Xing Yao

Hao Li, Daiwei Lu, Xing Yao et al.

In this paper, we present Endo-SemiS, a semi-supervised segmentation framework for providing reliable segmentation of endoscopic video frames with limited annotation. EndoSemiS uses 4 strategies to improve performance by effectively utilizing all available data, particularly unlabeled data: (1) Cross-supervision between two individual networks that supervise each other; (2) Uncertainty-guided pseudo-labels from unlabeled data, which are generated by selecting high-confidence regions to improve their quality; (3) Joint pseudolabel supervision, which aggregates reliable pixels from the pseudo-labels of both networks to provide accurate supervision for unlabeled data; and (4) Mutual learning, where both networks learn from each other at the feature and image levels, reducing variance and guiding them toward a consistent solution. Additionally, a separate corrective network that utilizes spatiotemporal information from endoscopy video to improve segmentation performance. Endo-SemiS is evaluated on two clinical applications: kidney stone laser lithotomy from ureteroscopy and polyp screening from colonoscopy. Compared to state-of-the-art segmentation methods, Endo-SemiS substantially achieves superior results on both datasets with limited labeled data. The code is publicly available at https://github.com/MedICL-VU/Endo-SemiS

Dewei Hu, Xing Yao, Jiacheng Wang et al.

Among the research efforts to segment the retinal vasculature from fundus images, deep learning models consistently achieve superior performance. However, this data-driven approach is very sensitive to domain shifts. For fundus images, such data distribution changes can easily be caused by variations in illumination conditions as well as the presence of disease-related features such as hemorrhages and drusen. Since the source domain may not include all possible types of pathological cases, a model that can robustly recognize vessels on unseen domains is desirable but remains elusive, despite many proposed segmentation networks of ever-increasing complexity. In this work, we propose a contrastive variational auto-encoder that can filter out irrelevant features and synthesize a latent image, named deep angiogram, representing only the retinal vessels. Then segmentation can be readily accomplished by thresholding the deep angiogram. The generalizability of the synthetic network is improved by the contrastive loss that makes the model less sensitive to variations of image contrast and noisy features. Compared to baseline deep segmentation networks, our model achieves higher segmentation performance via simple thresholding. Our experiments show that the model can generate stable angiograms on different target domains, providing excellent visualization of vessels and a non-invasive, safe alternative to fluorescein angiography.

Jiacheng Wang, Hao Li, Xing Yao et al.

Quantitative magnetization transfer (qMT) imaging provides myelin-sensitive biomarkers, such as the pool size ratio (PSR), which is valuable for multiple sclerosis (MS) assessment. However, qMT requires specialized 20-30 minute scans. We propose DEMIST to synthesize PSR maps from standard T1w and FLAIR images using a 3D latent diffusion model with three complementary conditioning mechanisms. Our approach has two stages: first, we train separate autoencoders for PSR and anatomical images to learn aligned latent representations. Second, we train a conditional diffusion model in this latent space on top of a frozen diffusion foundation backbone. Conditioning is decoupled into: (i) \textbf{semantic} tokens via cross-attention, (ii) \textbf{spatial} per-scale residual hints via a 3D ControlNet branch, and (iii) \textbf{adaptive} LoRA-modulated attention. We include edge-aware loss terms to preserve lesion boundaries and alignment losses to maintain quantitative consistency, while keeping the number of trainable parameters low and retaining the inductive bias of the pretrained model. We evaluate on 163 scans from 99 subjects using 5-fold cross-validation. Our method outperforms VAE, GAN and diffusion baselines on multiple metrics, producing sharper boundaries and better quantitative agreement with ground truth. Our code is publicly available at https://github.com/MedICL-VU/MS-Synthesis-3DcLDM.

Ruining Deng, Yihe Yang, David J. Pisapia et al.

Multi-class cell segmentation in high-resolution gigapixel whole slide images (WSIs) is crucial for various clinical applications. However, training such models typically requires labor-intensive, pixel-wise annotations by domain experts. Recent efforts have democratized this process by involving lay annotators without medical expertise. However, conventional non-corrective approaches struggle to handle annotation noise adaptively because they lack mechanisms to mitigate false positives (FP) and false negatives (FN) at both the image-feature and pixel levels. In this paper, we propose a consensus-aware self-corrective AI agent that leverages the Consensus Matrix to guide its learning process. The Consensus Matrix defines regions where both the AI and annotators agree on cell and non-cell annotations, which are prioritized with stronger supervision. Conversely, areas of disagreement are adaptively weighted based on their feature similarity to high-confidence consensus regions, with more similar regions receiving greater attention. Additionally, contrastive learning is employed to separate features of noisy regions from those of reliable consensus regions by maximizing their dissimilarity. This paradigm enables the model to iteratively refine noisy labels, enhancing its robustness. Validated on one real-world lay-annotated cell dataset and two reasoning-guided simulated noisy datasets, our method demonstrates improved segmentation performance, effectively correcting FP and FN errors and showcasing its potential for training robust models on noisy datasets. The official implementation and cell annotations are publicly available at https://github.com/ddrrnn123/CASC-AI.

Xing Yao, Vinayak Pathak, Haoran Xi et al.

This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth product (SBP) of conventional microscopes. Here, we show both in simulation and experiment that overlapped imaging and co-designed analysis software can achieve accurate detection of diagnostically-relevant features for several applications, including counting of white blood cells and the malaria parasite, leading to multi-fold increase in detection and processing throughput with minimal reduction in accuracy.