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1. Mastering SAM Prompts: A Large-Scale Empirical Study in Segmentation Refinement for Scientific Imaging

   Price, Stephen; Rundensteiner, Elke; Cote, Danielle (November 2025, Transactions on Machine Learning Research)

   Segment Anything Model (SAM) has emerged as a prevalent tool empowering advances in vision tasks from instance segmentation, panoptic segmentation, to interactive segmentation. Leveraging powerful zero-shot capabilities enabled by visual prompts such as masks placed on the image, SAM has been shown to significantly improve tasks. Yet, a poor prompt can worsen SAM performance, risking consequences such as misdiagnoses, autonomous driving failures, or manufacturing defects. However, recent studies on visual SAM prompting remain limited, cover only a small fraction of potential prompt configurations, adopt ad-hoc evaluation strategies, and come with limited or even no rigorous analysis of the statistical significance of prompt configurations. To address this gap, we undertake the first large-scale empirical study comprehensively evaluating the impact of SAM prompt configurations on segmentation refinement. This includes 2,688 prompt configurations, including points, boxes, and masks with diverse augmentations, on four initial segmentation models for a total of 10,752 evaluations. From these results, we draw statistically significant insights along with practical guidelines for prompt design on scientific images. In particular, we recommend including a bounding box, which raised AP@50-95 by 0.320 and advise against using a coarse mask, which lowers AP@50-95 by -0.133 across all four models on microscopy data sets. We showcase that our recommended prompt configuration enables SAM to outperform leading refinement methods on multiple scientific benchmark datasets. 

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2. All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning

   Can Cui, Ruining Deng (July 2023, Asia Conference on Computers and Communications, ACCC)

   The Segment Anything Model (SAM) is a recently proposed prompt-based segmentation model in a generic zero-shot segmentation approach. With the zero-shot segmentation capacity, SAM achieved impressive flexibility and precision on various segmentation tasks. However, the current pipeline requires manual prompts during the inference stage, which is still resource intensive for biomedical image segmentation. In this paper, instead of using prompts during the inference stage, we introduce a pipeline that utilizes the SAM, called all-in-SAM, through the entire AI development workflow (from annotation generation to model finetuning) without requiring manual prompts during the inference stage. Specifically, SAM is first employed to generate pixel-level annotations from weak prompts (e.g., points, bounding box). Then, the pixel-level annotations are used to finetune the SAM segmentation model rather than training from scratch. Our experimental results reveal two key findings: 1) the proposed pipeline surpasses the state-of-the-art (SOTA) methods in a nuclei segmentation task on the public Monuseg dataset, and 2) the utilization of weak and few annotations for SAM finetuning achieves competitive performance compared to using strong pixel-wise annotated data. 

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3. GeoSAM: Fine-Tuning SAM with Multi-Modal Prompts for Mobility Infrastructure Segmentation

   https://doi.org/10.3233/FAIA250844  

   Sultan, Rafi Ibn; Li, Chengyin; Zhu, Hui; Khanduri, Prashant; Brocanelli, Marco; Zhu, Dongxiao (October 2025, IOS Press)

   In geographical image segmentation, performance is often constrained by the limited availability of training data and a lack of generalizability, particularly for segmenting mobility infrastructure such as roads, sidewalks, and crosswalks. Vision foundation models like the Segment Anything Model (SAM), pre-trained on millions of natural images, have demonstrated impressive zero-shot segmentation performance, providing a potential solution. However, SAM struggles with geographical images, such as aerial and satellite imagery, due to its training being confined to natural images and the narrow features and textures of these objects blending into their surroundings. To address these challenges, we propose Geographical SAM (GeoSAM), a SAM-based framework that fine-tunes SAM using automatically generated multi-modal prompts. Specifically, GeoSAM integrates point prompts from a pre-trained task-specific model as primary visual guidance, and text prompts generated by a large language model as secondary semantic guidance, enabling the model to better capture both spatial structure and contextual meaning. GeoSAM outperforms existing approaches for mobility infrastructure segmentation in both familiar and completely unseen regions by at least 5% in mIoU, representing a significant leap in leveraging foundation models to segment mobility infrastructure, including both road and pedestrian infrastructure in geographical images. The source code is publicly available. 

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4. Tuning-Free Amodal Segmentation via the Occlusion-Free Bias of Inpainting Models

   https://doi.org/10.1609/aaai.v40i7.37509  

   Lee, Jae Joong; Benes, Bedrich; Yeh, Raymond A (March 2026, Proceedings of the AAAI Conference on Artificial Intelligence)

   Amodal segmentation is an image-based algorithm that aims to predict masks for both visible and occluded parts of objects. Existing methods typically rely on supervised learning with annotated amodal masks or synthetic data. The effectiveness of these methods relies heavily on the quality of the datasets. This dependence can unintentionally restrict their generalization capabilities due to insufficient diversity and size. Although existing zero-shot methods perform well on their reported datasets, their performance does not necessarily transfer to other datasets. We propose a tuning-free approach that re-purposes diffusion-based inpainting foundation models for amodal segmentation. Our approach is motivated by the “occlusion-free bias” of inpainting models, i.e., the inpainted objects tend to be complete and without occlusions. We reconstruct the occluded regions of an object via inpainting and then apply segmentation, all without additional training or fine-tuning. Experiments on five datasets, three previously unreported, demonstrate the generalizability of our approach. On average, our approach achieves 5.3% more accurate masks in mIoU compared to the publicly available state-of-the-art, pix2gestalt. 

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5. NudgeSeg: Zero-Shot Object Segmentation by Repeated Physical Interaction

   https://doi.org/10.1109/IROS51168.2021.9635832  

   Singh, Chahat Deep; Sanket, Nitin J.; Parameshwara, Chethan M.; Fermuller, Cornelia; Aloimonos, Yiannis (September 2021, 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS))

   Recent advances in object segmentation have demonstrated that deep neural networks excel at object segmentation for specific classes in color and depth images. However, their performance is dictated by the number of classes and objects used for training, thereby hindering generalization to never seen objects or zero-shot samples. To exacerbate the problem further, object segmentation using image frames rely on recognition and pattern matching cues. Instead, we utilize the ‘active’ nature of a robot and their ability to ‘interact’ with the environment to induce additional geometric constraints for segmenting zero-shot samples. In this paper, we present the first framework to segment unknown objects in a cluttered scene by repeatedly ‘nudging’ at the objects and moving them to obtain additional motion cues at every step using only a monochrome monocular camera. We call our framework NudgeSeg. These motion cues are used to refine the segmentation masks. We successfully test our approach to segment novel objects in various cluttered scenes and provide an extensive study with image and motion segmentation methods. We show an impressive average detection rate of over 86% on zero-shot objects. 

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