography, the gold standard in the field. However, EEG signals are prone to artifacts caused by both internal (device-specific) factors and external (environmental) interferences. As sleep studies are becoming larger, most rely on automatic sleep staging, a process highly susceptible to artifacts, leading to erroneous sleep scores. This paper addresses this challenge by introducing eegFloss, an open-source Python package to utilize eegUsability, a novel machine learning (ML) model designed to detect segments with artifacts in sleep EEG recordings. eegUsability has been trained and evaluated on manually artifact-labeled EEG data collected from 15 participants over 127 nights using the Zmax headband. It demonstrates solid overall classification performance (F1-score is approximately 0.85, Cohens kappa is 0.78), achieving a high recall rate of approximately 94% in identifying channel-wise usable EEG data, and extends beyond Zmax. Additionally, eegFloss offers features such as automatic time-in-bed detection using another ML model named eegMobility, filtering out certain artifacts, and generating hypnograms and sleep statistics. By addressing a fundamental challenge faced by most sleep studies, eegFloss can enhance the precision and rigor of their analysis as well as the accuracy and reliability of their outcomes.

In modern cancer diagnostics, Whole Slide Imaging (WSI) is widely used to digitize tissue specimens for detailed, high-resolution examination; however, other diagnostic approaches, such as liquid biopsy and molecular testing, are also utilized based on the cancer type and clinical context. While WSI has revolutionized digital histopathology by enabling automated, precise analysis, it remains vulnerable to artifacts introduced during slide preparation and scanning. These artifacts can compromise downstream image analysis. To address this challenge, we propose and compare three robust artifact detection approaches for WSIs: (1) a foundation model-based approach (FMA) using a fine-tuned Unified Neural Image (UNI) architecture, (2) a deep learning approach (DLA) built on a ResNet50 backbone, and (3) a knowledge-based approach (KBA) leveraging handcrafted features from texture, color, and frequency-based metrics. The methods target six common artifact types: tissue folds, out-of-focus regions, air bubbles, tissue damage, marker traces, and blood contamination. Evaluations were conducted on 50,000+ image patches from diverse scanners (Hamamatsu, Philips, Leica Aperio AT2) across multiple sites. The FMA achieved the highest patch-wise AUROC of 0.995 (95% CI [0.994, 0.995]), outperforming the ResNet50-based method (AUROC: 0.977, 95% CI [0.977, 0.978]) and the KBA (AUROC: 0.940, 95% CI [0.933, 0.946]). To translate detection into actionable insights, we developed a quality report scorecard that quantifies high-quality patches and visualizes artifact distributions.

Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, yet their impact on spatial proteomics, imaging that maps proteins at single-cell resolution, remains limited. Here, we introduce KRONOS, a foundation model built for spatial proteomics. KRONOS was trained in a self-supervised manner on over 47 million image patches covering 175 protein markers, 16 tissue types, and 8 fluorescence-based imaging platforms. We introduce key architectural adaptations to address the high-dimensional, multi-channel, and heterogeneous nature of multiplex imaging. We demonstrate that KRONOS learns biologically meaningful representations across multiple scales, ranging from cellular and microenvironment to tissue levels, enabling it to address diverse downstream tasks, including cell phenotyping, region classification, and patient stratification. Evaluated across 11 independent cohorts, KRONOS achieves state-of-the-art performance across cell phenotyping, treatment response prediction, and retrieval tasks, and is highly data-efficient. KRONOS also introduces the paradigm of segmentation-free patch-level processing for efficient and scalable spatial proteomics analysis, allowing cross-institutional comparisons, and as an image reverse search engine for spatial patterns.

Artifacts in the electroencephalogram (EEG) degrade signal quality and impact the analysis of brain activity. Current methods for detecting artifacts in sleep EEG rely on simple threshold-based algorithms that require manual intervention, which is time-consuming and impractical due to the vast volume of data that novel mobile recording systems generate. We propose a convolutional neural network (CNN) model incorporating a convolutional block attention module (CNN-CBAM) to detect and identify the location of artifacts in the sleep EEG with attention maps. We benchmarked this model against six other machine learning and signal processing approaches. We trained/tuned all models on 72 manually annotated EEG recordings obtained during home-based monitoring from 18 healthy participants with a mean (SD) age of 68.05 y ($\pm$5.02). We tested them on 26 separate recordings from 6 healthy participants with a mean (SD) age of 68.33 y ($\pm$4.08), with contained artifacts in 4\% of epochs. CNN-CBAM achieved the highest area under the receiver operating characteristic curve (0.88), sensitivity (0.81), and specificity (0.86) when compared to the other approaches. The attention maps from CNN-CBAM localized artifacts within the epoch with a sensitivity of 0.71 and specificity of 0.67. This work demonstrates the feasibility of automating the detection and localization of artifacts in wearable sleep EEG.

In intracoronary optical coherence tomography (OCT), blood residues and gas bubbles cause attenuation artifacts that can obscure critical vessel structures. The presence and severity of these artifacts may warrant re-acquisition, prolonging procedure time and increasing use of contrast agent. Accurate detection of these artifacts can guide targeted re-acquisition, reducing the amount of repeated scans needed to achieve diagnostically viable images. However, the highly heterogeneous appearance of these artifacts poses a challenge for the automated detection of the affected image regions. To enable automatic detection of the attenuation artifacts caused by blood residues and gas bubbles based on their severity, we propose a convolutional neural network that performs classification of the attenuation lines (A-lines) into three classes: no artifact, mild artifact and severe artifact. Our model extracts and merges features from OCT images in both Cartesian and polar coordinates, where each column of the image represents an A-line. Our method detects the presence of attenuation artifacts in OCT frames reaching F-scores of 0.77 and 0.94 for mild and severe artifacts, respectively. The inference time over a full OCT scan is approximately 6 seconds. Our experiments show that analysis of images represented in both Cartesian and polar coordinate systems outperforms the analysis in polar coordinates only, suggesting that these representations contain complementary features. This work lays the foundation for automated artifact assessment and image acquisition guidance in intracoronary OCT imaging.

EEG signals convey important information about brain activity both in healthy and pathological conditions. However, they are inherently noisy, which poses significant challenges for accurate analysis and interpretation. Traditional EEG artifact removal methods, while effective, often require extensive expert intervention. This study presents LSTEEG, a novel LSTM-based autoencoder designed for the detection and correction of artifacts in EEG signals. Leveraging deep learning, particularly LSTM layers, LSTEEG captures non-linear dependencies in sequential EEG data. LSTEEG demonstrates superior performance in both artifact detection and correction tasks compared to other state-of-the-art convolutional autoencoders. Our methodology enhances the interpretability and utility of the autoencoder's latent space, enabling data-driven automated artefact removal in EEG its application in downstream tasks. This research advances the field of efficient and accurate multi-channel EEG preprocessing, and promotes the implementation and usage of automated EEG analysis pipelines for brain health applications.

Overcoming this challenge requires developing quality control algorithms, that are hindered by the limited availability of relevant annotated data in histopathology. The manual annotation of ground-truth for artifact detection methods is expensive and time-consuming. This work addresses the issue by proposing a method dedicated to augmenting whole slide images with artifacts. The tool seamlessly generates and blends artifacts from an external library to a given histopathology dataset. The augmented datasets are then utilized to train artifact classification methods. The evaluation shows their usefulness in classification of the artifacts, where they show an improvement from 0.10 to 0.01 AUROC depending on the artifact type. The framework, model, weights, and ground-truth annotations are freely released to facilitate open science and reproducible research.

Recent research at CHU Sainte Justine's Pediatric Critical Care Unit (PICU) has revealed that traditional machine learning methods, such as semi-supervised label propagation and K-nearest neighbors, outperform Transformer-based models in artifact detection from PPG signals, mainly when data is limited. This study addresses the underutilization of abundant unlabeled data by employing self-supervised learning (SSL) to extract latent features from these data, followed by fine-tuning on labeled data. Our experiments demonstrate that SSL significantly enhances the Transformer model's ability to learn representations, improving its robustness in artifact classification tasks. Among various SSL techniques, including masking, contrastive learning, and DINO (self-distillation with no labels)-contrastive learning exhibited the most stable and superior performance in small PPG datasets. Further, we delve into optimizing contrastive loss functions, which are crucial for contrastive SSL. Inspired by InfoNCE, we introduce a novel contrastive loss function that facilitates smoother training and better convergence, thereby enhancing performance in artifact classification. In summary, this study establishes the efficacy of SSL in leveraging unlabeled data, particularly in enhancing the capabilities of the Transformer model. This approach holds promise for broader applications in PICU environments, where annotated data is often limited.