Domain adaptation (DA) for cardiac ultrasound image segmentation is clinically significant and valuable. However, previous domain adaptation methods are prone to be affected by the incomplete pseudo-label and low-quality target to source images. Human-centric domain adaptation has great advantages of human cognitive guidance to help model adapt to target domain and reduce reliance on labels. Doctor gaze trajectories contains a large amount of cross-domain human guidance. To leverage gaze information and human cognition for guiding domain adaptation, we propose gaze-assisted human-centric domain adaptation (GAHCDA), which reliably guides the domain adaptation of cardiac ultrasound images. GAHCDA includes following modules: (1) Gaze Augment Alignment (GAA): GAA enables the model to obtain human cognition general features to recognize segmentation target in different domain of cardiac ultrasound images like humans. (2) Gaze Balance Loss (GBL): GBL fused gaze heatmap with outputs which makes the segmentation result structurally closer to the target domain. The experimental results illustrate that our proposed framework is able to segment cardiac ultrasound images more effectively in the target domain than GAN-based methods and other self-train based methods, showing great potential in clinical application.
Purpose: To develop and evaluate a deep learning-based method that allows to perform myocardial infarct segmentation in a fully-automated way. Materials and Methods: For this retrospective study, a cascaded framework of two and three-dimensional convolutional neural networks (CNNs), specialized on identifying ischemic myocardial scars on late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) images, was trained on an in-house training dataset consisting of 144 examinations. On a separate test dataset from the same institution, including images from 152 examinations obtained between 2021 and 2023, a quantitative comparison between artificial intelligence (AI)-based segmentations and manual segmentations was performed. Further, qualitative assessment of segmentation accuracy was evaluated for both human and AI-generated contours by two CMR experts in a blinded experiment. Results: Excellent agreement could be found between manually and automatically calculated infarct volumes ($\rho_c$ = 0.9). The qualitative evaluation showed that compared to human-based measurements, the experts rated the AI-based segmentations to better represent the actual extent of infarction significantly (p < 0.001) more often (33.4% AI, 25.1% human, 41.5% equal). On the contrary, for segmentation of microvascular obstruction (MVO), manual measurements were still preferred (11.3% AI, 55.6% human, 33.1% equal). Conclusion: This fully-automated segmentation pipeline enables CMR infarct size to be calculated in a very short time and without requiring any pre-processing of the input images while matching the segmentation quality of trained human observers. In a blinded experiment, experts preferred automated infarct segmentations more often than manual segmentations, paving the way for a potential clinical application.
This study proposes a new loss function for deep neural networks, L1-weighted Dice Focal Loss (L1DFL), that leverages L1 norms for adaptive weighting of voxels based on their classification difficulty, towards automated detection and segmentation of metastatic prostate cancer lesions in PET/CT scans. We obtained 380 PSMA [18-F] DCFPyL PET/CT scans of patients diagnosed with biochemical recurrence metastatic prostate cancer. We trained two 3D convolutional neural networks, Attention U-Net and SegResNet, and concatenated the PET and CT volumes channel-wise as input. The performance of our custom loss function was evaluated against the Dice and Dice Focal Loss functions. For clinical significance, we considered a detected region of interest (ROI) as a true positive if at least the voxel with the maximum standardized uptake value falls within the ROI. We assessed the models' performance based on the number of lesions in an image, tumour volume, activity, and extent of spread. The L1DFL outperformed the comparative loss functions by at least 13% on the test set. In addition, the F1 scores of the Dice Loss and the Dice Focal Loss were lower than that of L1DFL by at least 6% and 34%, respectively. The Dice Focal Loss yielded more false positives, whereas the Dice Loss was more sensitive to smaller volumes and struggled to segment larger lesions accurately. They also exhibited network-specific variations and yielded declines in segmentation accuracy with increased tumour spread. Our results demonstrate the potential of L1DFL to yield robust segmentation of metastatic prostate cancer lesions in PSMA PET/CT images. The results further highlight potential complexities arising from the variations in lesion characteristics that may influence automated prostate cancer tumour detection and segmentation. The code is publicly available at: https://github.com/ObedDzik/pca_segment.git.
Deep learning-based medical image segmentation models, such as U-Net, rely on high-quality annotated datasets to achieve accurate predictions. However, the increasing use of generative models for synthetic data augmentation introduces potential risks, particularly in the absence of rigorous quality control. In this paper, we investigate the impact of synthetic MRI data on the robustness and segmentation accuracy of U-Net models for brain tumor segmentation. Specifically, we generate synthetic T1-contrast-enhanced (T1-Ce) MRI scans using a GAN-based model with a shared encoding-decoding framework and shortest-path regularization. To quantify the effect of synthetic data contamination, we train U-Net models on progressively "poisoned" datasets, where synthetic data proportions range from 16.67% to 83.33%. Experimental results on a real MRI validation set reveal a significant performance degradation as synthetic data increases, with Dice coefficients dropping from 0.8937 (33.33% synthetic) to 0.7474 (83.33% synthetic). Accuracy and sensitivity exhibit similar downward trends, demonstrating the detrimental effect of synthetic data on segmentation robustness. These findings underscore the importance of quality control in synthetic data integration and highlight the risks of unregulated synthetic augmentation in medical image analysis. Our study provides critical insights for the development of more reliable and trustworthy AI-driven medical imaging systems.
Service robots operating in unstructured environments must effectively recognize and segment unknown objects to enhance their functionality. Traditional supervised learningbased segmentation techniques require extensive annotated datasets, which are impractical for the diversity of objects encountered in real-world scenarios. Unseen Object Instance Segmentation (UOIS) methods aim to address this by training models on synthetic data to generalize to novel objects, but they often suffer from the simulation-to-reality gap. This paper proposes a novel approach (ZISVFM) for solving UOIS by leveraging the powerful zero-shot capability of the segment anything model (SAM) and explicit visual representations from a selfsupervised vision transformer (ViT). The proposed framework operates in three stages: (1) generating object-agnostic mask proposals from colorized depth images using SAM, (2) refining these proposals using attention-based features from the selfsupervised ViT to filter non-object masks, and (3) applying K-Medoids clustering to generate point prompts that guide SAM towards precise object segmentation. Experimental validation on two benchmark datasets and a self-collected dataset demonstrates the superior performance of ZISVFM in complex environments, including hierarchical settings such as cabinets, drawers, and handheld objects. Our source code is available at https://github.com/Yinmlmaoliang/zisvfm.
Industrial defect segmentation is critical for manufacturing quality control. Due to the scarcity of training defect samples, few-shot semantic segmentation (FSS) holds significant value in this field. However, existing studies mostly apply FSS to tackle defects on simple textures, without considering more diverse scenarios. This paper aims to address this gap by exploring FSS in broader industrial products with various defect types. To this end, we contribute a new real-world dataset and reorganize some existing datasets to build a more comprehensive few-shot defect segmentation (FDS) benchmark. On this benchmark, we thoroughly investigate metric learning-based FSS methods, including those based on meta-learning and those based on Vision Foundation Models (VFMs). We observe that existing meta-learning-based methods are generally not well-suited for this task, while VFMs hold great potential. We further systematically study the applicability of various VFMs in this task, involving two paradigms: feature matching and the use of Segment Anything (SAM) models. We propose a novel efficient FDS method based on feature matching. Meanwhile, we find that SAM2 is particularly effective for addressing FDS through its video track mode. The contributed dataset and code will be available at: https://github.com/liutongkun/GFDS.
Segment Anything Model (SAM) represents a large-scale segmentation model that enables powerful zero-shot capabilities with flexible prompts. While SAM can segment any object in zero-shot, it requires user-provided prompts for each target image and does not attach any label information to masks. Few-shot segmentation models addressed these issues by inputting annotated reference images as prompts to SAM and can segment specific objects in target images without user-provided prompts. Previous SAM-based few-shot segmentation models only use annotated reference images as prompts, resulting in limited accuracy due to a lack of reference information. In this paper, we propose a novel few-shot segmentation model, Vision and Language reference Prompt into SAM (VLP-SAM), that utilizes the visual information of the reference images and the semantic information of the text labels by inputting not only images but also language as reference information. In particular, VLP-SAM is a simple and scalable structure with minimal learnable parameters, which inputs prompt embeddings with vision-language information into SAM using a multimodal vision-language model. To demonstrate the effectiveness of VLP-SAM, we conducted experiments on the PASCAL-5i and COCO-20i datasets, and achieved high performance in the few-shot segmentation task, outperforming the previous state-of-the-art model by a large margin (6.3% and 9.5% in mIoU, respectively). Furthermore, VLP-SAM demonstrates its generality in unseen objects that are not included in the training data. Our code is available at https://github.com/kosukesakurai1/VLP-SAM.
Segmentation is an important analysis task for biomedical images, enabling the study of individual organelles, cells or organs. Deep learning has massively improved segmentation methods, but challenges remain in generalization to new conditions, requiring costly data annotation. Vision foundation models, such as Segment Anything Model (SAM), address this issue through broad segmentation capabilities. However, these models still require finetuning on annotated data, although with less annotations, to achieve optimal results for new conditions. As a downside, they require more computational resources. This makes parameter-efficient finetuning (PEFT) relevant for their application. We contribute the first comprehensive study of PEFT for SAM applied to biomedical segmentation by evaluating 9 PEFT methods on diverse datasets. We also provide an implementation of QLoRA for vision transformers and a new approach for resource-efficient finetuning of SAM. Our code is publicly available at https://github.com/computational-cell-analytics/peft-sam.
We introduce Lifting By Gaussians (LBG), a novel approach for open-world instance segmentation of 3D Gaussian Splatted Radiance Fields (3DGS). Recently, 3DGS Fields have emerged as a highly efficient and explicit alternative to Neural Field-based methods for high-quality Novel View Synthesis. Our 3D instance segmentation method directly lifts 2D segmentation masks from SAM (alternately FastSAM, etc.), together with features from CLIP and DINOv2, directly fusing them onto 3DGS (or similar Gaussian radiance fields such as 2DGS). Unlike previous approaches, LBG requires no per-scene training, allowing it to operate seamlessly on any existing 3DGS reconstruction. Our approach is not only an order of magnitude faster and simpler than existing approaches; it is also highly modular, enabling 3D semantic segmentation of existing 3DGS fields without requiring a specific parametrization of the 3D Gaussians. Furthermore, our technique achieves superior semantic segmentation for 2D semantic novel view synthesis and 3D asset extraction results while maintaining flexibility and efficiency. We further introduce a novel approach to evaluate individually segmented 3D assets from 3D radiance field segmentation methods.
This paper introduces the COCONut-PanCap dataset, created to enhance panoptic segmentation and grounded image captioning. Building upon the COCO dataset with advanced COCONut panoptic masks, this dataset aims to overcome limitations in existing image-text datasets that often lack detailed, scene-comprehensive descriptions. The COCONut-PanCap dataset incorporates fine-grained, region-level captions grounded in panoptic segmentation masks, ensuring consistency and improving the detail of generated captions. Through human-edited, densely annotated descriptions, COCONut-PanCap supports improved training of vision-language models (VLMs) for image understanding and generative models for text-to-image tasks. Experimental results demonstrate that COCONut-PanCap significantly boosts performance across understanding and generation tasks, offering complementary benefits to large-scale datasets. This dataset sets a new benchmark for evaluating models on joint panoptic segmentation and grounded captioning tasks, addressing the need for high-quality, detailed image-text annotations in multi-modal learning.
We tackle open-vocabulary 3D scene understanding by introducing a novel data generation pipeline and training framework. Our method addresses three critical requirements for effective training: precise 3D region segmentation, comprehensive textual descriptions, and sufficient dataset scale. By leveraging state-of-the-art open-vocabulary image segmentation models and region-aware Vision-Language Models, we develop an automatic pipeline that generates high-quality 3D mask-text pairs. Applying this pipeline to multiple 3D scene datasets, we create Mosaic3D-5.6M, a dataset of over 30K annotated scenes with 5.6M mask-text pairs, significantly larger than existing datasets. Building upon this data, we propose Mosaic3D, a foundation model combining a 3D encoder trained with contrastive learning and a lightweight mask decoder for open-vocabulary 3D semantic and instance segmentation. Our approach achieves state-of-the-art results on open-vocabulary 3D semantic and instance segmentation tasks including ScanNet200, Matterport3D, and ScanNet++, with ablation studies validating the effectiveness of our large-scale training data.
In this work, we extend the SEEDS superpixel algorithm from 2D images to 3D volumes, resulting in 3D SEEDS, a faster, better, and open-source supervoxel algorithm for medical image analysis. We compare 3D SEEDS with the widely used supervoxel algorithm SLIC on 13 segmentation tasks across 10 organs. 3D SEEDS accelerates supervoxel generation by a factor of 10, improves the achievable Dice score by +6.5%, and reduces the under-segmentation error by -0.16%. The code is available at https://github.com/Zch0414/3d_seeds
How to mitigate negative transfer in transfer learning is a long-standing and challenging issue, especially in the application of medical image segmentation. Existing methods for reducing negative transfer focus on classification or regression tasks, ignoring the non-uniform negative transfer risk in different image regions. In this work, we propose a simple yet effective weighted fine-tuning method that directs the model's attention towards regions with significant transfer risk for medical semantic segmentation. Specifically, we compute a transferability-guided transfer risk map to quantify the transfer hardness for each pixel and the potential risks of negative transfer. During the fine-tuning phase, we introduce a map-weighted loss function, normalized with image foreground size to counter class imbalance. Extensive experiments on brain segmentation datasets show our method significantly improves the target task performance, with gains of 4.37% on FeTS2021 and 1.81% on iSeg2019, avoiding negative transfer across modalities and tasks. Meanwhile, a 2.9% gain under a few-shot scenario validates the robustness of our approach.
Pre-training techniques significantly enhance the performance of semantic segmentation tasks with limited training data. However, the efficacy under a large domain gap between pre-training (e.g. RGB) and fine-tuning (e.g. infrared) remains underexplored. In this study, we first benchmark the infrared semantic segmentation performance of various pre-training methods and reveal several phenomena distinct from the RGB domain. Next, our layerwise analysis of pre-trained attention maps uncovers that: (1) There are three typical attention patterns (local, hybrid, and global); (2) Pre-training tasks notably influence the pattern distribution across layers; (3) The hybrid pattern is crucial for semantic segmentation as it attends to both nearby and foreground elements; (4) The texture bias impedes model generalization in infrared tasks. Building on these insights, we propose UNIP, a UNified Infrared Pre-training framework, to enhance the pre-trained model performance. This framework uses the hybrid-attention distillation NMI-HAD as the pre-training target, a large-scale mixed dataset InfMix for pre-training, and a last-layer feature pyramid network LL-FPN for fine-tuning. Experimental results show that UNIP outperforms various pre-training methods by up to 13.5\% in average mIoU on three infrared segmentation tasks, evaluated using fine-tuning and linear probing metrics. UNIP-S achieves performance on par with MAE-L while requiring only 1/10 of the computational cost. Furthermore, UNIP significantly surpasses state-of-the-art (SOTA) infrared or RGB segmentation methods and demonstrates broad potential for application in other modalities, such as RGB and depth. Our code is available at https://github.com/casiatao/UNIP.
Following the gaze of other people and analyzing the target they are looking at can help us understand what they are thinking, and doing, and predict the actions that may follow. Existing methods for gaze following struggle to perform well in natural scenes with diverse objects, and focus on gaze points rather than objects, making it difficult to deliver clear semantics and accurate scope of the targets. To address this shortcoming, we propose a novel gaze target prediction solution named GazeSeg, that can fully utilize the spatial visual field of the person as guiding information and lead to a progressively coarse-to-fine gaze target segmentation and recognition process. Specifically, a prompt-based visual foundation model serves as the encoder, working in conjunction with three distinct decoding modules (e.g. FoV perception, heatmap generation, and segmentation) to form the framework for gaze target prediction. Then, with the head bounding box performed as an initial prompt, GazeSeg obtains the FoV map, heatmap, and segmentation map progressively, leading to a unified framework for multiple tasks (e.g. direction estimation, gaze target segmentation, and recognition). In particular, to facilitate this research, we construct and release a new dataset, comprising 72k images with pixel-level annotations and 270 categories of gaze targets, built upon the GazeFollow dataset. The quantitative evaluation shows that our approach achieves the Dice of 0.325 in gaze target segmentation and 71.7% top-5 recognition. Meanwhile, our approach also outperforms previous state-of-the-art methods, achieving 0.953 in AUC on the gaze-following task. The dataset and code will be released.
3D cell segmentation methods are often hindered by \emph{oversegmentation}, where a single cell is incorrectly split into multiple fragments. This degrades the final segmentation quality and is notoriously difficult to resolve, as oversegmentation errors often resemble \emph{natural gaps} between adjacent cells. Our work makes two key contributions. First, for 3D cell segmentation, we are the first work to formulate oversegmentation as a concrete problem and propose a geometric framework to identify and correct these errors. Our approach builds a pre-trained classifier using both 2D geometric and 3D topological features extracted from flawed 3D segmentation results. Second, we introduce a novel metric, \emph{Geo-Wasserstein} divergence, to quantify changes in 2D geometries. This captures the evolving trends in cell mask shape changes in a geometry-aware manner. We validate our method through extensive experiments on in-domain plant datasets, including both synthesized and real cases, as well as on out-of-domain animal datasets to demonstrate transfer learning performance. An ablation study further highlights the contribution of the \emph{Geo-Wasserstein} divergence. A clear pipeline is provided for end-users to build pre-trained models to any labeled dataset.
Segmentation of brain tumors is a critical step in treatment planning, yet manual segmentation is both time-consuming and subjective, relying heavily on the expertise of radiologists. In Sub-Saharan Africa, this challenge is magnified by overburdened medical systems and limited access to advanced imaging modalities and expert radiologists. Automating brain tumor segmentation using deep learning offers a promising solution. Convolutional Neural Networks (CNNs), especially the U-Net architecture, have shown significant potential. However, a major challenge remains: achieving generalizability across different datasets. This study addresses this gap by developing a deep learning ensemble that integrates UNet3D, V-Net, and MSA-VNet models for the semantic segmentation of gliomas. By initially training on the BraTS-GLI dataset and fine-tuning with the BraTS-SSA dataset, we enhance model performance. Our ensemble approach significantly outperforms individual models, achieving DICE scores of 0.8358 for Tumor Core, 0.8521 for Whole Tumor, and 0.8167 for Enhancing Tumor. These results underscore the potential of ensemble methods in improving the accuracy and reliability of automated brain tumor segmentation, particularly in resource-limited settings.
Prostate cancer is a major cause of cancer-related deaths in men, where early detection greatly improves survival rates. Although MRI-TRUS fusion biopsy offers superior accuracy by combining MRI's detailed visualization with TRUS's real-time guidance, it is a complex and time-intensive procedure that relies heavily on manual annotations, leading to potential errors. To address these challenges, we propose a fully automatic MRI-TRUS fusion-based segmentation method that identifies prostate tumors directly in TRUS images without requiring manual annotations. Unlike traditional multimodal fusion approaches that rely on naive data concatenation, our method integrates a registration-segmentation framework to align and leverage spatial information between MRI and TRUS modalities. This alignment enhances segmentation accuracy and reduces reliance on manual effort. Our approach was validated on a dataset of 1,747 patients from Stanford Hospital, achieving an average Dice coefficient of 0.212, outperforming TRUS-only (0.117) and naive MRI-TRUS fusion (0.132) methods, with significant improvements (p $<$ 0.01). This framework demonstrates the potential for reducing the complexity of prostate cancer diagnosis and provides a flexible architecture applicable to other multimodal medical imaging tasks.
Nucleus segmentation is an important analysis task in digital pathology. However, methods for automatic segmentation often struggle with new data from a different distribution, requiring users to manually annotate nuclei and retrain data-specific models. Vision foundation models (VFMs), such as the Segment Anything Model (SAM), offer a more robust alternative for automatic and interactive segmentation. Despite their success in natural images, a foundation model for nucleus segmentation in histopathology is still missing. Initial efforts to adapt SAM have shown some success, but did not yet introduce a comprehensive model for diverse segmentation tasks. To close this gap, we introduce PathoSAM, a VFM for nucleus segmentation, based on training SAM on a diverse dataset. Our extensive experiments show that it is the new state-of-the-art model for automatic and interactive nucleus instance segmentation in histopathology. We also demonstrate how it can be adapted for other segmentation tasks, including semantic nucleus segmentation. For this task, we show that it yields results better than popular methods, while not yet beating the state-of-the-art, CellViT. Our models are open-source and compatible with popular tools for data annotation. We also provide scripts for whole-slide image segmentation. Our code and models are publicly available at https://github.com/computational-cell-analytics/patho-sam.
The retroperitoneum hosts a variety of tumors, including rare benign and malignant types, which pose diagnostic and treatment challenges due to their infrequency and proximity to vital structures. Estimating tumor volume is difficult due to their irregular shapes, and manual segmentation is time-consuming. Automatic segmentation using U-Net and its variants, incorporating Vision Transformer (ViT) elements, has shown promising results but struggles with high computational demands. To address this, architectures like the Mamba State Space Model (SSM) and Extended Long-Short Term Memory (xLSTM) offer efficient solutions by handling long-range dependencies with lower resource consumption. This study evaluates U-Net enhancements, including CNN, ViT, Mamba, and xLSTM, on a new in-house CT dataset and a public organ segmentation dataset. The proposed ViLU-Net model integrates Vi-blocks for improved segmentation. Results highlight xLSTM's efficiency in the U-Net framework. The code is publicly accessible on GitHub.