In this work, we address various segmentation tasks, each traditionally tackled by distinct or partially unified models. We propose OMG-Seg, One Model that is Good enough to efficiently and effectively handle all the segmentation tasks, including image semantic, instance, and panoptic segmentation, as well as their video counterparts, open vocabulary settings, prompt-driven, interactive segmentation like SAM, and video object segmentation. To our knowledge, this is the first model to handle all these tasks in one model and achieve satisfactory performance. We show that OMG-Seg, a transformer-based encoder-decoder architecture with task-specific queries and outputs, can support over ten distinct segmentation tasks and yet significantly reduce computational and parameter overhead across various tasks and datasets. We rigorously evaluate the inter-task influences and correlations during co-training. Code and models are available at https://github.com/lxtGH/OMG-Seg.
Advanced by transformer architecture, vision foundation models (VFMs) achieve remarkable progress in performance and generalization ability. Segment Anything Model (SAM) is one remarkable model that can achieve generalized segmentation. However, most VFMs cannot run in realtime, which makes it difficult to transfer them into several products. On the other hand, current real-time segmentation mainly has one purpose, such as semantic segmentation on the driving scene. We argue that diverse outputs are needed for real applications. Thus, this work explores a new real-time segmentation setting, named all-purpose segmentation in real-time, to transfer VFMs in real-time deployment. It contains three different tasks, including interactive segmentation, panoptic segmentation, and video segmentation. We aim to use one model to achieve the above tasks in real-time. We first benchmark several strong baselines. Then, we present Real-Time All Purpose SAM (RAP-SAM). It contains an efficient encoder and an efficient decoupled decoder to perform prompt-driven decoding. Moreover, we further explore different training strategies and tuning methods to boost co-training performance further. Our code and model are available at https://github.com/xushilin1/RAP-SAM/.
Panoptic and instance segmentation networks are often trained with specialized object detection modules, complex loss functions, and ad-hoc post-processing steps to manage the permutation-invariance of the instance masks. This work builds upon Stable Diffusion and proposes a latent diffusion approach for panoptic segmentation, resulting in a simple architecture that omits these complexities. Our training consists of two steps: (1) training a shallow autoencoder to project the segmentation masks to latent space; (2) training a diffusion model to allow image-conditioned sampling in latent space. This generative approach unlocks the exploration of mask completion or inpainting. The experimental validation on COCO and ADE20k yields strong segmentation results. Finally, we demonstrate our model's adaptability to multi-tasking by introducing learnable task embeddings.
Interactive segmentation has gained significant attention for its application in human-computer interaction and data annotation. To address the target scale variation issue in interactive segmentation, a novel multi-scale token adaptation algorithm is proposed. By performing top-k operations across multi-scale tokens, the computational complexity is greatly simplified while ensuring performance. To enhance the robustness of multi-scale token selection, we also propose a token learning algorithm based on contrastive loss. This algorithm can effectively improve the performance of multi-scale token adaptation. Extensive benchmarking shows that the algorithm achieves state-of-the-art (SOTA) performance, compared to current methods. An interactive demo and all reproducible codes will be released at https://github.com/hahamyt/mst.
The CLIP and Segment Anything Model (SAM) are remarkable vision foundation models (VFMs). SAM excels in segmentation tasks across diverse domains, whereas CLIP is renowned for its zero-shot recognition capabilities. This paper presents an in-depth exploration of integrating these two models into a unified framework. Specifically, we introduce the Open-Vocabulary SAM, a SAM-inspired model designed for simultaneous interactive segmentation and recognition, leveraging two unique knowledge transfer modules: SAM2CLIP and CLIP2SAM. The former adapts SAM's knowledge into the CLIP via distillation and learnable transformer adapters, while the latter transfers CLIP knowledge into SAM, enhancing its recognition capabilities. Extensive experiments on various datasets and detectors show the effectiveness of Open-Vocabulary SAM in both segmentation and recognition tasks, significantly outperforming the na\"{i}ve baselines of simply combining SAM and CLIP. Furthermore, aided with image classification data training, our method can segment and recognize approximately 22,000 classes.
In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.
Biomedical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific biomedical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive and requires domain expertise. We present \emph{ScribblePrompt}, a flexible neural network based interactive segmentation tool for biomedical imaging that enables human annotators to segment previously unseen structures using scribbles, clicks, and bounding boxes. Through rigorous quantitative experiments, we demonstrate that given comparable amounts of interaction, ScribblePrompt produces more accurate segmentations than previous methods on datasets unseen during training. In a user study with domain experts, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to the next best method. ScribblePrompt's success rests on a set of careful design decisions. These include a training strategy that incorporates both a highly diverse set of images and tasks, novel algorithms for simulated user interactions and labels, and a network that enables fast inference. We showcase ScribblePrompt in an interactive demo, provide code, and release a dataset of scribble annotations at https://scribbleprompt.csail.mit.edu
Segmentation is the assigning of a semantic class to every pixel in an image and is a prerequisite for various statistical analysis tasks in materials science, like phase quantification, physics simulations or morphological characterization. The wide range of length scales, imaging techniques and materials studied in materials science means any segmentation algorithm must generalise to unseen data and support abstract, user-defined semantic classes. Trainable segmentation is a popular interactive segmentation paradigm where a classifier is trained to map from image features to user drawn labels. SAMBA is a trainable segmentation tool that uses Meta's Segment Anything Model (SAM) for fast, high-quality label suggestions and a random forest classifier for robust, generalizable segmentations. It is accessible in the browser (https://www.sambasegment.com/) without the need to download any external dependencies. The segmentation backend is run in the cloud, so does not require the user to have powerful hardware.
Deep learning has revolutionized the accurate segmentation of diseases in medical imaging. However, achieving such results requires training with numerous manual voxel annotations. This requirement presents a challenge for whole-body Positron Emission Tomography (PET) imaging, where lesions are scattered throughout the body. To tackle this problem, we introduce SW-FastEdit - an interactive segmentation framework that accelerates the labeling by utilizing only a few user clicks instead of voxelwise annotations. While prior interactive models crop or resize PET volumes due to memory constraints, we use the complete volume with our sliding window-based interactive scheme. Our model outperforms existing non-sliding window interactive models on the AutoPET dataset and generalizes to the previously unseen HECKTOR dataset. A user study revealed that annotators achieve high-quality predictions with only 10 click iterations and a low perceived NASA-TLX workload. Our framework is implemented using MONAI Label and is available: https://github.com/matt3o/AutoPET2-Submission/
Interactive segmentation model leverages prompts from users to produce robust segmentation. This advancement is facilitated by prompt engineering, where interactive prompts serve as strong priors during test-time. However, this is an inherently subjective and hard-to-reproduce process. The variability in user expertise and inherently ambiguous boundaries in medical images can lead to inconsistent prompt selections, potentially affecting segmentation accuracy. This issue has not yet been extensively explored for medical imaging. In this paper, we assess the test-time variability for interactive medical image segmentation with diverse point prompts. For a given target region, the point is classified into three sub-regions: boundary, margin, and center. Our goal is to identify a straightforward and efficient approach for optimal prompt selection during test-time based on three considerations: (1) benefits of additional prompts, (2) effects of prompt placement, and (3) strategies for optimal prompt selection. We conduct extensive experiments on the public Medical Segmentation Decathlon dataset for challenging colon tumor segmentation task. We suggest an optimal strategy for prompt selection during test-time, supported by comprehensive results. The code is publicly available at https://github.com/MedICL-VU/variability
We present Set-of-Mark (SoM), a new visual prompting method, to unleash the visual grounding abilities of large multimodal models (LMMs), such as GPT-4V. As illustrated in Fig. 1 (right), we employ off-the-shelf interactive segmentation models, such as SEEM/SAM, to partition an image into regions at different levels of granularity, and overlay these regions with a set of marks e.g., alphanumerics, masks, boxes. Using the marked image as input, GPT-4V can answer the questions that require visual grounding. We perform a comprehensive empirical study to validate the effectiveness of SoM on a wide range of fine-grained vision and multimodal tasks. For example, our experiments show that GPT-4V with SoM in zero-shot setting outperforms the state-of-the-art fully-finetuned referring expression comprehension and segmentation model on RefCOCOg. Code for SoM prompting is made public at: https://github.com/microsoft/SoM.
Vision Foundation Models (VFMs) such as the Segment Anything Model (SAM) allow zero-shot or interactive segmentation of visual contents, thus they are quickly applied in a variety of visual scenes. However, their direct use in many Remote Sensing (RS) applications is often unsatisfactory due to the special imaging characteristics of RS images. In this work, we aim to utilize the strong visual recognition capabilities of VFMs to improve the change detection of high-resolution Remote Sensing Images (RSIs). We employ the visual encoder of FastSAM, an efficient variant of the SAM, to extract visual representations in RS scenes. To adapt FastSAM to focus on some specific ground objects in the RS scenes, we propose a convolutional adaptor to aggregate the task-oriented change information. Moreover, to utilize the semantic representations that are inherent to SAM features, we introduce a task-agnostic semantic learning branch to model the semantic latent in bi-temporal RSIs. The resulting method, SAMCD, obtains superior accuracy compared to the SOTA methods and exhibits a sample-efficient learning ability that is comparable to semi-supervised CD methods. To the best of our knowledge, this is the first work that adapts VFMs for the CD of HR RSIs.
The Segment Anything Model (SAM) represents a state-of-the-art research advancement in natural image segmentation, achieving impressive results with input prompts such as points and bounding boxes. However, our evaluation and recent research indicate that directly applying the pretrained SAM to medical image segmentation does not yield satisfactory performance. This limitation primarily arises from significant domain gap between natural images and medical images. To bridge this gap, we introduce SAM-Med2D, the most comprehensive studies on applying SAM to medical 2D images. Specifically, we first collect and curate approximately 4.6M images and 19.7M masks from public and private datasets, constructing a large-scale medical image segmentation dataset encompassing various modalities and objects. Then, we comprehensively fine-tune SAM on this dataset and turn it into SAM-Med2D. Unlike previous methods that only adopt bounding box or point prompts as interactive segmentation approach, we adapt SAM to medical image segmentation through more comprehensive prompts involving bounding boxes, points, and masks. We additionally fine-tune the encoder and decoder of the original SAM to obtain a well-performed SAM-Med2D, leading to the most comprehensive fine-tuning strategies to date. Finally, we conducted a comprehensive evaluation and analysis to investigate the performance of SAM-Med2D in medical image segmentation across various modalities, anatomical structures, and organs. Concurrently, we validated the generalization capability of SAM-Med2D on 9 datasets from MICCAI 2023 challenge. Overall, our approach demonstrated significantly superior performance and generalization capability compared to SAM.
Interactive segmentation, a computer vision technique where a user provides guidance to help an algorithm segment a feature of interest in an image, has achieved outstanding accuracy and efficient human-computer interaction. However, few studies have discussed its application to remote sensing imagery, where click-based interactive segmentation could greatly facilitate the analysis of complicated landscapes. This study aims to bridge the gap between click-based interactive segmentation and remote sensing image analysis by conducting a benchmark study on various click-based interactive segmentation models. We assessed the performance of five state-of-the-art interactive segmentation methods (Reviving Iterative Training with Mask Guidance for Interactive Segmentation (RITM), FocalClick, SimpleClick, Iterative Click Loss (ICL), and Segment Anything (SAM)) on two high-resolution aerial imagery datasets. The Cascade-Forward Refinement (CFR) approach, an innovative inference strategy for interactive segmentation, was also introduced to enhance the segmentation results without requiring manual efforts. We further integrated CFR into all models for comparison. The performance of these methods on various land cover types, different object sizes, and multiple band combinations in the datasets was evaluated. The SimpleClick-CFR model consistently outperformed the other methods in our experiments. Building upon these findings, we developed a dedicated online tool called SegMap for interactive segmentation of remote sensing data. SegMap incorporates a well-performing interactive model that is fine-tuned with remote sensing data. Unlike existing interactive segmentation tools, SegMap offers robust interactivity, modifiability, and adaptability to analyze remote sensing imagery.
Tongue segmentation serves as the primary step in automated TCM tongue diagnosis, which plays a significant role in the diagnostic results. Currently, numerous deep learning based methods have achieved promising results. However, when confronted with tongue images that differ from the training set or possess challenging backgrounds, these methods demonstrate limited performance. To address this issue, this paper proposes a universal tongue segmentation model named TongueSAM based on SAM (Segment Anything Model). SAM is a large-scale pretrained interactive segmentation model known for its powerful zero-shot generalization capability. Applying SAM to tongue segmentation leverages its learned prior knowledge from natural images, enabling the achievement of zero-shot segmentation for various types of tongue images. In this study, a Prompt Generator based on object detection is integrated into SAM to enable an end-to-end automated tongue segmentation method. Experiments demonstrate that TongueSAM achieves exceptional performance across various of tongue segmentation datasets, particularly under zero-shot. Even when dealing with challenging background tongue images, TongueSAM achieves a mIoU of 95.23\% under zero-shot conditions, surpassing other segmentation methods. As far as we know, this is the first application of large-scale pretrained model for tongue segmentation. The project mentioned in this paper is currently publicly available.
Interactive image segmentation aims to segment the target from the background with the manual guidance, which takes as input multimodal data such as images, clicks, scribbles, and bounding boxes. Recently, vision transformers have achieved a great success in several downstream visual tasks, and a few efforts have been made to bring this powerful architecture to interactive segmentation task. However, the previous works neglect the relations between two modalities and directly mock the way of processing purely visual information with self-attentions. In this paper, we propose a simple yet effective network for click-based interactive segmentation with cross-modality vision transformers. Cross-modality transformers exploits mutual information to better guide the learning process. The experiments on several benchmarks show that the proposed method achieves superior performance in comparison to the previous state-of-the-art models. The stability of our method in term of avoiding failure cases shows its potential to be a practical annotation tool. The code and pretrained models will be released under https://github.com/lik1996/iCMFormer.
Integration of diverse visual prompts like clicks, scribbles, and boxes in interactive image segmentation significantly facilitates users' interaction as well as improves interaction efficiency. However, existing studies primarily encode the position or pixel regions of prompts without considering the contextual areas around them, resulting in insufficient prompt feedback, which is not conducive to performance acceleration. To tackle this problem, this paper proposes a simple yet effective Probabilistic Visual Prompt Unified Transformer (PVPUFormer) for interactive image segmentation, which allows users to flexibly input diverse visual prompts with the probabilistic prompt encoding and feature post-processing to excavate sufficient and robust prompt features for performance boosting. Specifically, we first propose a Probabilistic Prompt-unified Encoder (PPuE) to generate a unified one-dimensional vector by exploring both prompt and non-prompt contextual information, offering richer feedback cues to accelerate performance improvement. On this basis, we further present a Prompt-to-Pixel Contrastive (P$^2$C) loss to accurately align both prompt and pixel features, bridging the representation gap between them to offer consistent feature representations for mask prediction. Moreover, our approach designs a Dual-cross Merging Attention (DMA) module to implement bidirectional feature interaction between image and prompt features, generating notable features for performance improvement. A comprehensive variety of experiments on several challenging datasets demonstrates that the proposed components achieve consistent improvements, yielding state-of-the-art interactive segmentation performance. Our code is available at https://github.com/XuZhang1211/PVPUFormer.
In this work, we explore regions as a potential visual analogue of words for self-supervised image representation learning. Inspired by Masked Autoencoding (MAE), a generative pre-training baseline, we propose masked region autoencoding to learn from groups of pixels or regions. Specifically, we design an architecture which efficiently addresses the one-to-many mapping between images and regions, while being highly effective especially with high-quality regions. When integrated with MAE, our approach (R-MAE) demonstrates consistent improvements across various pre-training datasets and downstream detection and segmentation benchmarks, with negligible computational overheads. Beyond the quantitative evaluation, our analysis indicates the models pre-trained with masked region autoencoding unlock the potential for interactive segmentation. The code is provided at https://github.com/facebookresearch/r-mae.
Automatic segmentation of medical images is a key step for diagnostic and interventional tasks. However, achieving this requires large amounts of annotated volumes, which can be tedious and time-consuming task for expert annotators. In this paper, we introduce DeepEdit, a deep learning-based method for volumetric medical image annotation, that allows automatic and semi-automatic segmentation, and click-based refinement. DeepEdit combines the power of two methods: a non-interactive (i.e. automatic segmentation using nnU-Net, UNET or UNETR) and an interactive segmentation method (i.e. DeepGrow), into a single deep learning model. It allows easy integration of uncertainty-based ranking strategies (i.e. aleatoric and epistemic uncertainty computation) and active learning. We propose and implement a method for training DeepEdit by using standard training combined with user interaction simulation. Once trained, DeepEdit allows clinicians to quickly segment their datasets by using the algorithm in auto segmentation mode or by providing clicks via a user interface (i.e. 3D Slicer, OHIF). We show the value of DeepEdit through evaluation on the PROSTATEx dataset for prostate/prostatic lesions and the Multi-Atlas Labeling Beyond the Cranial Vault (BTCV) dataset for abdominal CT segmentation, using state-of-the-art network architectures as baseline for comparison. DeepEdit could reduce the time and effort annotating 3D medical images compared to DeepGrow alone. Source code is available at https://github.com/Project-MONAI/MONAILabel
Large foundation models, known for their strong zero-shot generalization, have excelled in visual and language applications. However, applying them to medical image segmentation, a domain with diverse imaging types and target labels, remains an open challenge. Current approaches, such as adapting interactive segmentation models like Segment Anything Model (SAM), require user prompts for each sample during inference. Alternatively, transfer learning methods like few/one-shot models demand labeled samples, leading to high costs. This paper introduces a new paradigm toward the universal medical image segmentation, termed 'One-Prompt Segmentation.' One-Prompt Segmentation combines the strengths of one-shot and interactive methods. In the inference stage, with just \textbf{one prompted sample}, it can adeptly handle the unseen task in a single forward pass. We train One-Prompt Model on 64 open-source medical datasets, accompanied by the collection of over 3,000 clinician-labeled prompts. Tested on 14 previously unseen datasets, the One-Prompt Model showcases superior zero-shot segmentation capabilities, outperforming a wide range of related methods. The code and data is released as https://github.com/KidsWithTokens/one-prompt.