Adapting a Segmentation Foundation Model for Medical Image Classification

Recent advancements in foundation models, such as the Segment Anything Model (SAM), have shown strong performance in various vision tasks, particularly image segmentation, due to their impressive zero-shot segmentation capabilities. However, effectively adapting such models for medical image classification is still a less explored topic. In this paper, we introduce a new framework to adapt SAM for medical image classification. First, we utilize the SAM image encoder as a feature extractor to capture segmentation-based features that convey important spatial and contextual details of the image, while freezing its weights to avoid unnecessary overhead during training. Next, we propose a novel Spatially Localized Channel Attention (SLCA) mechanism to compute spatially localized attention weights for the feature maps. The features extracted from SAM's image encoder are processed through SLCA to compute attention weights, which are then integrated into deep learning classification models to enhance their focus on spatially relevant or meaningful regions of the image, thus improving classification performance. Experimental results on three public medical image classification datasets demonstrate the effectiveness and data-efficiency of our approach.

CaRaFFusion: Improving 2D Semantic Segmentation with Camera-Radar Point Cloud Fusion and Zero-Shot Image Inpainting

Segmenting objects in an environment is a crucial task for autonomous driving and robotics, as it enables a better understanding of the surroundings of each agent. Although camera sensors provide rich visual details, they are vulnerable to adverse weather conditions. In contrast, radar sensors remain robust under such conditions, but often produce sparse and noisy data. Therefore, a promising approach is to fuse information from both sensors. In this work, we propose a novel framework to enhance camera-only baselines by integrating a diffusion model into a camera-radar fusion architecture. We leverage radar point features to create pseudo-masks using the Segment-Anything model, treating the projected radar points as point prompts. Additionally, we propose a noise reduction unit to denoise these pseudo-masks, which are further used to generate inpainted images that complete the missing information in the original images. Our method improves the camera-only segmentation baseline by 2.63% in mIoU and enhances our camera-radar fusion architecture by 1.48% in mIoU on the Waterscenes dataset. This demonstrates the effectiveness of our approach for semantic segmentation using camera-radar fusion under adverse weather conditions.

Pro2SAM: Mask Prompt to SAM with Grid Points for Weakly Supervised Object Localization

Weakly Supervised Object Localization (WSOL), which aims to localize objects by only using image-level labels, has attracted much attention because of its low annotation cost in real applications. Current studies focus on the Class Activation Map (CAM) of CNN and the self-attention map of transformer to identify the region of objects. However, both CAM and self-attention maps can not learn pixel-level fine-grained information on the foreground objects, which hinders the further advance of WSOL. To address this problem, we initiatively leverage the capability of zero-shot generalization and fine-grained segmentation in Segment Anything Model (SAM) to boost the activation of integral object regions. Further, to alleviate the semantic ambiguity issue accrued in single point prompt-based SAM, we propose an innovative mask prompt to SAM (Pro2SAM) network with grid points for WSOL task. First, we devise a Global Token Transformer (GTFormer) to generate a coarse-grained foreground map as a flexible mask prompt, where the GTFormer jointly embeds patch tokens and novel global tokens to learn foreground semantics. Secondly, we deliver grid points as dense prompts into SAM to maximize the probability of foreground mask, which avoids the lack of objects caused by a single point/box prompt. Finally, we propose a pixel-level similarity metric to come true the mask matching from mask prompt to SAM, where the mask with the highest score is viewed as the final localization map. Experiments show that the proposed Pro2SAM achieves state-of-the-art performance on both CUB-200-2011 and ILSVRC, with 84.03\% and 66.85\% Top-1 Loc, respectively.

Advancing Generalizable Tumor Segmentation with Anomaly-Aware Open-Vocabulary Attention Maps and Frozen Foundation Diffusion Models

We explore Generalizable Tumor Segmentation, aiming to train a single model for zero-shot tumor segmentation across diverse anatomical regions. Existing methods face limitations related to segmentation quality, scalability, and the range of applicable imaging modalities. In this paper, we uncover the potential of the internal representations within frozen medical foundation diffusion models as highly efficient zero-shot learners for tumor segmentation by introducing a novel framework named DiffuGTS. DiffuGTS creates anomaly-aware open-vocabulary attention maps based on text prompts to enable generalizable anomaly segmentation without being restricted by a predefined training category list. To further improve and refine anomaly segmentation masks, DiffuGTS leverages the diffusion model, transforming pathological regions into high-quality pseudo-healthy counterparts through latent space inpainting, and applies a novel pixel-level and feature-level residual learning approach, resulting in segmentation masks with significantly enhanced quality and generalization. Comprehensive experiments on four datasets and seven tumor categories demonstrate the superior performance of our method, surpassing current state-of-the-art models across multiple zero-shot settings. Codes are available at https://github.com/Yankai96/DiffuGTS.

AI-Driven Segmentation and Analysis of Microbial Cells

Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an AI-driven image analysis system to efficiently segment individual cells and quantitatively analyze key cellular features. This system is comprised of four main modules. First, a denoising algorithm enhances contrast and suppresses noise while preserving fine cellular details. Second, the Segment Anything Model (SAM) enables accurate, zero-shot segmentation of cells without additional training. Third, post-processing is applied to refine segmentation results by removing over-segmented masks. Finally, quantitative analysis algorithms extract essential cellular features, including average intensity, length, width, and volume. The results show that denoising and post-processing significantly improved the segmentation accuracy of SAM in this new domain. Without human annotations, the AI-driven pipeline automatically and efficiently outlines cellular boundaries, indexes them, and calculates key cellular parameters with high accuracy. This framework will enable efficient and automated quantitative analysis of high-resolution fluorescence microscopy images to advance research into microbial adaptations to grow and metabolism that allow extremophiles to thrive in their harsh habitats.

RESAnything: Attribute Prompting for Arbitrary Referring Segmentation

We present an open-vocabulary and zero-shot method for arbitrary referring expression segmentation (RES), targeting input expressions that are more general than what prior works were designed to handle. Specifically, our inputs encompass both object- and part-level labels as well as implicit references pointing to properties or qualities of object/part function, design, style, material, etc. Our model, coined RESAnything, leverages Chain-of-Thoughts (CoT) reasoning, where the key idea is attribute prompting. We generate detailed descriptions of object/part attributes including shape, color, and location for potential segment proposals through systematic prompting of a large language model (LLM), where the proposals are produced by a foundational image segmentation model. Our approach encourages deep reasoning about object or part attributes related to function, style, design, etc., enabling the system to handle implicit queries without any part annotations for training or fine-tuning. As the first zero-shot and LLM-based RES method, RESAnything achieves clearly superior performance among zero-shot methods on traditional RES benchmarks and significantly outperforms existing methods on challenging scenarios involving implicit queries and complex part-level relations. Finally, we contribute a new benchmark dataset to offer ~3K carefully curated RES instances to assess part-level, arbitrary RES solutions.

SAM-Guided Robust Representation Learning for One-Shot 3D Medical Image Segmentation

One-shot medical image segmentation (MIS) is crucial for medical analysis due to the burden of medical experts on manual annotation. The recent emergence of the segment anything model (SAM) has demonstrated remarkable adaptation in MIS but cannot be directly applied to one-shot medical image segmentation (MIS) due to its reliance on labor-intensive user interactions and the high computational cost. To cope with these limitations, we propose a novel SAM-guided robust representation learning framework, named RRL-MedSAM, to adapt SAM to one-shot 3D MIS, which exploits the strong generalization capabilities of the SAM encoder to learn better feature representation. We devise a dual-stage knowledge distillation (DSKD) strategy to distill general knowledge between natural and medical images from the foundation model to train a lightweight encoder, and then adopt a mutual exponential moving average (mutual-EMA) to update the weights of the general lightweight encoder and medical-specific encoder. Specifically, pseudo labels from the registration network are used to perform mutual supervision for such two encoders. Moreover, we introduce an auto-prompting (AP) segmentation decoder which adopts the mask generated from the general lightweight model as a prompt to assist the medical-specific model in boosting the final segmentation performance. Extensive experiments conducted on three public datasets, i.e., OASIS, CT-lung demonstrate that the proposed RRL-MedSAM outperforms state-of-the-art one-shot MIS methods for both segmentation and registration tasks. Especially, our lightweight encoder uses only 3\% of the parameters compared to the encoder of SAM-Base.

Can Foundation Models Really Segment Tumors? A Benchmarking Odyssey in Lung CT Imaging

Accurate lung tumor segmentation is crucial for improving diagnosis, treatment planning, and patient outcomes in oncology. However, the complexity of tumor morphology, size, and location poses significant challenges for automated segmentation. This study presents a comprehensive benchmarking analysis of deep learning-based segmentation models, comparing traditional architectures such as U-Net and DeepLabV3, self-configuring models like nnUNet, and foundation models like MedSAM, and MedSAM~2. Evaluating performance across two lung tumor segmentation datasets, we assess segmentation accuracy and computational efficiency under various learning paradigms, including few-shot learning and fine-tuning. The results reveal that while traditional models struggle with tumor delineation, foundation models, particularly MedSAM~2, outperform them in both accuracy and computational efficiency. These findings underscore the potential of foundation models for lung tumor segmentation, highlighting their applicability in improving clinical workflows and patient outcomes.

AI-Driven High-Resolution Cell Segmentation and Quantitative Analysis

Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an AI-driven image analysis system to efficiently segment individual cells and quantitatively analyze key cellular features. This system is comprised of four main modules. First, a denoising algorithm enhances contrast and suppresses noise while preserving fine cellular details. Second, the Segment Anything Model (SAM) enables accurate, zero-shot segmentation of cells without additional training. Third, post-processing is applied to refine segmentation results by removing over-segmented masks. Finally, quantitative analysis algorithms extract essential cellular features, including average intensity, length, width, and volume. The results show that denoising and post-processing significantly improved the segmentation accuracy of SAM in this new domain. Without human annotations, the AI-driven pipeline automatically and efficiently outlines cellular boundaries, indexes them, and calculates key cellular parameters with high accuracy. This framework will enable efficient and automated quantitative analysis of high-resolution fluorescence microscopy images to advance research into microbial adaptations to grow and metabolism that allow extremophiles to thrive in their harsh habitats.

Common3D: Self-Supervised Learning of 3D Morphable Models for Common Objects in Neural Feature Space

3D morphable models (3DMMs) are a powerful tool to represent the possible shapes and appearances of an object category. Given a single test image, 3DMMs can be used to solve various tasks, such as predicting the 3D shape, pose, semantic correspondence, and instance segmentation of an object. Unfortunately, 3DMMs are only available for very few object categories that are of particular interest, like faces or human bodies, as they require a demanding 3D data acquisition and category-specific training process. In contrast, we introduce a new method, Common3D, that learns 3DMMs of common objects in a fully self-supervised manner from a collection of object-centric videos. For this purpose, our model represents objects as a learned 3D template mesh and a deformation field that is parameterized as an image-conditioned neural network. Different from prior works, Common3D represents the object appearance with neural features instead of RGB colors, which enables the learning of more generalizable representations through an abstraction from pixel intensities. Importantly, we train the appearance features using a contrastive objective by exploiting the correspondences defined through the deformable template mesh. This leads to higher quality correspondence features compared to related works and a significantly improved model performance at estimating 3D object pose and semantic correspondence. Common3D is the first completely self-supervised method that can solve various vision tasks in a zero-shot manner.