Placenta volume measured from 3D ultrasound (3DUS) images is an important tool for tracking the growth trajectory and is associated with pregnancy outcomes. Manual segmentation is the gold standard, but it is time-consuming and subjective. Although fully automated deep learning algorithms perform well, they do not always yield high-quality results for each case. Interactive segmentation models could address this issue. However, there is limited work on interactive segmentation models for the placenta. Despite their segmentation accuracy, these methods may not be feasible for clinical use as they require relatively large computational power which may be especially prohibitive in low-resource environments, or on mobile devices. In this paper, we propose a lightweight interactive segmentation model aiming for clinical use to interactively segment the placenta from 3DUS images in real-time. The proposed model adopts the segmentation from our fully automated model for initialization and is designed in a human-in-the-loop manner to achieve iterative improvements. The Dice score and normalized surface Dice are used as evaluation metrics. The results show that our model can achieve superior performance in segmentation compared to state-of-the-art models while using significantly fewer parameters. Additionally, the proposed model is much faster for inference and robust to poor initial masks. The code is available at https://github.com/MedICL-VU/PRISM-placenta.
Interactive segmentation algorithms based on click points have garnered significant attention from researchers in recent years. However, existing studies typically use sparse click maps as model inputs to segment specific target objects, which primarily affect local regions and have limited abilities to focus on the whole target object, leading to increased times of clicks. In addition, most existing algorithms can not balance well between high performance and efficiency. To address this issue, we propose a click attention algorithm that expands the influence range of positive clicks based on the similarity between positively-clicked regions and the whole input. We also propose a discriminative affinity loss to reduce the attention coupling between positive and negative click regions to avoid an accuracy decrease caused by mutual interference between positive and negative clicks. Extensive experiments demonstrate that our approach is superior to existing methods and achieves cutting-edge performance in fewer parameters. An interactive demo and all reproducible codes will be released at https://github.com/hahamyt/ClickAttention.
Medical image segmentation plays a pivotal role in clinical diagnostics and treatment planning, yet existing models often face challenges in generalization and in handling both 2D and 3D data uniformly. In this paper, we introduce Medical SAM 2 (MedSAM-2), a generalized auto-tracking model for universal 2D and 3D medical image segmentation. The core concept is to leverage the Segment Anything Model 2 (SAM2) pipeline to treat all 2D and 3D medical segmentation tasks as a video object tracking problem. To put it into practice, we propose a novel \emph{self-sorting memory bank} mechanism that dynamically selects informative embeddings based on confidence and dissimilarity, regardless of temporal order. This mechanism not only significantly improves performance in 3D medical image segmentation but also unlocks a \emph{One-Prompt Segmentation} capability for 2D images, allowing segmentation across multiple images from a single prompt without temporal relationships. We evaluated MedSAM-2 on five 2D tasks and nine 3D tasks, including white blood cells, optic cups, retinal vessels, mandibles, coronary arteries, kidney tumors, liver tumors, breast cancer, nasopharynx cancer, vestibular schwannoma, mediastinal lymph nodules, cerebral artery, inferior alveolar nerve, and abdominal organs, comparing it against state-of-the-art (SOTA) models in task-tailored, general and interactive segmentation settings. Our findings demonstrate that MedSAM-2 surpasses a wide range of existing models and updates new SOTA on several benchmarks. The code is released on the project page: https://supermedintel.github.io/Medical-SAM2/.
Accurate segmentation of anatomical structures and pathological regions in medical images is crucial for diagnosis, treatment planning, and disease monitoring. While the Segment Anything Model (SAM) and its variants have demonstrated impressive interactive segmentation capabilities on image types not seen during training without the need for domain adaptation or retraining, their practical application in volumetric 3D medical imaging workflows has been hindered by the lack of a user-friendly interface. To address this challenge, we introduce FastSAM-3DSlicer, a 3D Slicer extension that integrates both 2D and 3D SAM models, including SAM-Med2D, MedSAM, SAM-Med3D, and FastSAM-3D. Building on the well-established open-source 3D Slicer platform, our extension enables efficient, real-time segmentation of 3D volumetric medical images, with seamless interaction and visualization. By automating the handling of raw image data, user prompts, and segmented masks, FastSAM-3DSlicer provides a streamlined, user-friendly interface that can be easily incorporated into medical image analysis workflows. Performance evaluations reveal that the FastSAM-3DSlicer extension running FastSAM-3D achieves low inference times of only 1.09 seconds per volume on CPU and 0.73 seconds per volume on GPU, making it well-suited for real-time interactive segmentation. Moreover, we introduce an uncertainty quantification scheme that leverages the rapid inference capabilities of FastSAM-3D for practical implementation, further enhancing its reliability and applicability in medical settings. FastSAM-3DSlicer offers an interactive platform and user interface for 2D and 3D interactive volumetric medical image segmentation, offering a powerful combination of efficiency, precision, and ease of use with SAMs. The source code and a video demonstration are publicly available at https://github.com/arcadelab/FastSAM3D_slicer.
In this paper we introduce a new dataset containing instance segmentation masks for ten different categories of winter sports equipment, called WSESeg (Winter Sports Equipment Segmentation). Furthermore, we carry out interactive segmentation experiments on said dataset to explore possibilities for efficient further labeling. The SAM and HQ-SAM models are conceptualized as foundation models for performing user guided segmentation. In order to measure their claimed generalization capability we evaluate them on WSESeg. Since interactive segmentation offers the benefit of creating easily exploitable ground truth data during test-time, we are going to test various online adaptation methods for the purpose of exploring potentials for improvements without having to fine-tune the models explicitly. Our experiments show that our adaptation methods drastically reduce the Failure Rate (FR) and Number of Clicks (NoC) metrics, which generally leads faster to better interactive segmentation results.
Placenta volume measurement from 3D ultrasound images is critical for predicting pregnancy outcomes, and manual annotation is the gold standard. However, such manual annotation is expensive and time-consuming. Automated segmentation algorithms can often successfully segment the placenta, but these methods may not consistently produce robust segmentations suitable for practical use. Recently, inspired by the Segment Anything Model (SAM), deep learning-based interactive segmentation models have been widely applied in the medical imaging domain. These models produce a segmentation from visual prompts provided to indicate the target region, which may offer a feasible solution for practical use. However, none of these models are specifically designed for interactively segmenting 3D ultrasound images, which remain challenging due to the inherent noise of this modality. In this paper, we evaluate publicly available state-of-the-art 3D interactive segmentation models in contrast to a human-in-the-loop approach for the placenta segmentation task. The Dice score, normalized surface Dice, averaged symmetric surface distance, and 95-percent Hausdorff distance are used as evaluation metrics. We consider a Dice score of 0.95 a successful segmentation. Our results indicate that the human-in-the-loop segmentation model reaches this standard. Moreover, we assess the efficiency of the human-in-the-loop model as a function of the amount of prompts. Our results demonstrate that the human-in-the-loop model is both effective and efficient for interactive placenta segmentation. The code is available at \url{https://github.com/MedICL-VU/PRISM-placenta}.
The Segment Anything Model (SAM) has advanced interactive segmentation but is limited by the high computational cost on high-resolution images. This requires downsampling to meet GPU constraints, sacrificing the fine-grained details needed for high-precision interactive segmentation. To address SAM's limitations, we focus on visual length extrapolation and propose a lightweight model named HRSAM. The extrapolation enables HRSAM trained on low resolutions to generalize to high resolutions. We begin by finding the link between the extrapolation and attention scores, which leads us to base HRSAM on Swin attention. We then introduce the Flexible Local Attention (FLA) framework, using CUDA-optimized Efficient Memory Attention to accelerate HRSAM. Within FLA, we implement Flash Swin attention, achieving over a 35% speedup compared to traditional Swin attention, and propose a KV-only padding mechanism to enhance extrapolation. We also develop the Cycle-scan module that uses State Space models to efficiently expand HRSAM's receptive field. We further develop the HRSAM++ within FLA by adding an anchor map, providing multi-scale data augmentation for the extrapolation and a larger receptive field at slight computational cost. Experiments show that, under standard training, HRSAMs surpass the previous SOTA with only 38% of the latency. With SAM-distillation, the extrapolation enables HRSAMs to outperform the teacher model at lower latency. Further finetuning achieves performance significantly exceeding the previous SOTA.
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 parameters compared to previous SAM methods based on large multimodal models.
Herein, we present CoDA, the Coral Dendroid structure Analyzer, a visual analytics suite that allows for the first time to investigate the ontogenetic morphological development of complex dendroid coral colonies, exemplified on three important framework-forming dendroid cold-water corals: Lophelia pertusa (Linnaeus, 1758), Madrepora oculata (Linnaeus, 1758), and Goniocorella dumosa (Alcock, 1902). Input to CoDA is an initial instance segmentation of the coral polyp cavities (calices), from which it estimates the skeleton tree of the colony and extracts classical morphological measurements and advanced shape features of the individual corallites. CoDA also works as a proofreading and error correction tool by helping to identify wrong parts in the skeleton tree and providing tools to quickly correct these errors. The final skeleton tree enables the derivation of additional information about the calices/corallite instances that otherwise could not be obtained, including their ontogenetic generation and branching patterns - the basis of a fully quantitative statistical analysis of the coral colony morphology. Part of CoDA is CoDAGraph, a feature-rich link-and-brush user interface for visualizing the extracted features and 2D graph layouts of the skeleton tree, enabling the real-time exploration of complex coral colonies and their building blocks, the individual corallites and branches. In the future, we expect CoDA to greatly facilitate the analysis of large stony corals of different species and morphotypes, as well as other dendroid structures, enabling new insights into the influence of genetic and environmental factors on their ontogenetic morphological development.
Medical image segmentation is a core component of precision medicine, and 3D computed tomography (CT) is one of the most important imaging techniques. A highly accurate and clinically applicable segmentation foundation model will greatly facilitate clinicians and researchers using CT images. Although existing foundation models have attracted great interest, none are adequate for 3D CT, either because they lack accurate automatic segmentation for large cohort analysis or the ability to segment novel classes. An ideal segmentation solution should possess two features: accurate out-of-the-box performance covering major organ classes, and effective adaptation or zero-shot ability to novel structures. To achieve this goal, we introduce Versatile Imaging SegmenTation and Annotation model (VISTA3D). VISTA3D is trained systematically on 11454 volumes and provides accurate out-of-the-box segmentation for 127 common types of human anatomical structures and various lesions. Additionally, VISTA3D supports 3D interactive segmentation, allowing convenient editing of automatic results and achieving state-of-the-art annotation results on unseen classes. The novel model design and training recipe represent a promising step toward developing a versatile medical image foundation model and will serve as a valuable foundation for CT image analysis. Code and model weights are available at https://github.com/Project-MONAI/VISTA
Removing reflection from a single image is challenging due to the absence of general reflection priors. Although existing methods incorporate extensive user guidance for satisfactory performance, they often lack the flexibility to adapt user guidance in different modalities, and dense user interactions further limit their practicality. To alleviate these problems, this paper presents FIRM, a novel framework for Flexible Interactive image Reflection reMoval with various forms of guidance, where users can provide sparse visual guidance (e.g., points, boxes, or strokes) or text descriptions for better reflection removal. Firstly, we design a novel user guidance conversion module (UGC) to transform different forms of guidance into unified contrastive masks. The contrastive masks provide explicit cues for identifying reflection and transmission layers in blended images. Secondly, we devise a contrastive mask-guided reflection removal network that comprises a newly proposed contrastive guidance interaction block (CGIB). This block leverages a unique cross-attention mechanism that merges contrastive masks with image features, allowing for precise layer separation. The proposed framework requires only 10\% of the guidance time needed by previous interactive methods, which makes a step-change in flexibility. Extensive results on public real-world reflection removal datasets validate that our method demonstrates state-of-the-art reflection removal performance. Code is avaliable at https://github.com/ShawnChenn/FlexibleReflectionRemoval.
The Segment Anything Model (SAM) marks a notable milestone in segmentation models, highlighted by its robust zero-shot capabilities and ability to handle diverse prompts. SAM follows a pipeline that separates interactive segmentation into image preprocessing through a large encoder and interactive inference via a lightweight decoder, ensuring efficient real-time performance. However, SAM faces stability issues in challenging samples upon this pipeline. These issues arise from two main factors. Firstly, the image preprocessing disables SAM from dynamically using image-level zoom-in strategies to refocus on the target object during interaction. Secondly, the lightweight decoder struggles to sufficiently integrate interactive information with image embeddings. To address these two limitations, we propose FocSAM with a pipeline redesigned on two pivotal aspects. First, we propose Dynamic Window Multi-head Self-Attention (Dwin-MSA) to dynamically refocus SAM's image embeddings on the target object. Dwin-MSA localizes attention computations around the target object, enhancing object-related embeddings with minimal computational overhead. Second, we propose Pixel-wise Dynamic ReLU (P-DyReLU) to enable sufficient integration of interactive information from a few initial clicks that have significant impacts on the overall segmentation results. Experimentally, FocSAM augments SAM's interactive segmentation performance to match the existing state-of-the-art method in segmentation quality, requiring only about 5.6% of this method's inference time on CPUs.
Click-point-based interactive segmentation has received widespread attention due to its efficiency. However, it's hard for existing algorithms to obtain precise and robust responses after multiple clicks. In this case, the segmentation results tend to have little change or are even worse than before. To improve the robustness of the response, we propose a structured click intent model based on graph neural networks, which adaptively obtains graph nodes via the global similarity of user-clicked Transformer tokens. Then the graph nodes will be aggregated to obtain structured interaction features. Finally, the dual cross-attention will be used to inject structured interaction features into vision Transformer features, thereby enhancing the control of clicks over segmentation results. Extensive experiments demonstrated the proposed algorithm can serve as a general structure in improving Transformer-based interactive segmenta?tion performance. The code and data will be released at https://github.com/hahamyt/scc.
Interactive Segmentation (IS) segments specific objects or parts in the image according to user input. Current IS pipelines fall into two categories: single-granularity output and multi-granularity output. The latter aims to alleviate the spatial ambiguity present in the former. However, the multi-granularity output pipeline suffers from limited interaction flexibility and produces redundant results. In this work, we introduce Granularity-Controllable Interactive Segmentation (GraCo), a novel approach that allows precise control of prediction granularity by introducing additional parameters to input. This enhances the customization of the interactive system and eliminates redundancy while resolving ambiguity. Nevertheless, the exorbitant cost of annotating multi-granularity masks and the lack of available datasets with granularity annotations make it difficult for models to acquire the necessary guidance to control output granularity. To address this problem, we design an any-granularity mask generator that exploits the semantic property of the pre-trained IS model to automatically generate abundant mask-granularity pairs without requiring additional manual annotation. Based on these pairs, we propose a granularity-controllable learning strategy that efficiently imparts the granularity controllability to the IS model. Extensive experiments on intricate scenarios at object and part levels demonstrate that our GraCo has significant advantages over previous methods. This highlights the potential of GraCo to be a flexible annotation tool, capable of adapting to diverse segmentation scenarios. The project page: https://zhao-yian.github.io/GraCo.
In recent interactive segmentation algorithms, previous probability maps are used as network input to help predictions in the current segmentation round. However, despite the utilization of previous masks, useful information contained in the probability maps is not well propagated to the current predictions. In this paper, to overcome this limitation, we propose a novel and effective algorithm for click-based interactive image segmentation, called MFP, which attempts to make full use of probability maps. We first modulate previous probability maps to enhance their representations of user-specified objects. Then, we feed the modulated probability maps as additional input to the segmentation network. We implement the proposed MFP algorithm based on the ResNet-34, HRNet-18, and ViT-B backbones and assess the performance extensively on various datasets. It is demonstrated that MFP meaningfully outperforms the existing algorithms using identical backbones. The source codes are available at \href{https://github.com/cwlee00/MFP}{https://github.com/cwlee00/MFP}.
In this paper, we present PRISM, a Promptable and Robust Interactive Segmentation Model, aiming for precise segmentation of 3D medical images. PRISM accepts various visual inputs, including points, boxes, and scribbles as sparse prompts, as well as masks as dense prompts. Specifically, PRISM is designed with four principles to achieve robustness: (1) Iterative learning. The model produces segmentations by using visual prompts from previous iterations to achieve progressive improvement. (2) Confidence learning. PRISM employs multiple segmentation heads per input image, each generating a continuous map and a confidence score to optimize predictions. (3) Corrective learning. Following each segmentation iteration, PRISM employs a shallow corrective refinement network to reassign mislabeled voxels. (4) Hybrid design. PRISM integrates hybrid encoders to better capture both the local and global information. Comprehensive validation of PRISM is conducted using four public datasets for tumor segmentation in the colon, pancreas, liver, and kidney, highlighting challenges caused by anatomical variations and ambiguous boundaries in accurate tumor identification. Compared to state-of-the-art methods, both with and without prompt engineering, PRISM significantly improves performance, achieving results that are close to human levels. The code is publicly available at https://github.com/MedICL-VU/PRISM.
The goal of interactive image segmentation is to delineate specific regions within an image via visual or language prompts. Low-latency and high-quality interactive segmentation with diverse prompts remain challenging for existing specialist and generalist models. Specialist models, with their limited prompts and task-specific designs, experience high latency because the image must be recomputed every time the prompt is updated, due to the joint encoding of image and visual prompts. Generalist models, exemplified by the Segment Anything Model (SAM), have recently excelled in prompt diversity and efficiency, lifting image segmentation to the foundation model era. However, for high-quality segmentations, SAM still lags behind state-of-the-art specialist models despite SAM being trained with x100 more segmentation masks. In this work, we delve deep into the architectural differences between the two types of models. We observe that dense representation and fusion of visual prompts are the key design choices contributing to the high segmentation quality of specialist models. In light of this, we reintroduce this dense design into the generalist models, to facilitate the development of generalist models with high segmentation quality. To densely represent diverse visual prompts, we propose to use a dense map to capture five types: clicks, boxes, polygons, scribbles, and masks. Thus, we propose SegNext, a next-generation interactive segmentation approach offering low latency, high quality, and diverse prompt support. Our method outperforms current state-of-the-art methods on HQSeg-44K and DAVIS, both quantitatively and qualitatively.
Prominent solutions for medical image segmentation are typically tailored for automatic or interactive setups, posing challenges in facilitating progress achieved in one task to another.$_{\!}$ This$_{\!}$ also$_{\!}$ necessitates$_{\!}$ separate$_{\!}$ models for each task, duplicating both training time and parameters.$_{\!}$ To$_{\!}$ address$_{\!}$ above$_{\!}$ issues,$_{\!}$ we$_{\!}$ introduce$_{\!}$ S2VNet,$_{\!}$ a$_{\!}$ universal$_{\!}$ framework$_{\!}$ that$_{\!}$ leverages$_{\!}$ Slice-to-Volume$_{\!}$ propagation$_{\!}$ to$_{\!}$ unify automatic/interactive segmentation within a single model and one training session. Inspired by clustering-based segmentation techniques, S2VNet makes full use of the slice-wise structure of volumetric data by initializing cluster centers from the cluster$_{\!}$ results$_{\!}$ of$_{\!}$ previous$_{\!}$ slice.$_{\!}$ This enables knowledge acquired from prior slices to assist in the segmentation of the current slice, further efficiently bridging the communication between remote slices using mere 2D networks. Moreover, such a framework readily accommodates interactive segmentation with no architectural change, simply by initializing centroids from user inputs. S2VNet distinguishes itself by swift inference speeds and reduced memory consumption compared to prevailing 3D solutions. It can also handle multi-class interactions with each of them serving to initialize different centroids. Experiments on three benchmarks demonstrate S2VNet surpasses task-specified solutions on both automatic/interactive setups.
Segment anything model (SAM) demonstrates strong generalization ability on natural image segmentation. However, its direct adaptation in medical image segmentation tasks shows significant performance drops. It also requires an excessive number of prompt points to obtain a reasonable accuracy. Although quite a few studies explore adapting SAM into medical image volumes, the efficiency of 2D adaptation methods is unsatisfactory and 3D adaptation methods are only capable of segmenting specific organs/tumors. In this work, we propose a comprehensive and scalable 3D SAM model for whole-body CT segmentation, named CT-SAM3D. Instead of adapting SAM, we propose a 3D promptable segmentation model using a (nearly) fully labeled CT dataset. To train CT-SAM3D effectively, ensuring the model's accurate responses to higher-dimensional spatial prompts is crucial, and 3D patch-wise training is required due to GPU memory constraints. Therefore, we propose two key technical developments: 1) a progressively and spatially aligned prompt encoding method to effectively encode click prompts in local 3D space; and 2) a cross-patch prompt scheme to capture more 3D spatial context, which is beneficial for reducing the editing workloads when interactively prompting on large organs. CT-SAM3D is trained using a curated dataset of 1204 CT scans containing 107 whole-body anatomies and extensively validated using five datasets, achieving significantly better results against all previous SAM-derived models. Code, data, and our 3D interactive segmentation tool with quasi-real-time responses are available at https://github.com/alibaba-damo-academy/ct-sam3d.
Interactive segmentation, an integration of AI algorithms and human expertise, premises to improve the accuracy and efficiency of curating large-scale, detailed-annotated datasets in healthcare. Human experts revise the annotations predicted by AI, and in turn, AI improves its predictions by learning from these revised annotations. This interactive process continues to enhance the quality of annotations until no major revision is needed from experts. The key challenge is how to leverage AI predicted and expert revised annotations to iteratively improve the AI. Two problems arise: (1) The risk of catastrophic forgetting--the AI tends to forget the previously learned classes if it is only retrained using the expert revised classes. (2) Computational inefficiency when retraining the AI using both AI predicted and expert revised annotations; moreover, given the dominant AI predicted annotations in the dataset, the contribution of newly revised annotations--often account for a very small fraction--to the AI training remains marginal. This paper proposes Continual Tuning to address the problems from two perspectives: network design and data reuse. Firstly, we design a shared network for all classes followed by class-specific networks dedicated to individual classes. To mitigate forgetting, we freeze the shared network for previously learned classes and only update the class-specific network for revised classes. Secondly, we reuse a small fraction of data with previous annotations to avoid over-computing. The selection of such data relies on the importance estimate of each data. The importance score is computed by combining the uncertainty and consistency of AI predictions. Our experiments demonstrate that Continual Tuning achieves a speed 16x greater than repeatedly training AI from scratch without compromising the performance.