Recent progress in interactive point prompt based Image Segmentation allows to significantly reduce the manual effort to obtain high quality semantic labels. State-of-the-art unsupervised methods use self-supervised pre-trained models to obtain pseudo-labels which are used in training a prompt-based segmentation model. In this paper, we propose a novel unsupervised and training-free approach based solely on the self-attention of Stable Diffusion. We interpret the self-attention tensor as a Markov transition operator, which enables us to iteratively construct a Markov chain. Pixel-wise counting of the required number of iterations along the Markov-chain to reach a relative probability threshold yields a Markov-iteration-map, which we simply call a Markov-map. Compared to the raw attention maps, we show that our proposed Markov-map has less noise, sharper semantic boundaries and more uniform values within semantically similar regions. We integrate the Markov-map in a simple yet effective truncated nearest neighbor framework to obtain interactive point prompt based segmentation. Despite being training-free, we experimentally show that our approach yields excellent results in terms of Number of Clicks (NoC), even outperforming state-of-the-art training based unsupervised methods in most of the datasets.
Automatic melanoma segmentation is essential for early skin cancer detection, yet challenges arise from the heterogeneity of melanoma, as well as interfering factors like blurred boundaries, low contrast, and imaging artifacts. While numerous algorithms have been developed to address these issues, previous approaches have often overlooked the need to jointly capture spatial and sequential features within dermatological images. This limitation hampers segmentation accuracy, especially in cases with indistinct borders or structurally similar lesions. Additionally, previous models lacked both a global receptive field and high computational efficiency. In this work, we present the xLSTM-VMUNet Model, which jointly capture spatial and sequential features within dermatological images successfully. xLSTM-VMUNet can not only specialize in extracting spatial features from images, focusing on the structural characteristics of skin lesions, but also enhance contextual understanding, allowing more effective handling of complex medical image structures. Experiment results on the ISIC2018 dataset demonstrate that xLSTM-VMUNet outperforms VMUNet by 4.85% on DSC and 6.41% on IoU on the ISIC2017 dataset, by 1.25% on DSC and 2.07% on IoU on the ISIC2018 dataset, with faster convergence and consistently high segmentation performance. Our code is available at https://github.com/FangZhuoyi/XLSTM-VMUNet.
Accurate segmentation of retinal images plays a crucial role in aiding ophthalmologists in diagnosing retinopathy of prematurity (ROP) and assessing its severity. However, due to their underdeveloped, thinner vessels, manual annotation in infant fundus images is very complex, and this presents challenges for fully supervised learning. To address the scarcity of annotations, we propose a semi supervised segmentation framework designed to advance ROP studies without the need for extensive manual vessel annotation. Unlike previous methods that rely solely on limited labeled data, our approach leverages teacher student learning by integrating two powerful components: an uncertainty weighted vessel unveiling module and domain adversarial learning. The vessel unveiling module helps the model effectively reveal obscured and hard to detect vessel structures, while adversarial training aligns feature representations across different domains, ensuring robust and generalizable vessel segmentations. We validate our approach on public datasets (CHASEDB, STARE) and an in-house ROP dataset, demonstrating its superior performance across multiple evaluation metrics. Additionally, we extend the model's utility to a downstream task of ROP multi-stage classification, where vessel masks extracted by our segmentation model improve diagnostic accuracy. The promising results in classification underscore the model's potential for clinical application, particularly in early-stage ROP diagnosis and intervention. Overall, our work offers a scalable solution for leveraging unlabeled data in pediatric ophthalmology, opening new avenues for biomarker discovery and clinical research.
Accurate left atrium (LA) segmentation from pre-operative scans is crucial for diagnosing atrial fibrillation, treatment planning, and supporting surgical interventions. While deep learning models are key in medical image segmentation, they often require extensive manually annotated data. Foundation models trained on larger datasets have reduced this dependency, enhancing generalizability and robustness through transfer learning. We explore DINOv2, a self-supervised learning vision transformer trained on natural images, for LA segmentation using MRI. The challenges for LA's complex anatomy, thin boundaries, and limited annotated data make accurate segmentation difficult before & during the image-guided intervention. We demonstrate DINOv2's ability to provide accurate & consistent segmentation, achieving a mean Dice score of .871 & a Jaccard Index of .792 for end-to-end fine-tuning. Through few-shot learning across various data sizes & patient counts, DINOv2 consistently outperforms baseline models. These results suggest that DINOv2 effectively adapts to MRI with limited data, highlighting its potential as a competitive tool for segmentation & encouraging broader use in medical imaging.
3D microscopic cerebrovascular images are characterized by their high resolution, presenting significant annotation challenges, large data volumes, and intricate variations in detail. Together, these factors make achieving high-quality, efficient whole-brain segmentation particularly demanding. In this paper, we propose a novel Vessel-Pattern-Based Semi-Supervised Distillation pipeline (VpbSD) to address the challenges of 3D microscopic cerebrovascular segmentation. This pipeline initially constructs a vessel-pattern codebook that captures diverse vascular structures from unlabeled data during the teacher model's pretraining phase. In the knowledge distillation stage, the codebook facilitates the transfer of rich knowledge from a heterogeneous teacher model to a student model, while the semi-supervised approach further enhances the student model's exposure to diverse learning samples. Experimental results on real-world data, including comparisons with state-of-the-art methods and ablation studies, demonstrate that our pipeline and its individual components effectively address the challenges inherent in microscopic cerebrovascular segmentation.
Despite significant advancements, segmentation based on deep neural networks in medical and surgical imaging faces several challenges, two of which we aim to address in this work. First, acquiring complete pixel-level segmentation labels for medical images is time-consuming and requires domain expertise. Second, typical segmentation pipelines cannot detect out-of-distribution (OOD) pixels, leaving them prone to spurious outputs during deployment. In this work, we propose a novel segmentation approach exploiting OOD detection that learns only from sparsely annotated pixels from multiple positive-only classes. These multi-class positive annotations naturally fall within the in-distribution (ID) set. Unlabelled pixels may contain positive classes but also negative ones, including what is typically referred to as \emph{background} in standard segmentation formulations. Here, we forgo the need for background annotation and consider these together with any other unseen classes as part of the OOD set. Our framework can integrate, at a pixel-level, any OOD detection approaches designed for classification tasks. To address the lack of existing OOD datasets and established evaluation metric for medical image segmentation, we propose a cross-validation strategy that treats held-out labelled classes as OOD. Extensive experiments on both multi-class hyperspectral and RGB surgical imaging datasets demonstrate the robustness and generalisation capability of our proposed framework.
Remote sensing (RS) involves the acquisition of data about objects or areas from a distance, primarily to monitor environmental changes, manage resources, and support planning and disaster response. A significant challenge in RS segmentation is the scarcity of high-quality labeled images due to the diversity and complexity of RS image, which makes pixel-level annotation difficult and hinders the development of effective supervised segmentation algorithms. To solve this problem, we propose Adaptively Augmented Consistency Learning (AACL), a semi-supervised segmentation framework designed to enhances RS segmentation accuracy under condictions of limited labeled data. AACL extracts additional information embedded in unlabeled images through the use of Uniform Strength Augmentation (USAug) and Adaptive Cut-Mix (AdaCM). Evaluations across various RS datasets demonstrate that AACL achieves competitive performance in semi-supervised segmentation, showing up to a 20% improvement in specific categories and 2% increase in overall performance compared to state-of-the-art frameworks.
Thoracic trauma often results in rib fractures, which demand swift and accurate diagnosis for effective treatment. However, detecting these fractures on rib CT scans poses considerable challenges, involving the analysis of many image slices in sequence. Despite notable advancements in algorithms for automated fracture segmentation, the persisting challenges stem from the diverse shapes and sizes of these fractures. To address these issues, this study introduces a sophisticated deep-learning model with an auxiliary classification task designed to enhance the accuracy of rib fracture segmentation. The auxiliary classification task is crucial in distinguishing between fractured ribs and negative regions, encompassing non-fractured ribs and surrounding tissues, from the patches obtained from CT scans. By leveraging this auxiliary task, the model aims to improve feature representation at the bottleneck layer by highlighting the regions of interest. Experimental results on the RibFrac dataset demonstrate significant improvement in segmentation performance.
Vision Transformers (ViT) have recently brought a new wave of research in the field of computer vision. These models have done particularly well in the field of image classification and segmentation. Research on semantic and instance segmentation has emerged to accelerate with the inception of the new architecture, with over 80\% of the top 20 benchmarks for the iSAID dataset being either based on the ViT architecture or the attention mechanism behind its success. This paper focuses on the heuristic comparison of three key factors of using (or not using) ViT for semantic segmentation of remote sensing aerial images on the iSAID. The experimental results observed during the course of the research were under the scrutinization of the following objectives: 1. Use of weighted fused loss function for the maximum mean Intersection over Union (mIoU) score, Dice score, and minimization or conservation of entropy or class representation, 2. Comparison of transfer learning on Meta's MaskFormer, a ViT-based semantic segmentation model, against generic UNet Convolutional Neural Networks (CNNs) judged over mIoU, Dice scores, training efficiency, and inference time, and 3. What do we lose for what we gain? i.e., the comparison of the two models against current state-of-art segmentation models. We show the use of the novel combined weighted loss function significantly boosts the CNN model's performance capacities as compared to transfer learning the ViT. The code for this implementation can be found on \url{https://github.com/ashimdahal/ViT-vs-CNN-ImageSegmentation}.
While Contrastive Language-Image Pre-training (CLIP) has advanced open-vocabulary predictions, its performance on semantic segmentation remains suboptimal. This shortfall primarily stems from its spatial-invariant semantic features and constrained resolution. While previous adaptations addressed spatial invariance semantic by modifying the self-attention in CLIP's image encoder, the issue of limited resolution remains unexplored. Different from previous segment-then-splice methods that segment sub-images via a sliding window and splice the results, we introduce a splice-then-segment paradigm that incorporates Segment-Anything Model (SAM) to tackle the resolution issue since SAM excels at extracting fine-grained semantic correlations from high-resolution images. Specifically, we introduce Trident, a training-free framework that first splices features extracted by CLIP and DINO from sub-images, then leverages SAM's encoder to create a correlation matrix for global aggregation, enabling a broadened receptive field for effective segmentation. Besides, we propose a refinement strategy for CLIP's coarse segmentation outputs by transforming them into prompts for SAM, further enhancing the segmentation performance. Trident achieves a significant improvement in the mIoU across eight benchmarks compared with the current SOTA, increasing from 44.4 to 48.6.Code is available at https://github.com/YuHengsss/Trident.
The Segment Anything Model (SAM) and similar models build a family of promptable foundation models (FMs) for image and video segmentation. The object of interest is identified using prompts, such as bounding boxes or points. With these FMs becoming part of medical image segmentation, extensive evaluation studies are required to assess their strengths and weaknesses in clinical setting. Since the performance is highly dependent on the chosen prompting strategy, it is important to investigate different prompting techniques to define optimal guidelines that ensure effective use in medical image segmentation. Currently, no dedicated evaluation studies exist specifically for bone segmentation in CT scans, leaving a gap in understanding the performance for this task. Thus, we use non-iterative, ``optimal'' prompting strategies composed of bounding box, points and combinations to test the zero-shot capability of SAM-family models for bone CT segmentation on three different skeletal regions. Our results show that the best settings depend on the model type and size, dataset characteristics and objective to optimize. Overall, SAM and SAM2 prompted with a bounding box in combination with the center point for all the components of an object yield the best results across all tested settings. As the results depend on multiple factors, we provide a guideline for informed decision-making in 2D prompting with non-interactive, ''optimal'' prompts.
Morphological methods play a crucial role in remote sensing image processing, due to their ability to capture and preserve small structural details. However, most of the existing deep learning models for semantic segmentation are based on the encoder-decoder architecture including U-net and Segment Anything Model (SAM), where the downsampling process tends to discard fine details. In this paper, we propose a new approach that integrates learnable morphological skeleton prior into deep neural networks using the variational method. To address the difficulty in backpropagation in neural networks caused by the non-differentiability presented in classical morphological operations, we provide a smooth representation of the morphological skeleton and design a variational segmentation model integrating morphological skeleton prior by employing operator splitting and dual methods. Then, we integrate this model into the network architecture of SAM, which is achieved by adding a token to mask decoder and modifying the final sigmoid layer, ensuring the final segmentation results preserve the skeleton structure as much as possible. Experimental results on remote sensing datasets, including buildings and roads, demonstrate that our method outperforms the original SAM on slender object segmentation and exhibits better generalization capability.
AI-based music generation has progressed significantly in recent years. However, creating symbolic music that is both long-structured and expressive remains a considerable challenge. In this paper, we propose PerceiverS (Segmentation and Scale), a novel architecture designed to address this issue by leveraging both Effective Segmentation and Multi-Scale attention mechanisms. Our approach enhances symbolic music generation by simultaneously learning long-term structural dependencies and short-term expressive details. By combining cross-attention and self-attention in a Multi-Scale setting, PerceiverS captures long-range musical structure while preserving musical diversity. The proposed model has been evaluated using the Maestro dataset and has demonstrated improvements in generating music of conventional length with expressive nuances. The project demos and the generated music samples can be accessed through the link: https://perceivers.github.io
White matter tract segmentation is crucial for studying brain structural connectivity and neurosurgical planning. However, segmentation remains challenging due to issues like class imbalance between major and minor tracts, structural similarity, subject variability, symmetric streamlines between hemispheres etc. To address these challenges, we propose TractoEmbed, a modular multi-level embedding framework, that encodes localized representations through learning tasks in respective encoders. In this paper, TractoEmbed introduces a novel hierarchical streamline data representation that captures maximum spatial information at each level i.e. individual streamlines, clusters, and patches. Experiments show that TractoEmbed outperforms state-of-the-art methods in white matter tract segmentation across different datasets, and spanning various age groups. The modular framework directly allows the integration of additional embeddings in future works.
Meningeal lymphatic vessels (MLVs) are responsible for the drainage of waste products from the human brain. An impairment in their functionality has been associated with aging as well as brain disorders like multiple sclerosis and Alzheimer's disease. However, MLVs have only recently been described for the first time in magnetic resonance imaging (MRI), and their ramified structure renders manual segmentation particularly difficult. Further, as there is no consistent notion of their appearance, human-annotated MLV structures contain a high inter-rater variability that most automatic segmentation methods cannot take into account. In this work, we propose a new rater-aware training scheme for the popular nnU-Net model, and we explore rater-based ensembling strategies for accurate and consistent segmentation of MLVs. This enables us to boost nnU-Net's performance while obtaining explicit predictions in different annotation styles and a rater-based uncertainty estimation. Our final model, MLV$^2$-Net, achieves a Dice similarity coefficient of 0.806 with respect to the human reference standard. The model further matches the human inter-rater reliability and replicates age-related associations with MLV volume.
Quality control of structures segmentation in volumetric medical images is important for identifying segmentation errors in clinical practice and for facilitating model development. This paper introduces SegQC, a novel framework for segmentation quality estimation and segmentation error detection. SegQC computes an estimate measure of the quality of a segmentation in volumetric scans and in their individual slices and identifies possible segmentation error regions within a slice. The key components include: 1. SegQC-Net, a deep network that inputs a scan and its segmentation mask and outputs segmentation error probabilities for each voxel in the scan; 2. three new segmentation quality metrics, two overlap metrics and a structure size metric, computed from the segmentation error probabilities; 3. a new method for detecting possible segmentation errors in scan slices computed from the segmentation error probabilities. We introduce a new evaluation scheme to measure segmentation error discrepancies based on an expert radiologist corrections of automatically produced segmentations that yields smaller observer variability and is closer to actual segmentation errors. We demonstrate SegQC on three fetal structures in 198 fetal MRI scans: fetal brain, fetal body and the placenta. To assess the benefits of SegQC, we compare it to the unsupervised Test Time Augmentation (TTA)-based quality estimation. Our studies indicate that SegQC outperforms TTA-based quality estimation in terms of Pearson correlation and MAE for fetal body and fetal brain structures segmentation. Our segmentation error detection method achieved recall and precision rates of 0.77 and 0.48 for fetal body, and 0.74 and 0.55 for fetal brain segmentation error detection respectively. SegQC enhances segmentation metrics estimation for whole scans and individual slices, as well as provides error regions detection.
We introduce GaussianCut, a new method for interactive multiview segmentation of scenes represented as 3D Gaussians. Our approach allows for selecting the objects to be segmented by interacting with a single view. It accepts intuitive user input, such as point clicks, coarse scribbles, or text. Using 3D Gaussian Splatting (3DGS) as the underlying scene representation simplifies the extraction of objects of interest which are considered to be a subset of the scene's Gaussians. Our key idea is to represent the scene as a graph and use the graph-cut algorithm to minimize an energy function to effectively partition the Gaussians into foreground and background. To achieve this, we construct a graph based on scene Gaussians and devise a segmentation-aligned energy function on the graph to combine user inputs with scene properties. To obtain an initial coarse segmentation, we leverage 2D image/video segmentation models and further refine these coarse estimates using our graph construction. Our empirical evaluations show the adaptability of GaussianCut across a diverse set of scenes. GaussianCut achieves competitive performance with state-of-the-art approaches for 3D segmentation without requiring any additional segmentation-aware training.
High-speed video (HSV) phase detection (PD) segmentation is crucial for monitoring vapor, liquid, and microlayer phases in industrial processes. While CNN-based models like U-Net have shown success in simplified shadowgraphy-based two-phase flow (TPF) analysis, their application to complex HSV PD tasks remains unexplored, and vision foundation models (VFMs) have yet to address the complexities of either shadowgraphy-based or PD TPF video segmentation. Existing uncertainty quantification (UQ) methods lack pixel-level reliability for critical metrics like contact line density and dry area fraction, and the absence of large-scale, multimodal experimental datasets tailored to PD segmentation further impedes progress. To address these gaps, we propose MSEG-VCUQ. This hybrid framework integrates U-Net CNNs with the transformer-based Segment Anything Model (SAM) to achieve enhanced segmentation accuracy and cross-modality generalization. Our approach incorporates systematic UQ for robust error assessment and introduces the first open-source multimodal HSV PD datasets. Empirical results demonstrate that MSEG-VCUQ outperforms baseline CNNs and VFMs, enabling scalable and reliable PD segmentation for real-world boiling dynamics.
Effortless and precise segmentation with minimal clinician effort could greatly streamline clinical workflows. Recent interactive segmentation models, inspired by METAs Segment Anything, have made significant progress but face critical limitations in 3D radiology. These include impractical human interaction requirements such as slice-by-slice operations for 2D models on 3D data and a lack of iterative refinement. Prior studies have been hindered by inadequate evaluation protocols, resulting in unreliable performance assessments and inconsistent findings across studies. The RadioActive benchmark addresses these challenges by providing a rigorous and reproducible evaluation framework for interactive segmentation methods in clinically relevant scenarios. It features diverse datasets, a wide range of target structures, and the most impactful 2D and 3D interactive segmentation methods, all within a flexible and extensible codebase. We also introduce advanced prompting techniques that reduce interaction steps, enabling fair comparisons between 2D and 3D models. Surprisingly, SAM2 outperforms all specialized medical 2D and 3D models in a setting requiring only a few interactions to generate prompts for a 3D volume. This challenges prevailing assumptions and demonstrates that general-purpose models surpass specialized medical approaches. By open-sourcing RadioActive, we invite researchers to integrate their models and prompting techniques, ensuring continuous and transparent evaluation of 3D medical interactive models.
Many open-ended conversations (e.g., tutoring lessons or business meetings) revolve around pre-defined reference materials, like worksheets or meeting bullets. To provide a framework for studying such conversation structure, we introduce Problem-Oriented Segmentation & Retrieval (POSR), the task of jointly breaking down conversations into segments and linking each segment to the relevant reference item. As a case study, we apply POSR to education where effectively structuring lessons around problems is critical yet difficult. We present LessonLink, the first dataset of real-world tutoring lessons, featuring 3,500 segments, spanning 24,300 minutes of instruction and linked to 116 SAT math problems. We define and evaluate several joint and independent approaches for POSR, including segmentation (e.g., TextTiling), retrieval (e.g., ColBERT), and large language models (LLMs) methods. Our results highlight that modeling POSR as one joint task is essential: POSR methods outperform independent segmentation and retrieval pipelines by up to +76% on joint metrics and surpass traditional segmentation methods by up to +78% on segmentation metrics. We demonstrate POSR's practical impact on downstream education applications, deriving new insights on the language and time use in real-world lesson structures.