Tumor volume segmentation on MRI is a challenging and time-consuming process that is performed manually in typical clinical settings. This work presents an approach to automated delineation of head and neck tumors on MRI scans, developed in the context of the MICCAI Head and Neck Tumor Segmentation for MR-Guided Applications (HNTS-MRG) 2024 Challenge. Rather than designing a new, task-specific convolutional neural network, the focus of this research was to propose improvements to the configuration commonly used in medical segmentation tasks, relying solely on the traditional U-Net architecture. The empirical results presented in this article suggest the superiority of patch-wise normalization used for both training and sliding window inference. They also indicate that the performance of segmentation models can be enhanced by applying a scheduled data augmentation policy during training. Finally, it is shown that a small improvement in quality can be achieved by using Gaussian weighting to combine predictions for individual patches during sliding window inference. The model with the best configuration obtained an aggregated Dice Similarity Coefficient (DSCagg) of 0.749 in Task 1 and 0.710 in Task 2 on five cross-validation folds. The ensemble of five models (one best model per validation fold) showed consistent results on a private test set of 50 patients with an DSCagg of 0.752 in Task 1 and 0.718 in Task 2 (team name: andrei.iantsen). The source code and model weights are freely available at www.github.com/iantsen/hntsmrg.
Contactless fingerprint recognition systems offer a hygienic, user-friendly, and efficient alternative to traditional contact-based methods. However, their accuracy heavily relies on precise fingertip detection and segmentation, particularly under challenging background conditions. This paper introduces TipSegNet, a novel deep learning model that achieves state-of-the-art performance in segmenting fingertips directly from grayscale hand images. TipSegNet leverages a ResNeXt-101 backbone for robust feature extraction, combined with a Feature Pyramid Network (FPN) for multi-scale representation, enabling accurate segmentation across varying finger poses and image qualities. Furthermore, we employ an extensive data augmentation strategy to enhance the model's generalizability and robustness. TipSegNet outperforms existing methods, achieving a mean Intersection over Union (mIoU) of 0.987 and an accuracy of 0.999, representing a significant advancement in contactless fingerprint segmentation. This enhanced accuracy has the potential to substantially improve the reliability and effectiveness of contactless biometric systems in real-world applications.
Deep Anterior Lamellar Keratoplasty (DALK) is a partial-thickness corneal transplant procedure used to treat corneal stromal diseases. A crucial step in this procedure is the precise separation of the deep stroma from Descemet's membrane (DM) using the Big Bubble technique. To simplify the tasks of needle insertion and pneumo-dissection in this technique, we previously developed an Optical Coherence Tomography (OCT)-guided, eye-mountable robot that uses real-time tracking of corneal layers from M-mode OCT signals for control. However, signal noise and instability during manipulation of the OCT fiber sensor-integrated needle have hindered the performance of conventional deep-learning segmentation methods, resulting in rough and inaccurate detection of corneal layers. To address these challenges, we have developed a topology-based deep-learning segmentation method that integrates a topological loss function with a modified network architecture. This approach effectively reduces the effects of noise and improves segmentation speed, precision, and stability. Validation using in vivo, ex vivo, and hybrid rabbit eye datasets demonstrates that our method outperforms traditional loss-based techniques, providing fast, accurate, and robust segmentation of the epithelium and DM to guide surgery.
Foreground segmentation is a fundamental task in computer vision, encompassing various subdivision tasks. Previous research has typically designed task-specific architectures for each task, leading to a lack of unification. Moreover, they primarily focus on recognizing foreground objects without effectively distinguishing them from the background. In this paper, we emphasize the importance of the background and its relationship with the foreground. We introduce FOCUS, the Foreground ObjeCts Universal Segmentation framework that can handle multiple foreground tasks. We develop a multi-scale semantic network using the edge information of objects to enhance image features. To achieve boundary-aware segmentation, we propose a novel distillation method, integrating the contrastive learning strategy to refine the prediction mask in multi-modal feature space. We conduct extensive experiments on a total of 13 datasets across 5 tasks, and the results demonstrate that FOCUS consistently outperforms the state-of-the-art task-specific models on most metrics.
This study presents an open-source toolkit to address critical challenges in preprocessing data for self-supervised learning (SSL) for 3D medical imaging, focusing on data privacy and computational efficiency. The toolkit comprises two main components: a segmentation network that delineates foreground regions to optimize data sampling and thus reduce training time, and a segmentation network that identifies anonymized regions, preventing erroneous supervision in reconstruction-based SSL methods. Experimental results demonstrate high robustness, with mean Dice scores exceeding 98.5 across all anonymization methods and surpassing 99.5 for foreground segmentation tasks, highlighting the efficacy of the toolkit in supporting SSL applications in 3D medical imaging for both CT and MRI images. The weights and code is available at https://github.com/MIC-DKFZ/Foreground-and-Anonymization-Area-Segmentation.
We present Seg-TTO, a novel framework for zero-shot, open-vocabulary semantic segmentation (OVSS), designed to excel in specialized domain tasks. While current open vocabulary approaches show impressive performance on standard segmentation benchmarks under zero-shot settings, they fall short of supervised counterparts on highly domain-specific datasets. We focus on segmentation-specific test-time optimization to address this gap. Segmentation requires an understanding of multiple concepts within a single image while retaining the locality and spatial structure of representations. We propose a novel self-supervised objective adhering to these requirements and use it to align the model parameters with input images at test time. In the textual modality, we learn multiple embeddings for each category to capture diverse concepts within an image, while in the visual modality, we calculate pixel-level losses followed by embedding aggregation operations specific to preserving spatial structure. Our resulting framework termed Seg-TTO is a plug-in-play module. We integrate Seg-TTO with three state-of-the-art OVSS approaches and evaluate across 22 challenging OVSS tasks covering a range of specialized domains. Our Seg-TTO demonstrates clear performance improvements across these establishing new state-of-the-art. Code: https://github.com/UlinduP/SegTTO.
Automated fish documentation processes are in the near future expected to play an essential role in sustainable fisheries management and for addressing challenges of overfishing. In this paper, we present a novel and publicly available dataset named AutoFish designed for fine-grained fish analysis. The dataset comprises 1,500 images of 454 specimens of visually similar fish placed in various constellations on a white conveyor belt and annotated with instance segmentation masks, IDs, and length measurements. The data was collected in a controlled environment using an RGB camera. The annotation procedure involved manual point annotations, initial segmentation masks proposed by the Segment Anything Model (SAM), and subsequent manual correction of the masks. We establish baseline instance segmentation results using two variations of the Mask2Former architecture, with the best performing model reaching an mAP of 89.15%. Additionally, we present two baseline length estimation methods, the best performing being a custom MobileNetV2-based regression model reaching an MAE of 0.62cm in images with no occlusion and 1.38cm in images with occlusion. Link to project page: https://vap.aau.dk/autofish/.
This study explores the potential of graph neural networks (GNNs) to enhance semantic segmentation across diverse image modalities. We evaluate the effectiveness of a novel GNN-based U-Net architecture on three distinct datasets: PascalVOC, a standard benchmark for natural image segmentation, WoodScape, a challenging dataset of fisheye images commonly used in autonomous driving, introducing significant geometric distortions; and ISIC2016, a dataset of dermoscopic images for skin lesion segmentation. We compare our proposed UNet-GNN model against established convolutional neural networks (CNNs) based segmentation models, including U-Net and U-Net++, as well as the transformer-based SwinUNet. Unlike these methods, which primarily rely on local convolutional operations or global self-attention, GNNs explicitly model relationships between image regions by constructing and operating on a graph representation of the image features. This approach allows the model to capture long-range dependencies and complex spatial relationships, which we hypothesize will be particularly beneficial for handling geometric distortions present in fisheye imagery and capturing intricate boundaries in medical images. Our analysis demonstrates the versatility of GNNs in addressing diverse segmentation challenges and highlights their potential to improve segmentation accuracy in various applications, including autonomous driving and medical image analysis.
Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a critical global health issue, necessitating timely diagnosis and treatment. Current methods for detecting tuberculosis bacilli from bright field microscopic sputum smear images suffer from low automation, inadequate segmentation performance, and limited classification accuracy. This paper proposes an efficient hybrid approach that combines deep learning for segmentation and an ensemble model for classification. An enhanced U-Net model incorporating attention blocks and residual connections is introduced to precisely segment microscopic sputum smear images, facilitating the extraction of Regions of Interest (ROIs). These ROIs are subsequently classified using an ensemble classifier comprising Support Vector Machine (SVM), Random Forest, and Extreme Gradient Boost (XGBoost), resulting in an accurate identification of bacilli within the images. Experiments conducted on a newly created dataset, along with public datasets, demonstrate that the proposed model achieves superior segmentation performance, higher classification accuracy, and enhanced automation compared to existing methods.
Prostate cancer is a leading cause of cancer-related mortality in men. The registration of magnetic resonance (MR) and transrectal ultrasound (TRUS) can provide guidance for the targeted biopsy of prostate cancer. In this study, we propose a salient region matching framework for fully automated MR-TRUS registration. The framework consists of prostate segmentation, rigid alignment and deformable registration. Prostate segmentation is performed using two segmentation networks on MR and TRUS respectively, and the predicted salient regions are used for the rigid alignment. The rigidly-aligned MR and TRUS images serve as initialization for the deformable registration. The deformable registration network has a dual-stream encoder with cross-modal spatial attention modules to facilitate multi-modality feature learning, and a salient region matching loss to consider both structure and intensity similarity within the prostate region. Experiments on a public MR-TRUS dataset demonstrate that our method achieves satisfactory registration results, outperforming several cutting-edge methods. The code is publicly available at https://github.com/mock1ngbrd/salient-region-matching.
Satisfactory progress has been achieved recently in universal segmentation of CT images. Following the success of vision-language methods, there is a growing trend towards utilizing text prompts and contrastive learning to develop universal segmentation models. However, there exists a significant imbalance in information density between 3D images and text prompts. Moreover, the standard fully connected layer segmentation approach faces significant challenges in handling multiple classes and exhibits poor generalizability. To address these challenges, we propose the VOxel Interacting with LAnguage method (VOILA) for universal CT image segmentation. Initially, we align voxels and language into a shared representation space and classify voxels on the basis of cosine similarity. Subsequently, we develop the Voxel-Language Interaction framework to mitigate the impact of class imbalance caused by foreground-background discrepancies and variations in target volumes. Furthermore, a Complexity-Aware Sampling method is proposed to focus on region hard to segment, achieved by generating pseudo-heatmaps from a trainable Gaussian mixture distribution. Our results indicate the proposed VOILA is capable to achieve improved performance with reduced parameters and computational cost during training. Furthermore, it demonstrates significant generalizability across diverse datasets without additional fine-tuning.
Retinal vascular morphology is crucial for diagnosing diseases such as diabetes, glaucoma, and hypertension, making accurate segmentation of retinal vessels essential for early intervention. Traditional segmentation methods assume that training and testing data share similar distributions, which can lead to poor performance on unseen domains due to domain shifts caused by variations in imaging devices and patient demographics. This paper presents a novel approach, DGSSA, for retinal vessel image segmentation that enhances model generalization by combining structural and style augmentation strategies. We utilize a space colonization algorithm to generate diverse vascular-like structures that closely mimic actual retinal vessels, which are then used to generate pseudo-retinal images with an improved Pix2Pix model, allowing the segmentation model to learn a broader range of structure distributions. Additionally, we utilize PixMix to implement random photometric augmentations and introduce uncertainty perturbations, thereby enriching stylistic diversity and significantly enhancing the model's adaptability to varying imaging conditions. Our framework has been rigorously evaluated on four challenging datasets-DRIVE, CHASEDB, HRF, and STARE-demonstrating state-of-the-art performance that surpasses existing methods. This validates the effectiveness of our proposed approach, highlighting its potential for clinical application in automated retinal vessel analysis.
This work presents Sa2VA, the first unified model for dense grounded understanding of both images and videos. Unlike existing multi-modal large language models, which are often limited to specific modalities and tasks, Sa2VA supports a wide range of image and video tasks, including referring segmentation and conversation, with minimal one-shot instruction tuning. Sa2VA combines SAM-2, a foundation video segmentation model, with LLaVA, an advanced vision-language model, and unifies text, image, and video into a shared LLM token space. Using the LLM, Sa2VA generates instruction tokens that guide SAM-2 in producing precise masks, enabling a grounded, multi-modal understanding of both static and dynamic visual content. Additionally, we introduce Ref-SAV, an auto-labeled dataset containing over 72k object expressions in complex video scenes, designed to boost model performance. We also manually validate 2k video objects in the Ref-SAV datasets to benchmark referring video object segmentation in complex environments. Experiments show that Sa2VA achieves state-of-the-art across multiple tasks, particularly in referring video object segmentation, highlighting its potential for complex real-world applications.
With the rapid advancement of deep learning, computational pathology has made significant progress in cancer diagnosis and subtyping. Tissue segmentation is a core challenge, essential for prognosis and treatment decisions. Weakly supervised semantic segmentation (WSSS) reduces the annotation requirement by using image-level labels instead of pixel-level ones. However, Class Activation Map (CAM)-based methods still suffer from low spatial resolution and unclear boundaries. To address these issues, we propose a multi-level superpixel correction algorithm that refines CAM boundaries using superpixel clustering and floodfill. Experimental results show that our method achieves great performance on breast cancer segmentation dataset with mIoU of 71.08%, significantly improving tumor microenvironment boundary delineation.
Current medical image segmentation approaches have limitations in deeply exploring multi-scale information and effectively combining local detail textures with global contextual semantic information. This results in over-segmentation, under-segmentation, and blurred segmentation boundaries. To tackle these challenges, we explore multi-scale feature representations from different perspectives, proposing a novel, lightweight, and multi-scale architecture (LM-Net) that integrates advantages of both Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) to enhance segmentation accuracy. LM-Net employs a lightweight multi-branch module to capture multi-scale features at the same level. Furthermore, we introduce two modules to concurrently capture local detail textures and global semantics with multi-scale features at different levels: the Local Feature Transformer (LFT) and Global Feature Transformer (GFT). The LFT integrates local window self-attention to capture local detail textures, while the GFT leverages global self-attention to capture global contextual semantics. By combining these modules, our model achieves complementarity between local and global representations, alleviating the problem of blurred segmentation boundaries in medical image segmentation. To evaluate the feasibility of LM-Net, extensive experiments have been conducted on three publicly available datasets with different modalities. Our proposed model achieves state-of-the-art results, surpassing previous methods, while only requiring 4.66G FLOPs and 5.4M parameters. These state-of-the-art results on three datasets with different modalities demonstrate the effectiveness and adaptability of our proposed LM-Net for various medical image segmentation tasks.
Accurate segmentation of pulmonary structures iscrucial in clinical diagnosis, disease study, and treatment planning. Significant progress has been made in deep learning-based segmentation techniques, but most require much labeled data for training. Consequently, developing precise segmentation methods that demand fewer labeled datasets is paramount in medical image analysis. The emergence of pre-trained vision-language foundation models, such as CLIP, recently opened the door for universal computer vision tasks. Exploiting the generalization ability of these pre-trained foundation models on downstream tasks, such as segmentation, leads to unexpected performance with a relatively small amount of labeled data. However, exploring these models for pulmonary artery-vein segmentation is still limited. This paper proposes a novel framework called Language-guided self-adaptive Cross-Attention Fusion Framework. Our method adopts pre-trained CLIP as a strong feature extractor for generating the segmentation of 3D CT scans, while adaptively aggregating the cross-modality of text and image representations. We propose a s pecially designed adapter module to fine-tune pre-trained CLIP with a self-adaptive learning strategy to effectively fuse the two modalities of embeddings. We extensively validate our method on a local dataset, which is the largest pulmonary artery-vein CT dataset to date and consists of 718 labeled data in total. The experiments show that our method outperformed other state-of-the-art methods by a large margin. Our data and code will be made publicly available upon acceptance.
In this paper, we introduce an unsupervised approach for Speech Segmentation, which builds on previously researched approaches, e.g., Speaker Diarization, while being applicable to an inclusive set of acoustic-semantic distinctions, paving a path towards a general Unsupervised Speech Segmentation approach. Unlike traditional speech and audio segmentation, which mainly focuses on spectral changes in the input signal, e.g., phone segmentation, our approach tries to segment the spoken utterance into chunks with differing acoustic-semantic styles, focusing on acoustic-semantic information that does not translate well into text, e.g., emotion or speaker. While most Speech Segmentation tasks only handle one style change, e.g., emotion diarization, our approach tries to handle multiple acoustic-semantic style changes. Leveraging recent advances in Speech Language Models (SLMs), we propose a simple unsupervised method to segment a given speech utterance. We empirically demonstrate the effectiveness of the proposed approach by considering several setups. Results suggest that the proposed method is superior to the evaluated baselines on boundary detection, segment purity, and over-segmentation. Code is available at https://github.com/avishaiElmakies/unsupervised_speech_segmentation_using_slm.
Model checking, a formal verification technique, ensures systems meet predefined requirements, playing a crucial role in minimizing errors and enhancing quality during development. This paper introduces a novel hybrid framework integrating model checking with deep learning for brain tumor detection and validation in medical imaging. By combining model-checking principles with CNN-based feature extraction and K-FCM clustering for segmentation, the proposed approach enhances the reliability of tumor detection and segmentation. Experimental results highlight the framework's effectiveness, achieving 98\% accuracy, 96.15\% precision, and 100\% recall, demonstrating its potential as a robust tool for advanced medical image analysis.
Semantic segmentation is a computer vision task where classification is performed at a pixel level. Due to this, the process of labeling images for semantic segmentation is time-consuming and expensive. To mitigate this cost there has been a surge in the use of synthetically generated data -- usually created using simulators or videogames -- which, in combination with domain adaptation methods, can effectively learn how to segment real data. Still, these datasets have a particular limitation: due to their closed-set nature, it is not possible to include novel classes without modifying the tool used to generate them, which is often not public. Concurrently, generative models have made remarkable progress, particularly with the introduction of diffusion models, enabling the creation of high-quality images from text prompts without additional supervision. In this work, we propose an unsupervised pipeline that leverages Stable Diffusion and Segment Anything Module to generate class examples with an associated segmentation mask, and a method to integrate generated cutouts for novel classes in semantic segmentation datasets, all with minimal user input. Our approach aims to improve the performance of unsupervised domain adaptation methods by introducing novel samples into the training data without modifications to the underlying algorithms. With our methods, we show how models can not only effectively learn how to segment novel classes, with an average performance of 51% IoU, but also reduce errors for other, already existing classes, reaching a higher performance level overall.
This paper introduces Tree-NET, a novel framework for medical image segmentation that leverages bottleneck feature supervision to enhance both segmentation accuracy and computational efficiency. While previous studies have employed bottleneck feature supervision, their applications have largely been limited to the training phase, offering no computational benefits during training or evaluation. To the best of our knowledge, this study is the first to propose a framework that incorporates two additional training phases for segmentation models, utilizing bottleneck features at both input and output stages. This approach significantly improves computational performance by reducing input and output dimensions with a negligible addition to parameter count, without compromising accuracy. Tree-NET features a three-layer architecture comprising Encoder-Net and Decoder-Net, which are autoencoders designed to compress input and label data, respectively, and Bridge-Net, a segmentation framework that supervises the bottleneck features. By focusing on dense, compressed representations, Tree-NET enhances operational efficiency and can be seamlessly integrated into existing segmentation models without altering their internal structures or increasing model size. We evaluate Tree-NET on two critical segmentation tasks -- skin lesion and polyp segmentation -- using various backbone models, including U-NET variants and Polyp-PVT. Experimental results demonstrate that Tree-NET reduces FLOPs by a factor of 4 to 13 and decreases memory usage, while achieving comparable or superior accuracy compared to the original architectures. These findings underscore Tree-NET's potential as a robust and efficient solution for medical image segmentation.