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Segment Anything Model (SAM) has demonstrated impressive zero-shot performance and brought a range of unexplored capabilities to natural image segmentation tasks. However, as a very important branch of image segmentation, the performance of SAM remains uncertain when applied to medical image segmentation due to the significant differences between natural images and medical images. Meanwhile, it is harsh to meet the SAM's requirements of extra prompts provided, such as points or boxes to specify medical regions. In this paper, we propose a novel self-prompt SAM adaptation framework for medical image segmentation, named Self-Prompt-SAM. We design a multi-scale prompt generator combined with the image encoder in SAM to generate auxiliary masks. Then, we use the auxiliary masks to generate bounding boxes as box prompts and use Distance Transform to select the most central points as point prompts. Meanwhile, we design a 3D depth-fused adapter (DfusedAdapter) and inject the DFusedAdapter into each transformer in the image encoder and mask decoder to enable pre-trained 2D SAM models to extract 3D information and adapt to 3D medical images. Extensive experiments demonstrate that our method

Interactive medical image segmentation (IMIS) has shown significant potential in enhancing segmentation accuracy by integrating iterative feedback from medical professionals. However, the limited availability of enough 3D medical data restricts the generalization and robustness of most IMIS methods. The Segment Anything Model (SAM), though effective for 2D images, requires expensive semi-auto slice-by-slice annotations for 3D medical images. In this paper, we explore the zero-shot capabilities of SAM 2, the next-generation Meta SAM model trained on videos, for 3D medical image segmentation. By treating sequential 2D slices of 3D images as video frames, SAM 2 can fully automatically propagate annotations from a single frame to the entire 3D volume. We propose a practical pipeline for using SAM 2 in 3D medical image segmentation and present key findings highlighting its efficiency and potential for further optimization. Concretely, numerical experiments on the BraTS2020 and the medical segmentation decathlon datasets demonstrate that SAM 2 still has a gap with supervised methods but can narrow the gap in specific settings and organ types, significantly reducing the annotation burden

Recently, developing unified medical image segmentation models gains increasing attention, especially with the advent of the Segment Anything Model (SAM). SAM has shown promising binary segmentation performance in natural domains, however, transferring it to the medical domain remains challenging, as medical images often possess substantial inter-category overlaps. To address this, we propose the SEmantic-Guided SAM (SEG-SAM), a unified medical segmentation model that incorporates semantic medical knowledge to enhance medical segmentation performance. First, to avoid the potential conflict between binary and semantic predictions, we introduce a semantic-aware decoder independent of SAM's original decoder, specialized for both semantic segmentation on the prompted object and classification on unprompted objects in images. To further enhance the model's semantic understanding, we solicit key characteristics of medical categories from large language models and incorporate them into SEG-SAM through a text-to-vision semantic module, adaptively transferring the language information into the visual segmentation task. In the end, we introduce the cross-mask spatial alignment strategy to en

With the proposal of the Segment Anything Model (SAM), fine-tuning SAM for medical image segmentation (MIS) has become popular. However, due to the large size of the SAM model and the significant domain gap between natural and medical images, fine-tuning-based strategies are costly with potential risk of instability, feature damage and catastrophic forgetting. Furthermore, some methods of transferring SAM to a domain-specific MIS through fine-tuning strategies disable the model's prompting capability, severely limiting its utilization scenarios. In this paper, we propose an Auto-Prompting Module (APM), which provides SAM-based foundation model with Euclidean adaptive prompts in the target domain. Our experiments demonstrate that such adaptive prompts significantly improve SAM's non-fine-tuned performance in MIS. In addition, we propose a novel non-invasive method called Incremental Pattern Shifting (IPS) to adapt SAM to specific medical domains. Experimental results show that the IPS enables SAM to achieve state-of-the-art or competitive performance in MIS without the need for fine-tuning. By coupling these two methods, we propose ProMISe, an end-to-end non-fine-tuned framework for

Emerging of visual language models, such as the segment anything model (SAM), have made great breakthroughs in the field of universal semantic segmentation and significantly aid the improvements of medical image segmentation, in particular with the help of Medical SAM adaptor (Med-SA). However, Med-SA still can be improved, as it fine-tunes SAM in a partial adaption manner. To resolve this problem, we present a novel global medical SAM adaptor (GMed-SA) with full adaption, which can adapt SAM globally. We further combine GMed-SA and Med-SA to propose a global-local medical SAM adaptor (GLMed-SA) to adapt SAM both globally and locally. Extensive experiments have been performed on the challenging public 2D melanoma segmentation dataset. The results show that GLMed-SA outperforms several state-of-the-art semantic segmentation methods on various evaluation metrics, demonstrating the superiority of our methods.

Manual annotation of volumetric medical images, such as magnetic resonance imaging (MRI) and computed tomography (CT), is a labor-intensive and time-consuming process. Recent advancements in foundation models for video object segmentation, such as Segment Anything Model 2 (SAM 2), offer a potential opportunity to significantly speed up the annotation process by manually annotating one or a few slices and then propagating target masks across the entire volume. However, the performance of SAM 2 in this context varies. Our experiments show that relying on a single memory bank and attention module is prone to error propagation, particularly at boundary regions where the target is present in the previous slice but absent in the current one. To address this problem, we propose Short-Long Memory SAM 2 (SLM-SAM 2), a novel architecture that integrates distinct short-term and long-term memory banks with separate attention modules to improve segmentation accuracy. We evaluate SLM-SAM 2 on four public datasets covering organs, bones, and muscles across MRI, CT, and ultrasound videos. We show that the proposed method markedly outperforms the default SAM 2, achieving an average Dice Similarity

The Segment Anything Model (SAM) has achieved a notable success in two-dimensional image segmentation in natural images. However, the substantial gap between medical and natural images hinders its direct application to medical image segmentation tasks. Particularly in 3D medical images, SAM struggles to learn contextual relationships between slices, limiting its practical applicability. Moreover, applying 2D SAM to 3D images requires prompting the entire volume, which is time- and label-consuming. To address these problems, we propose Slide-SAM, which treats a stack of three adjacent slices as a prediction window. It firstly takes three slices from a 3D volume and point- or bounding box prompts on the central slice as inputs to predict segmentation masks for all three slices. Subsequently, the masks of the top and bottom slices are then used to generate new prompts for adjacent slices. Finally, step-wise prediction can be achieved by sliding the prediction window forward or backward through the entire volume. Our model is trained on multiple public and private medical datasets and demonstrates its effectiveness through extensive 3D segmetnation experiments, with the help of minimal

Semantic segmentation is a crucial task in medical imaging. Although supervised learning techniques have proven to be effective in performing this task, they heavily depend on large amounts of annotated training data. The recently introduced Segment Anything Model (SAM) enables prompt-based segmentation and offers zero-shot generalization to unfamiliar objects. In our work, we leverage SAM's abstract object understanding for medical image segmentation to provide pseudo labels for semi-supervised learning, thereby mitigating the need for extensive annotated training data. Our approach refines initial segmentations that are derived from a limited amount of annotated data (comprising up to 43 cases) by extracting bounding boxes and seed points as prompts forwarded to SAM. Thus, it enables the generation of dense segmentation masks as pseudo labels for unlabelled data. The results show that training with our pseudo labels yields an improvement in Dice score from $74.29\,\%$ to $84.17\,\%$ and from $66.63\,\%$ to $74.87\,\%$ for the segmentation of bones of the paediatric wrist and teeth in dental radiographs, respectively. As a result, our method outperforms intensity-based post-proces

The Segment Anything model (SAM) has shown a generalized ability to group image pixels into patches, but applying it to semantic-aware segmentation still faces major challenges. This paper presents SAM-CP, a simple approach that establishes two types of composable prompts beyond SAM and composes them for versatile segmentation. Specifically, given a set of classes (in texts) and a set of SAM patches, the Type-I prompt judges whether a SAM patch aligns with a text label, and the Type-II prompt judges whether two SAM patches with the same text label also belong to the same instance. To decrease the complexity in dealing with a large number of semantic classes and patches, we establish a unified framework that calculates the affinity between (semantic and instance) queries and SAM patches and merges patches with high affinity to the query. Experiments show that SAM-CP achieves semantic, instance, and panoptic segmentation in both open and closed domains. In particular, it achieves state-of-the-art performance in open-vocabulary segmentation. Our research offers a novel and generalized methodology for equipping vision foundation models like SAM with multi-grained semantic perception ab

Defect segmentation in additive manufacturing (AM) X-ray computed tomography (XCT) images remains challenging due to severe class imbalance and large distribution shifts across scan conditions. Although recent foundation models such as the Segment Anything Model (SAM) provide strong general-purpose segmentation priors, their natural-image pre-training transfers poorly to the AM XCT domain, where defects appear as subtle non-semantic microstructural anomalies. Moreover, adapting SAM to the AM domain is further limited by the large domain gap and scarcity of labeled real XCT data. We present XCT-SAM, a sequential parameter-efficient adaptation framework for AM XCT defect segmentation. Instead of adapting SAM directly from natural images to XCT data, we first fine-tune Conv-LoRA adapters on an alloy-microstructure dataset and subsequently transfer the adapted model to XCT images, progressively bridging the domain gap. Using Conv-LoRA adapters with rank r=2, the framework injects convolutional spatial inductive bias into SAM's backbone while training approximately 4.15M parameters and keeping over 99% of the model frozen. We evaluate XCT-SAM on out-of-distribution CycleGAN-XCT benchmar

Creating annotations for 3D medical data is time-consuming and often requires highly specialized expertise. Various tools have been implemented to aid this process. Segment Anything Model 2 (SAM 2) offers a general-purpose prompt-based segmentation algorithm designed to annotate videos. In this paper, we adapt this model to the annotation of 3D medical images and offer our implementation in the form of an extension to the popular annotation software: 3D Slicer. Our extension allows users to place point prompts on 2D slices to generate annotation masks and propagate these annotations across entire volumes in either single-directional or bi-directional manners. Our code is publicly available on https://github.com/mazurowski-lab/SlicerSegmentWithSAM and can be easily installed directly from the Extension Manager of 3D Slicer as well.

Access to diverse, well-annotated medical images with interactive learning tools is fundamental for training practitioners in medicine and related fields to improve their diagnostic skills and understanding of anatomical structures. While medical atlases are valuable, they are often impractical due to their size and lack of interactivity, whereas online image search may provide mislabeled or incomplete material. To address this, we propose MIRAGE, a multimodal medical text and image retrieval and generation system that allows users to find and generate clinically relevant images from trustworthy sources by mapping both text and images to a shared latent space, enabling semantically meaningful queries. The system is based on a fine-tuned medical version of CLIP (MedICaT-ROCO), trained with the ROCO dataset, obtained from PubMed Central. MIRAGE allows users to give prompts to retrieve images, generate synthetic ones through a medical diffusion model (Prompt2MedImage) and receive enriched descriptions from a large language model (Dolly-v2-3b). It also supports a dual search option, enabling the visual comparison of different medical conditions. A key advantage of the system is that it

The Segment Anything Model (SAM) has exhibited outstanding performance in various image segmentation tasks. Despite being trained with over a billion masks, SAM faces challenges in mask prediction quality in numerous scenarios, especially in real-world contexts. In this paper, we introduce a novel prompt-driven adapter into SAM, namely Prompt Adapter Segment Anything Model (PA-SAM), aiming to enhance the segmentation mask quality of the original SAM. By exclusively training the prompt adapter, PA-SAM extracts detailed information from images and optimizes the mask decoder feature at both sparse and dense prompt levels, improving the segmentation performance of SAM to produce high-quality masks. Experimental results demonstrate that our PA-SAM outperforms other SAM-based methods in high-quality, zero-shot, and open-set segmentation. We're making the source code and models available at https://github.com/xzz2/pa-sam.

Segment Anything Model (SAM) has attracted widespread attention for its superior interactive segmentation capabilities with visual prompts while lacking further exploration of text prompts. In this paper, we empirically investigate what text prompt encoders (e.g., CLIP or LLM) are good for adapting SAM for referring expression segmentation and introduce the Early Vision-language Fusion-based SAM (EVF-SAM). EVF-SAM is a simple yet effective referring segmentation method which exploits multimodal prompts (i.e., image and text) and comprises a pre-trained vision-language model to generate referring prompts and a SAM model for segmentation. Surprisingly, we observe that: (1) multimodal prompts and (2) vision-language models with early fusion (e.g., BEIT-3) are beneficial for prompting SAM for accurate referring segmentation. Our experiments show that the proposed EVF-SAM based on BEIT-3 can obtain state-of-the-art performance on RefCOCO/+/g for referring expression segmentation and demonstrate the superiority of prompting SAM with early vision-language fusion. In addition, the proposed EVF-SAM with 1.32B parameters achieves remarkably higher performance while reducing nearly 82% of par

Contrastive Language-Image Pre-training (CLIP) has demonstrated outstanding performance in global image understanding and zero-shot transfer through large-scale text-image alignment. However, the core of medical image analysis often lies in the fine-grained understanding of specific anatomical structures or lesion regions. Therefore, precisely comprehending region-of-interest (RoI) information provided by medical professionals or perception models becomes crucial. To address this need, we propose MedP-CLIP, a region-aware medical vision-language model (VLM). MedP-CLIP innovatively integrates medical prior knowledge and designs a feature-level region prompt integration mechanism, enabling it to flexibly respond to various prompt forms (e.g., points, bounding boxes, masks) while maintaining global contextual awareness when focusing on local regions. We pre-train the model on a meticulously constructed large-scale dataset (containing over 6.4 million medical images and 97.3 million region-level annotations), equipping it with cross-disease and cross-modality fine-grained spatial semantic understanding capabilities. Experiments demonstrate that MedP-CLIP significantly outperforms basel

The Segment Anything Model (SAM) has demonstrated remarkable capabilities of scaled-up segmentation models, enabling zero-shot generalization across a variety of domains. By leveraging large-scale foundational models as pre-trained models, it is a natural progression to fine-tune SAM for specific domains to further enhance performances. However, the adoption of foundational models in the medical domain presents a challenge due to the difficulty and expense of labeling sufficient data for adaptation within hospital systems. In this paper, we introduce an efficient and practical approach for fine-tuning SAM using a limited number of exemplars, making it suitable for such scenarios. Our approach combines two established techniques from the literature: an exemplar-guided synthesis module and the widely recognized Low-Rank Adaptation (LoRA) fine-tuning strategy, serving as data-level and model-level attempts respectively. Interestingly, our empirical findings suggest that SAM can be effectively aligned within the medical domain even with few labeled data. We validate our approach through experiments on brain tumor segmentation (BraTS) and multi-organ CT segmentation (Synapse). The compr

The Segment Anything Model (SAM), a profound vision foundation model pretrained on a large-scale dataset, breaks the boundaries of general segmentation and sparks various downstream applications. This paper introduces Hi-SAM, a unified model leveraging SAM for hierarchical text segmentation. Hi-SAM excels in segmentation across four hierarchies, including pixel-level text, word, text-line, and paragraph, while realizing layout analysis as well. Specifically, we first turn SAM into a high-quality pixel-level text segmentation (TS) model through a parameter-efficient fine-tuning approach. We use this TS model to iteratively generate the pixel-level text labels in a semi-automatical manner, unifying labels across the four text hierarchies in the HierText dataset. Subsequently, with these complete labels, we launch the end-to-end trainable Hi-SAM based on the TS architecture with a customized hierarchical mask decoder. During inference, Hi-SAM offers both automatic mask generation (AMG) mode and promptable segmentation (PS) mode. In the AMG mode, Hi-SAM segments pixel-level text foreground masks initially, then samples foreground points for hierarchical text mask generation and achieve

Segment Anything Model (SAM) exhibits remarkable zero-shot segmentation capability; however, its prohibitive computational costs make edge deployment challenging. Although post-training quantization (PTQ) offers a promising compression solution, existing methods yield unsatisfactory results when applied to SAM, owing to its specialized model components and promptable workflow: (i) The mask decoder's attention exhibits extreme activation outliers, and we find that aggressive clipping (even 100x), without smoothing or isolation, is effective in suppressing outliers while maintaining performance. Unfortunately, traditional distribution-based metrics (e.g., MSE) fail to provide such large-scale clipping. (ii) Existing quantization reconstruction methods neglect semantic interactivity of SAM, leading to misalignment between image feature and prompt intention. To address the above issues, we propose SAQ-SAM in this paper, which boosts PTQ for SAM from the perspective of semantic alignment. Specifically, we propose Perceptual-Consistency Clipping, which exploits attention focus overlap to promote aggressive clipping while preserving semantic capabilities. Furthermore, we propose Prompt-Aw

Segment Anything Model (SAM) has attracted significant attention due to its impressive zero-shot transfer performance and high versatility for numerous vision applications (like image editing with fine-grained control). Many of such applications need to be run on resource-constraint edge devices, like mobile phones. In this work, we aim to make SAM mobile-friendly by replacing the heavyweight image encoder with a lightweight one. A naive way to train such a new SAM as in the original SAM paper leads to unsatisfactory performance, especially when limited training sources are available. We find that this is mainly caused by the coupled optimization of the image encoder and mask decoder, motivated by which we propose decoupled distillation. Concretely, we distill the knowledge from the heavy image encoder (ViT-H in the original SAM) to a lightweight image encoder, which can be automatically compatible with the mask decoder in the original SAM. The training can be completed on a single GPU within less than one day, and the resulting lightweight SAM is termed MobileSAM which is more than 60 times smaller yet performs on par with the original SAM. For inference speed, With a single GPU,