Junlin Guo

Zhengyi Lu, Ming Lu, Chongyu Qu et al.

Metal implants in MRI cause severe artifacts that degrade image quality and hinder clinical diagnosis. Traditional approaches address metal artifact reduction (MAR) and accelerated MRI acquisition as separate problems. We propose MASC, a unified reinforcement learning framework that jointly optimizes metal-aware k-space sampling and artifact correction for accelerated MRI. To enable supervised training, we construct a paired MRI dataset using physics-based simulation, generating k-space data and reconstructions for phantoms with and without metal implants. This paired dataset provides simulated 3D MRI scans with and without metal implants, where each metal-corrupted sample has an exactly matched clean reference, enabling direct supervision for both artifact reduction and acquisition policy learning. We formulate active MRI acquisition as a sequential decision-making problem, where an artifact-aware Proximal Policy Optimization (PPO) agent learns to select k-space phase-encoding lines under a limited acquisition budget. The agent operates on undersampled reconstructions processed through a U-Net-based MAR network, learning patterns that maximize reconstruction quality. We further propose an end-to-end training scheme where the acquisition policy learns to select k-space lines that best support artifact removal while the MAR network simultaneously adapts to the resulting undersampling patterns. Experiments demonstrate that MASC's learned policies outperform conventional sampling strategies, and end-to-end training improves performance compared to using a frozen pre-trained MAR network, validating the benefit of joint optimization. Cross-dataset experiments on FastMRI with physics-based artifact simulation further confirm generalization to realistic clinical MRI data. The code and models of MASC have been made publicly available: https://github.com/hrlblab/masc

Can Cui, Ruining Deng, Junlin Guo et al.

The Vision Foundation Model has recently gained attention in medical image analysis. Its zero-shot learning capabilities accelerate AI deployment and enhance the generalizability of clinical applications. However, segmenting pathological images presents a special focus on the flexibility of segmentation targets. For instance, a single click on a Whole Slide Image (WSI) could signify a cell, a functional unit, or layers, adding layers of complexity to the segmentation tasks. Current models primarily predict potential outcomes but lack the flexibility needed for physician input. In this paper, we explore the potential of enhancing segmentation model flexibility by introducing various task prompts through a Large Language Model (LLM) alongside traditional task tokens. Our contribution is in four-fold: (1) we construct a computational-efficient pipeline that uses finetuned language prompts to guide flexible multi-class segmentation; (2) We compare segmentation performance with fixed prompts against free-text; (3) We design a multi-task kidney pathology segmentation dataset and the corresponding various free-text prompts; and (4) We evaluate our approach on the kidney pathology dataset, assessing its capacity to new cases during inference.

Juming Xiong, Ruining Deng, Jialin Yue et al.

Histological analysis plays a crucial role in understanding tissue structure and pathology. While recent advancements in registration methods have improved 2D histological analysis, they often struggle to preserve critical 3D spatial relationships, limiting their utility in both clinical and research applications. Specifically, constructing accurate 3D models from 2D slices remains challenging due to tissue deformation, sectioning artifacts, variability in imaging techniques, and inconsistent illumination. Deep learning-based registration methods have demonstrated improved performance but suffer from limited generalizability and require large-scale training data. In contrast, non-deep-learning approaches offer better generalizability but often compromise on accuracy. In this study, we introduced ZeroReg3D, a novel zero-shot registration pipeline tailored for accurate 3D reconstruction from serial histological sections. By combining zero-shot deep learning-based keypoint matching with optimization-based affine and non-rigid registration techniques, ZeroReg3D effectively addresses critical challenges such as tissue deformation, sectioning artifacts, staining variability, and inconsistent illumination without requiring retraining or fine-tuning. The code has been made publicly available at https://github.com/hrlblab/ZeroReg3D

Junlin Guo, James R. Zimmer-Dauphinee, Jordan M. Nieusma et al.

By mapping sites at large scales using remotely sensed data, archaeologists can generate unique insights into long-term demographic trends, inter-regional social networks, and past adaptations to climate change. Remote sensing surveys complement field-based approaches, and their reach can be especially great when combined with deep learning and computer vision techniques. However, conventional supervised deep learning methods face challenges in annotating fine-grained archaeological features at scale. While recent vision foundation models have shown remarkable success in learning large-scale remote sensing data with minimal annotations, most off-the-shelf solutions are designed for RGB images rather than multi-spectral satellite imagery, such as the 8-band data used in our study. In this paper, we introduce DeepAndes, a transformer-based vision foundation model trained on three million multi-spectral satellite images, specifically tailored for Andean archaeology. DeepAndes incorporates a customized DINOv2 self-supervised learning algorithm optimized for 8-band multi-spectral imagery, marking the first foundation model designed explicitly for the Andes region. We evaluate its image understanding performance through imbalanced image classification, image instance retrieval, and pixel-level semantic segmentation tasks. Our experiments show that DeepAndes achieves superior F1 scores, mean average precision, and Dice scores in few-shot learning scenarios, significantly outperforming models trained from scratch or pre-trained on smaller datasets. This underscores the effectiveness of large-scale self-supervised pre-training in archaeological remote sensing. Codes will be available on https://github.com/geopacha/DeepAndes.

Runchen Wang, Junlin Guo, Siqi Lu et al.

Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has evaluated early-generation AI cell foundation models in this domain, the effectiveness of recent cell foundation models remains unclear. In this study, we benchmark advanced AI cell foundation models (2025), including CellViT++ variants and Cellpose-SAM, against three widely used cell foundation models developed prior to 2024, using a diverse large-scale set of kidney image patches within a human-in-the-loop rating framework. We further performed fusion-based ensemble evaluation and model agreement analysis to assess the segmentation capabilities of the different models. Our results show that CellViT++ [Virchow] yields the highest standalone performance with 40.3% of predictions rated as "Good" on a curated set of 2,091 challenging samples, outperforming all prior models. In addition, our fused model achieves 62.2% "Good" predictions and only 0.4% "Bad", substantially reducing segmentation errors. Notably, the fusion model (2025) successfully resolved the majority of challenging cases that remained unaddressed in our previous study. These findings demonstrate the potential of AI cell foundation model development in renal pathology and provide a curated dataset of challenging samples to support future kidney-specific model refinement.

Jiachen Xu, Junlin Guo, James Zimmer-Dauphinee et al.

Archaeology has long faced fundamental issues of sampling and scalar representation. Traditionally, the local-to-regional-scale views of settlement patterns are produced through systematic pedestrian surveys. Recently, systematic manual survey of satellite and aerial imagery has enabled continuous distributional views of archaeological phenomena at interregional scales. However, such 'brute force' manual imagery survey methods are both time- and labor-intensive, as well as prone to inter-observer differences in sensitivity and specificity. The development of self-supervised learning methods offers a scalable learning scheme for locating archaeological features using unlabeled satellite and historical aerial images. However, archaeological features are generally only visible in a very small proportion relative to the landscape, while the modern contrastive-supervised learning approach typically yields an inferior performance on highly imbalanced datasets. In this work, we propose a framework to address this long-tail problem. As opposed to the existing contrastive learning approaches that treat the labelled and unlabeled data separately, our proposed method reforms the learning paradigm under a semi-supervised setting in order to utilize the precious annotated data (<7% in our setting). Specifically, the highly unbalanced nature of the data is employed as the prior knowledge in order to form pseudo negative pairs by ranking the similarities between unannotated image patches and annotated anchor images. In this study, we used 95,358 unlabeled images and 5,830 labelled images in order to solve the issues associated with detecting ancient buildings from a long-tailed satellite image dataset. From the results, our semi-supervised contrastive learning model achieved a promising testing balanced accuracy of 79.0%, which is a 3.8% improvement as compared to other state-of-the-art approaches.