Daily Papers

Root canal (RC) treatment is a highly delicate and technically complex procedure in clinical practice, heavily influenced by the clinicians' experience and subjective judgment. Deep learning has made significant advancements in the field of computer-aided diagnosis (CAD) because it can provide more objective and accurate diagnostic results. However, its application in RC treatment is still relatively rare, mainly due to the lack of public datasets in this field. To address this issue, in this paper, we established a First Molar Root Canal segmentation dataset called FMRC-2025. Additionally, to alleviate the workload of manual annotation for dentists and fully leverage the unlabeled data, we designed a Cross-Frequency Collaborative training semi-supervised learning (SSL) Network called CFC-Net. It consists of two components: (1) Cross-Frequency Collaborative Mean Teacher (CFC-MT), which introduces two specialized students (SS) and one comprehensive teacher (CT) for collaborative multi-frequency training. The CT and SS are trained on different frequency components while fully integrating multi-frequency knowledge through cross and full frequency consistency supervisions. (2) Uncertainty-guided Cross-Frequency Mix (UCF-Mix) mechanism enables the network to generate high-confidence pseudo-labels while learning to integrate multi-frequency information and maintaining the structural integrity of the targets. Extensive experiments on FMRC-2025 and three public dental datasets demonstrate that CFC-MT is effective for RC segmentation and can also exhibit strong generalizability on other dental segmentation tasks, outperforming state-of-the-art SSL medical image segmentation methods. Codes and dataset will be released.

Teeth segmentation and recognition are critical in various dental applications and dental diagnosis. Automatic and accurate segmentation approaches have been made possible by integrating deep learning models. Although teeth segmentation has been studied in the past, only some techniques were able to effectively classify and segment teeth simultaneously. This article offers a pipeline of two deep learning models, U-Net and YOLOv8, which results in BB-UNet, a new architecture for the classification and segmentation of teeth on panoramic X-rays that is efficient and reliable. We have improved the quality and reliability of teeth segmentation by utilising the YOLOv8 and U-Net capabilities. The proposed networks have been evaluated using the mean average precision (mAP) and dice coefficient for YOLOv8 and BB-UNet, respectively. We have achieved a 3\% increase in mAP score for teeth classification compared to existing methods, and a 10-15\% increase in dice coefficient for teeth segmentation compared to U-Net across different categories of teeth. A new Dental dataset was created based on UFBA-UESC dataset with Bounding-Box and Polygon annotations of 425 dental panoramic X-rays. The findings of this research pave the way for a wider adoption of object detection models in the field of dental diagnosis.

Deep learning (DL), a pivotal technology in artificial intelligence, has recently gained substantial traction in the domain of dental auxiliary diagnosis. However, its application has predominantly been confined to imaging modalities such as panoramic radiographs and Cone Beam Computed Tomography, with limited focus on auxiliary analysis specifically targeting Periapical Radiographs (PR). PR are the most extensively utilized imaging modality in endodontics and periodontics due to their capability to capture detailed local lesions at a low cost. Nevertheless, challenges such as resolution limitations and artifacts complicate the annotation and recognition of PR, leading to a scarcity of publicly available, large-scale, high-quality PR analysis datasets. This scarcity has somewhat impeded the advancement of DL applications in PR analysis. In this paper, we present PRAD-10K, a dataset for PR analysis. PRAD-10K comprises 10,000 clinical periapical radiograph images, with pixel-level annotations provided by professional dentists for nine distinct anatomical structures, lesions, and artificial restorations or medical devices, We also include classification labels for images with typical conditions or lesions. Furthermore, we introduce a DL network named PRNet to establish benchmarks for PR segmentation tasks. Experimental results demonstrate that PRNet surpasses previous state-of-the-art medical image segmentation models on the PRAD-10K dataset. The codes and dataset will be made publicly available.

Achieving meticulous segmentation of tooth point clouds from intra-oral scans stands as an indispensable prerequisite for various orthodontic applications. Given the labor-intensive nature of dental annotation, a significant amount of data remains unlabeled, driving increasing interest in semi-supervised approaches. One primary challenge of existing semi-supervised medical segmentation methods lies in noisy pseudo labels generated for unlabeled data. To address this challenge, we propose GeoT, the first framework that employs instance-dependent transition matrix (IDTM) to explicitly model noise in pseudo labels for semi-supervised dental segmentation. Specifically, to handle the extensive solution space of IDTM arising from tens of thousands of dental points, we introduce tooth geometric priors through two key components: point-level geometric regularization (PLGR) to enhance consistency between point adjacency relationships in 3D and IDTM spaces, and class-level geometric smoothing (CLGS) to leverage the fixed spatial distribution of tooth categories for optimal IDTM estimation. Extensive experiments performed on the public Teeth3DS dataset and private dataset demonstrate that our method can make full utilization of unlabeled data to facilitate segmentation, achieving performance comparable to fully supervised methods with only 20% of the labeled data.

Tooth segmentation is a pivotal step in modern digital dentistry, essential for applications across orthodontic diagnosis and treatment planning. Despite its importance, this process is fraught with challenges due to the high noise and low contrast inherent in 2D and 3D tooth data. Both Convolutional Neural Networks (CNNs) and Transformers has shown promise in medical image segmentation, yet each method has limitations in handling long-range dependencies and computational complexity. To address this issue, this paper introduces T-Mamba, integrating frequency-based features and shared bi-positional encoding into vision mamba to address limitations in efficient global feature modeling. Besides, we design a gate selection unit to integrate two features in spatial domain and one feature in frequency domain adaptively. T-Mamba is the first work to introduce frequency-based features into vision mamba, and its flexibility allows it to process both 2D and 3D tooth data without the need for separate modules. Also, the TED3, a large-scale public tooth 2D dental X-ray dataset, has been presented in this paper. Extensive experiments demonstrate that T-Mamba achieves new SOTA results on a public tooth CBCT dataset and outperforms previous SOTA methods on TED3 dataset. The code and models are publicly available at: https://github.com/isbrycee/T-Mamba.

Due to the necessity for precise treatment planning, the use of panoramic X-rays to identify different dental diseases has tremendously increased. Although numerous ML models have been developed for the interpretation of panoramic X-rays, there has not been an end-to-end model developed that can identify problematic teeth with dental enumeration and associated diagnoses at the same time. To develop such a model, we structure the three distinct types of annotated data hierarchically following the FDI system, the first labeled with only quadrant, the second labeled with quadrant-enumeration, and the third fully labeled with quadrant-enumeration-diagnosis. To learn from all three hierarchies jointly, we introduce a novel diffusion-based hierarchical multi-label object detection framework by adapting a diffusion-based method that formulates object detection as a denoising diffusion process from noisy boxes to object boxes. Specifically, to take advantage of the hierarchically annotated data, our method utilizes a novel noisy box manipulation technique by adapting the denoising process in the diffusion network with the inference from the previously trained model in hierarchical order. We also utilize a multi-label object detection method to learn efficiently from partial annotations and to give all the needed information about each abnormal tooth for treatment planning. Experimental results show that our method significantly outperforms state-of-the-art object detection methods, including RetinaNet, Faster R-CNN, DETR, and DiffusionDet for the analysis of panoramic X-rays, demonstrating the great potential of our method for hierarchically and partially annotated datasets. The code and the data are available at: https://github.com/ibrahimethemhamamci/HierarchicalDet.

Semi-supervised learning has become a compelling approach for 3D tooth segmentation from CBCT scans, where labeled data is minimal. However, existing methods still face two persistent challenges: limited corrective supervision in structurally ambiguous or mislabeled regions during supervised training and performance degradation caused by unreliable pseudo-labels on unlabeled data. To address these problems, we propose Region-Aware Instructive Learning (RAIL), a dual-group dual-student, semi-supervised framework. Each group contains two student models guided by a shared teacher network. By alternating training between the two groups, RAIL promotes intergroup knowledge transfer and collaborative region-aware instruction while reducing overfitting to the characteristics of any single model. Specifically, RAIL introduces two instructive mechanisms. Disagreement-Focused Supervision (DFS) Controller improves supervised learning by instructing predictions only within areas where student outputs diverge from both ground truth and the best student, thereby concentrating supervision on structurally ambiguous or mislabeled areas. In the unsupervised phase, Confidence-Aware Learning (CAL) Modulator reinforces agreement in regions with high model certainty while reducing the effect of low-confidence predictions during training. This helps prevent our model from learning unstable patterns and improves the overall reliability of pseudo-labels. Extensive experiments on four CBCT tooth segmentation datasets show that RAIL surpasses state-of-the-art methods under limited annotation. Our code will be available at https://github.com/Tournesol-Saturday/RAIL.

In this work, we focused on deep learning image processing in the context of oral rare diseases, which pose challenges due to limited data availability. A crucial step involves teeth detection, segmentation and numbering in panoramic radiographs. To this end, we used a dataset consisting of 156 panoramic radiographs from individuals with rare oral diseases and labeled by experts. We trained the Detection Transformer (DETR) neural network for teeth detection, segmentation, and numbering the 52 teeth classes. In addition, we used data augmentation techniques, including geometric transformations. Finally, we generated new panoramic images using inpainting techniques with stable diffusion, by removing teeth from a panoramic radiograph and integrating teeth into it. The results showed a mAP exceeding 0,69 for DETR without data augmentation. The mAP was improved to 0,82 when data augmentation techniques are used. Furthermore, we observed promising performances when using new panoramic radiographs generated with inpainting technique, with mAP of 0,76.

Detecting dental diseases through panoramic X-rays images is a standard procedure for dentists. Normally, a dentist need to identify diseases and find the infected teeth. While numerous machine learning models adopting this two-step procedure have been developed, there has not been an end-to-end model that can identify teeth and their associated diseases at the same time. To fill the gap, we develop YOLOrtho, a unified framework for teeth enumeration and dental disease detection. We develop our model on Dentex Challenge 2023 data, which consists of three distinct types of annotated data. The first part is labeled with quadrant, and the second part is labeled with quadrant and enumeration and the third part is labeled with quadrant, enumeration and disease. To further improve detection, we make use of Tufts Dental public dataset. To fully utilize the data and learn both teeth detection and disease identification simultaneously, we formulate diseases as attributes attached to their corresponding teeth. Due to the nature of position relation in teeth enumeration, We replace convolution layer with CoordConv in our model to provide more position information for the model. We also adjust the model architecture and insert one more upsampling layer in FPN in favor of large object detection. Finally, we propose a post-process strategy for teeth layout that corrects teeth enumeration based on linear sum assignment. Results from experiments show that our model exceeds large Diffusion-based model.

The increasing prevalence of lumbar spinal canal stenosis has resulted in a surge of MRI (Magnetic Resonance Imaging), leading to labor-intensive interpretation and significant inter-reader variability, even among expert radiologists. This paper introduces a novel and efficient deep-learning framework that fully automates the grading of lumbar spinal canal stenosis. We demonstrate state-of-the-art performance in grading spinal canal stenosis on a dataset of 1,975 unique studies, each containing three distinct types of 3D cross-sectional spine images: Axial T2, Sagittal T1, and Sagittal T2/STIR. Employing a distinctive training strategy, our proposed multistage approach effectively integrates sagittal and axial images. This strategy employs a multi-view model with a sequence-based architecture, optimizing feature extraction and cross-view alignment to achieve an AUROC (Area Under the Receiver Operating Characteristic Curve) of 0.971 in spinal canal stenosis grading surpassing other state-of-the-art methods.

Panoramic X-rays are frequently used in dentistry for treatment planning, but their interpretation can be both time-consuming and prone to error. Artificial intelligence (AI) has the potential to aid in the analysis of these X-rays, thereby improving the accuracy of dental diagnoses and treatment plans. Nevertheless, designing automated algorithms for this purpose poses significant challenges, mainly due to the scarcity of annotated data and variations in anatomical structure. To address these issues, the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge (DENTEX) has been organized in association with the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) in 2023. This challenge aims to promote the development of algorithms for multi-label detection of abnormal teeth, using three types of hierarchically annotated data: partially annotated quadrant data, partially annotated quadrant-enumeration data, and fully annotated quadrant-enumeration-diagnosis data, inclusive of four different diagnoses. In this paper, we present the results of evaluating participant algorithms on the fully annotated data, additionally investigating performance variation for quadrant, enumeration, and diagnosis labels in the detection of abnormal teeth. The provision of this annotated dataset, alongside the results of this challenge, may lay the groundwork for the creation of AI-powered tools that can offer more precise and efficient diagnosis and treatment planning in the field of dentistry. The evaluation code and datasets can be accessed at https://github.com/ibrahimethemhamamci/DENTEX

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

Medical image analysis is critical yet challenged by the need of jointly segmenting organs or tissues, and numerous instances for anatomical structures and tumor microenvironment analysis. Existing studies typically formulated different segmentation tasks in isolation, which overlooks the fundamental interdependencies between these tasks, leading to suboptimal segmentation performance and insufficient medical image understanding. To address this issue, we propose a Co-Seg++ framework for versatile medical segmentation. Specifically, we introduce a novel co-segmentation paradigm, allowing semantic and instance segmentation tasks to mutually enhance each other. We first devise a spatio-temporal prompt encoder (STP-Encoder) to capture long-range spatial and temporal relationships between segmentation regions and image embeddings as prior spatial constraints. Moreover, we devise a multi-task collaborative decoder (MTC-Decoder) that leverages cross-guidance to strengthen the contextual consistency of both tasks, jointly computing semantic and instance segmentation masks. Extensive experiments on diverse CT and histopathology datasets demonstrate that the proposed Co-Seg++ outperforms state-of-the-arts in the semantic, instance, and panoptic segmentation of dental anatomical structures, histopathology tissues, and nuclei instances. The source code is available at https://github.com/xq141839/Co-Seg-Plus.

We propose a minimal path method to simultaneously compute segmentation masks and extract centerlines of tubular structures with line-topology. Minimal path methods are commonly used for the segmentation of tubular structures in a wide variety of applications. Recent methods use features extracted by CNNs, and often outperform methods using hand-tuned features. However, for CNN-based methods, the samples used for training may be generated inappropriately, so that they can be very different from samples encountered during inference. We approach this discrepancy by introducing a novel iterative training scheme, which enables generating better training samples specifically tailored for the minimal path methods without changing existing annotations. In our method, segmentation masks and centerlines are not determined after one another by post-processing, but obtained using the same steps. Our method requires only very few annotated training images. Comparison with seven previous approaches on three public datasets, including satellite images and medical images, shows that our method achieves state-of-the-art results both for segmentation masks and centerlines.

Tooth arrangement is a crucial step in orthodontics treatment, in which aligning teeth could improve overall well-being, enhance facial aesthetics, and boost self-confidence. To improve the efficiency of tooth arrangement and minimize errors associated with unreasonable designs by inexperienced practitioners, some deep learning-based tooth arrangement methods have been proposed. Currently, most existing approaches employ MLPs to model the nonlinear relationship between tooth features and transformation matrices to achieve tooth arrangement automatically. However, the limited datasets (which to our knowledge, have not been made public) collected from clinical practice constrain the applicability of existing methods, making them inadequate for addressing diverse malocclusion issues. To address this challenge, we propose a general tooth arrangement neural network based on the diffusion probabilistic model. Conditioned on the features extracted from the dental model, the diffusion probabilistic model can learn the distribution of teeth transformation matrices from malocclusion to normal occlusion by gradually denoising from a random variable, thus more adeptly managing real orthodontic data. To take full advantage of effective features, we exploit both mesh and point cloud representations by designing different encoding networks to extract the tooth (local) and jaw (global) features, respectively. In addition to traditional metrics ADD, PA-ADD, CSA, and ME_{rot}, we propose a new evaluation metric based on dental arch curves to judge whether the generated teeth meet the individual normal occlusion. Experimental results demonstrate that our proposed method achieves state-of-the-art tooth alignment results and satisfactory occlusal relationships between dental arches. We will publish the code and dataset.

Segmentation of biomedical images can assist radiologists to make a better diagnosis and take decisions faster by helping in the detection of abnormalities, such as tumors. Manual or semi-automated segmentation, however, can be a time-consuming task. Most deep learning based automated segmentation methods are supervised and rely on manually segmented ground-truth. A possible solution for the problem would be an unsupervised deep learning based approach for automated segmentation, which this research work tries to address. We use a W-Net architecture and modified it, such that it can be applied to 3D volumes. In addition, to suppress noise in the segmentation we added attention gates to the skip connections. The loss for the segmentation output was calculated using soft N-Cuts and for the reconstruction output using SSIM. Conditional Random Fields were used as a post-processing step to fine-tune the results. The proposed method has shown promising results, with a dice coefficient of 0.88 for the liver segmentation compared against manual segmentation.

In this paper, we propose a hybrid approach for multi-object microbial cell segmentation. The approach combines an ML-based detection with a geometry-aware variational-based segmentation using B-splines that are parametrized based on a geometric model of the cell shape. The detection is done first using YOLOv5. In a second step, each detected cell is segmented individually. Thus, the segmentation only needs to be done on a per-cell basis, which makes it amenable to a variational approach that incorporates prior knowledge on the geometry. Here, the contour of the segmentation is modelled as closed uniform cubic B-spline, whose control points are parametrized using the known cell geometry. Compared to purely ML-based segmentation approaches, which need accurate segmentation maps as training data that are very laborious to produce, our method just needs bounding boxes as training data. Still, the proposed method performs on par with ML-based segmentation approaches usually used in this context. We study the performance of the proposed method on time-lapse microscopy data of Corynebacterium glutamicum.

Segmentation of surgical instruments is crucial for enhancing surgeon performance and ensuring patient safety. Conventional techniques such as binary, semantic, and instance segmentation share a common drawback: they do not accommodate the parts of instruments obscured by tissues or other instruments. Precisely predicting the full extent of these occluded instruments can significantly improve laparoscopic surgeries by providing critical guidance during operations and assisting in the analysis of potential surgical errors, as well as serving educational purposes. In this paper, we introduce Amodal Segmentation to the realm of surgical instruments in the medical field. This technique identifies both the visible and occluded parts of an object. To achieve this, we introduce a new Amoal Instruments Segmentation (AIS) dataset, which was developed by reannotating each instrument with its complete mask, utilizing the 2017 MICCAI EndoVis Robotic Instrument Segmentation Challenge dataset. Additionally, we evaluate several leading amodal segmentation methods to establish a benchmark for this new dataset.

The stability of mine dumps is contingent upon the precise arrangement of spoil piles, taking into account their geological and geotechnical attributes. Yet, on-site characterisation of individual piles poses a formidable challenge. The utilisation of image-based techniques for spoil pile characterisation, employing remotely acquired data through unmanned aerial systems, is a promising complementary solution. Image processing, such as object-based classification and feature extraction, are dependent upon effective segmentation. This study refines and juxtaposes various segmentation approaches, specifically colour-based and morphology-based techniques. The objective is to enhance and evaluate avenues for object-based analysis for spoil characterisation within the context of mining environments. Furthermore, a comparative analysis is conducted between conventional segmentation approaches and those rooted in deep learning methodologies. Among the diverse segmentation approaches evaluated, the morphology-based deep learning segmentation approach, Segment Anything Model (SAM), exhibited superior performance in comparison to other approaches. This outcome underscores the efficacy of incorporating advanced morphological and deep learning techniques for accurate and efficient spoil pile characterisation. The findings of this study contribute valuable insights to the optimisation of segmentation strategies, thereby advancing the application of image-based techniques for the characterisation of spoil piles in mining environments.

Precise image segmentation provides clinical study with meaningful and well-structured information. Despite the remarkable progress achieved in medical image segmentation, there is still an absence of foundation segmentation model that can segment a wide range of anatomical categories with easy user interaction. In this paper, we propose a universal and interactive volumetric medical image segmentation model, named SegVol. By training on 90k unlabeled Computed Tomography (CT) volumes and 6k labeled CTs, this foundation model supports the segmentation of over 200 anatomical categories using semantic and spatial prompts. Extensive experiments verify that SegVol outperforms the state of the art by a large margin on multiple segmentation benchmarks. Notably, on three challenging lesion datasets, our method achieves around 20% higher Dice score than nnU-Net. The model and data are publicly available at: https://github.com/BAAI-DCAI/SegVol.

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Despite the progress in medical image segmentation, most existing methods remain task-specific and lack interactivity. Although recent text-prompt-based segmentation approaches enhance user-driven and reasoning-based segmentation, they remain confined to single-round dialogues and fail to perform multi-round reasoning. In this work, we introduce Multi-Round Entity-Level Medical Reasoning Segmentation (MEMR-Seg), a new task that requires generating segmentation masks through multi-round queries with entity-level reasoning. To support this task, we construct MR-MedSeg, a large-scale dataset of 177K multi-round medical segmentation dialogues, featuring entity-based reasoning across rounds. Furthermore, we propose MediRound, an effective baseline model designed for multi-round medical reasoning segmentation. To mitigate the inherent error propagation in the chain-like pipeline of multi-round segmentation, we introduce a lightweight yet effective Judgment & Correction Mechanism during model inference. Experimental results demonstrate that our method effectively addresses the MEMR-Seg task and outperforms conventional medical referring segmentation methods.

The recent release of RadGenome-Chest CT has significantly advanced CT-based report generation. However, existing methods primarily focus on global features, making it challenging to capture region-specific details, which may cause certain abnormalities to go unnoticed. To address this, we propose MedRegion-CT, a region-focused Multi-Modal Large Language Model (MLLM) framework, featuring three key innovations. First, we introduce Region Representative (R^2) Token Pooling, which utilizes a 2D-wise pretrained vision model to efficiently extract 3D CT features. This approach generates global tokens representing overall slice features and region tokens highlighting target areas, enabling the MLLM to process comprehensive information effectively. Second, a universal segmentation model generates pseudo-masks, which are then processed by a mask encoder to extract region-centric features. This allows the MLLM to focus on clinically relevant regions, using six predefined region masks. Third, we leverage segmentation results to extract patient-specific attributions, including organ size, diameter, and locations. These are converted into text prompts, enriching the MLLM's understanding of patient-specific contexts. To ensure rigorous evaluation, we conducted benchmark experiments on report generation using the RadGenome-Chest CT. MedRegion-CT achieved state-of-the-art performance, outperforming existing methods in natural language generation quality and clinical relevance while maintaining interpretability. The code for our framework is publicly available.

Multimodal Large Language Models (MLLMs) have exhibited immense potential across numerous medical specialties; yet, dentistry remains underexplored, in part due to limited domain-specific data, scarce dental expert annotations, insufficient modality-specific modeling, and challenges in reliability. In this paper, we present OralGPT-Omni, the first dental-specialized MLLM designed for comprehensive and trustworthy analysis across diverse dental imaging modalities and clinical tasks. To explicitly capture dentists' diagnostic reasoning, we construct TRACE-CoT, a clinically grounded chain-of-thought dataset that mirrors dental radiologists' decision-making processes. This reasoning supervision, combined with our proposed four-stage training paradigm, substantially strengthens the model's capacity for dental image understanding and analysis. In parallel, we introduce MMOral-Uni, the first unified multimodal benchmark for dental image analysis. It comprises 2,809 open-ended question-answer pairs spanning five modalities and five tasks, offering a comprehensive evaluation suite to date for MLLMs in digital dentistry. OralGPT-Omni achieves an overall score of 51.84 on the MMOral-Uni benchmark and 45.31 on the MMOral-OPG benchmark, dramatically outperforming the scores of GPT-5. Our work promotes intelligent dentistry and paves the way for future advances in dental image analysis. All code, benchmark, and models will be made publicly available.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

Polyp segmentation, a contentious issue in medical imaging, has seen numerous proposed methods aimed at improving the quality of segmented masks. While current state-of-the-art techniques yield impressive results, the size and computational cost of these models create challenges for practical industry applications. To address this challenge, we present KDAS, a Knowledge Distillation framework that incorporates attention supervision, and our proposed Symmetrical Guiding Module. This framework is designed to facilitate a compact student model with fewer parameters, allowing it to learn the strengths of the teacher model and mitigate the inconsistency between teacher features and student features, a common challenge in Knowledge Distillation, via the Symmetrical Guiding Module. Through extensive experiments, our compact models demonstrate their strength by achieving competitive results with state-of-the-art methods, offering a promising approach to creating compact models with high accuracy for polyp segmentation and in the medical imaging field. The implementation is available on https://github.com/huyquoctrinh/KDAS.

Adolescent idiopathic scoliosis (AIS) is a lifetime disease that arises in children. Accurate estimation of Cobb angles of the scoliosis is essential for clinicians to make diagnosis and treatment decisions. The Cobb angles are measured according to the vertebrae landmarks. Existing regression-based methods for the vertebra landmark detection typically suffer from large dense mapping parameters and inaccurate landmark localization. The segmentation-based methods tend to predict connected or corrupted vertebra masks. In this paper, we propose a novel vertebra-focused landmark detection method. Our model first localizes the vertebra centers, based on which it then traces the four corner landmarks of the vertebra through the learned corner offset. In this way, our method is able to keep the order of the landmarks. The comparison results demonstrate the merits of our method in both Cobb angle measurement and landmark detection on low-contrast and ambiguous X-ray images. Code is available at: https://github.com/yijingru/Vertebra-Landmark-Detection.

We introduce Medal S, a medical segmentation foundation model that supports native-resolution spatial and textual prompts within an end-to-end trainable framework. Unlike text-only methods lacking spatial awareness, Medal S achieves channel-wise alignment between volumetric prompts and text embeddings, mitigating inaccuracies from resolution mismatches. By preserving full 3D context, it efficiently processes multiple native-resolution masks in parallel, enhancing multi-class segmentation performance. A lightweight 3D convolutional module enables precise voxel-space refinement guided by both prompt types, supporting up to 243 classes across CT, MRI, PET, ultrasound, and microscopy modalities in the BiomedSegFM dataset. Medal S offers two prompting modes: a text-only mode, where model predictions serve as spatial prompts for self-refinement without human input, and a hybrid mode, incorporating manual annotations for enhanced flexibility. For 24-class segmentation, parallel spatial prompting reduces inference time by more than 90% compared to sequential prompting. We propose dynamic resampling to address target-patch ratio imbalance, extending SAT and nnU-Net for data augmentation. Furthermore, we develop optimized text preprocessing, a two-stage inference strategy, and post-processing techniques to improve memory efficiency, precision, and inference speed. On the five-modality average on the validation set, Medal S outperforms SAT with a DSC of 75.44 (vs. 69.83), NSD of 77.34 (vs. 71.06), F1 of 38.24 (vs. 24.88), and DSC TP of 65.46 (vs. 46.97). Medal S achieves excellent performance by harmonizing spatial precision with semantic textual guidance, demonstrating superior efficiency and accuracy in multi-class medical segmentation tasks compared to sequential prompt-based approaches. Medal S will be publicly available at https://github.com/yinghemedical/Medal-S.

Rapid advancements in medical image segmentation performance have been significantly driven by the development of Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). These models follow the discriminative pixel-wise classification learning paradigm and often have limited ability to generalize across diverse medical imaging datasets. In this manuscript, we introduce Generative Medical Segmentation (GMS), a novel approach leveraging a generative model to perform image segmentation. Concretely, GMS employs a robust pre-trained vision foundation model to extract latent representations for images and corresponding ground truth masks, followed by a model that learns a mapping function from the image to the mask in the latent space. Once trained, the model generates an estimated segmentation mask using the pre-trained vision foundation model to decode the predicted latent representation back into the image space. The design of GMS leads to fewer trainable parameters in the model which reduces the risk of overfitting and enhances its generalization capability. Our experimental analysis across five public datasets in different medical imaging domains demonstrates GMS outperforms existing discriminative and generative segmentation models. Furthermore, GMS is able to generalize well across datasets from different centers within the same imaging modality. Our experiments suggest GMS offers a scalable and effective solution for medical image segmentation. GMS implementation and trained model weights are available at https://github.com/King-HAW/GMS.

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds millions voxels) of the pore space can be extracted, from grey level 3D CT scanner images, by means of simple image processing tools. Classical methods for numerical simulation of biological dynamics using mesh of voxels, such as Lattice Boltzmann Model (LBM), are too much time consuming. Thus, the use of more compact and reliable geometrical representations of pore space can drastically decrease the computational cost of the simulations. Several recent works propose basic analytic volume primitives (e.g. spheres, generalized cylinders, ellipsoids) to define a piece-wise approximation of pore space for numerical simulation of draining, diffusion and microbial decomposition. Such approaches work well but the drawback is that it generates approximation errors. In the present work, we study another alternative where pore space is described by means of geometrically relevant connected subsets of voxels (regions) computed from the curvilinear skeleton. Indeed, many works use the curvilinear skeleton (3D medial axis) for analyzing and partitioning 3D shapes within various domains (medicine, material sciences, petroleum engineering, etc.) but only a few ones in soil sciences. Within the context of soil sciences, most studies dealing with 3D medial axis focus on the determination of pore throats. Here, we segment pore space using curvilinear skeleton in order to achieve numerical simulation of microbial decomposition (including diffusion processes). We validate simulation outputs by comparison with other methods using different pore space geometrical representations (balls, voxels).

This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.

Leveraging the powerful capabilities of diffusion models has yielded quite effective results in medical image segmentation tasks. However, existing methods typically transfer the original training process directly without specific adjustments for segmentation tasks. Furthermore, the commonly used pre-trained diffusion models still have deficiencies in feature extraction. Based on these considerations, we propose LEAF, a medical image segmentation model grounded in latent diffusion models. During the fine-tuning process, we replace the original noise prediction pattern with a direct prediction of the segmentation map, thereby reducing the variance of segmentation results. We also employ a feature distillation method to align the hidden states of the convolutional layers with the features from a transformer-based vision encoder. Experimental results demonstrate that our method enhances the performance of the original diffusion model across multiple segmentation datasets for different disease types. Notably, our approach does not alter the model architecture, nor does it increase the number of parameters or computation during the inference phase, making it highly efficient.

The detailed images produced by Magnetic Resonance Imaging (MRI) provide life-critical information for the diagnosis and treatment of prostate cancer. To provide standardized acquisition, interpretation and usage of the complex MRI images, the PI-RADS v2 guideline was proposed. An automated segmentation following the guideline facilitates consistent and precise lesion detection, staging and treatment. The guideline recommends a division of the prostate into four zones, PZ (peripheral zone), TZ (transition zone), DPU (distal prostatic urethra) and AFS (anterior fibromuscular stroma). Not every zone shares a boundary with the others and is present in every slice. Further, the representations captured by a single model might not suffice for all zones. This motivated us to design a dual-branch convolutional neural network (CNN), where each branch captures the representations of the connected zones separately. Further, the representations from different branches act complementary to each other at the second stage of training, where they are fine-tuned through an unsupervised loss. The loss penalises the difference in predictions from the two branches for the same class. We also incorporate multi-task learning in our framework to further improve the segmentation accuracy. The proposed approach improves the segmentation accuracy of the baseline (mean absolute symmetric distance) by 7.56%, 11.00%, 58.43% and 19.67% for PZ, TZ, DPU and AFS zones respectively.

Colonoscopy is an effective technique for detecting colorectal polyps, which are highly related to colorectal cancer. In clinical practice, segmenting polyps from colonoscopy images is of great importance since it provides valuable information for diagnosis and surgery. However, accurate polyp segmentation is a challenging task, for two major reasons: (i) the same type of polyps has a diversity of size, color and texture; and (ii) the boundary between a polyp and its surrounding mucosa is not sharp. To address these challenges, we propose a parallel reverse attention network (PraNet) for accurate polyp segmentation in colonoscopy images. Specifically, we first aggregate the features in high-level layers using a parallel partial decoder (PPD). Based on the combined feature, we then generate a global map as the initial guidance area for the following components. In addition, we mine the boundary cues using a reverse attention (RA) module, which is able to establish the relationship between areas and boundary cues. Thanks to the recurrent cooperation mechanism between areas and boundaries, our PraNet is capable of calibrating any misaligned predictions, improving the segmentation accuracy. Quantitative and qualitative evaluations on five challenging datasets across six metrics show that our PraNet improves the segmentation accuracy significantly, and presents a number of advantages in terms of generalizability, and real-time segmentation efficiency.

In this paper, we propose a novel text promptable surgical instrument segmentation approach to overcome challenges associated with diversity and differentiation of surgical instruments in minimally invasive surgeries. We redefine the task as text promptable, thereby enabling a more nuanced comprehension of surgical instruments and adaptability to new instrument types. Inspired by recent advancements in vision-language models, we leverage pretrained image and text encoders as our model backbone and design a text promptable mask decoder consisting of attention- and convolution-based prompting schemes for surgical instrument segmentation prediction. Our model leverages multiple text prompts for each surgical instrument through a new mixture of prompts mechanism, resulting in enhanced segmentation performance. Additionally, we introduce a hard instrument area reinforcement module to improve image feature comprehension and segmentation precision. Extensive experiments on EndoVis2017 and EndoVis2018 datasets demonstrate our model's superior performance and promising generalization capability. To our knowledge, this is the first implementation of a promptable approach to surgical instrument segmentation, offering significant potential for practical application in the field of robotic-assisted surgery.

Reliable interpretation of multimodal data in dentistry is essential for automated oral healthcare, yet current multimodal large language models (MLLMs) struggle to capture fine-grained dental visual details and lack sufficient reasoning ability for precise diagnosis. To address these limitations, we present DentalGPT, a specialized dental MLLM developed through high-quality domain knowledge injection and reinforcement learning. Specifically, the largest annotated multimodal dataset for dentistry to date was constructed by aggregating over 120k dental images paired with detailed descriptions that highlight diagnostically relevant visual features, making it the multimodal dataset with the most extensive collection of dental images to date. Training on this dataset significantly enhances the MLLM's visual understanding of dental conditions, while the subsequent reinforcement learning stage further strengthens its capability for multimodal complex reasoning. Comprehensive evaluations on intraoral and panoramic benchmarks, along with dental subsets of medical VQA benchmarks, show that DentalGPT achieves superior performance in disease classification and dental VQA tasks, outperforming many state-of-the-art MLLMs despite having only 7B parameters. These results demonstrate that high-quality dental data combined with staged adaptation provides an effective pathway for building capable and domain-specialized dental MLLMs.

Medical image segmentation allows quantifying target structure size and shape, aiding in disease diagnosis, prognosis, surgery planning, and comprehension.Building upon recent advancements in foundation Vision-Language Models (VLMs) from natural image-text pairs, several studies have proposed adapting them to Vision-Language Segmentation Models (VLSMs) that allow using language text as an additional input to segmentation models. Introducing auxiliary information via text with human-in-the-loop prompting during inference opens up unique opportunities, such as open vocabulary segmentation and potentially more robust segmentation models against out-of-distribution data. Although transfer learning from natural to medical images has been explored for image-only segmentation models, the joint representation of vision-language in segmentation problems remains underexplored. This study introduces the first systematic study on transferring VLSMs to 2D medical images, using carefully curated 11 datasets encompassing diverse modalities and insightful language prompts and experiments. Our findings demonstrate that although VLSMs show competitive performance compared to image-only models for segmentation after finetuning in limited medical image datasets, not all VLSMs utilize the additional information from language prompts, with image features playing a dominant role. While VLSMs exhibit enhanced performance in handling pooled datasets with diverse modalities and show potential robustness to domain shifts compared to conventional segmentation models, our results suggest that novel approaches are required to enable VLSMs to leverage the various auxiliary information available through language prompts. The code and datasets are available at https://github.com/naamiinepal/medvlsm.

Glaucoma is one of the leading causes of irreversible but preventable blindness in working age populations. Color fundus photography (CFP) is the most cost-effective imaging modality to screen for retinal disorders. However, its application to glaucoma has been limited to the computation of a few related biomarkers such as the vertical cup-to-disc ratio. Deep learning approaches, although widely applied for medical image analysis, have not been extensively used for glaucoma assessment due to the limited size of the available data sets. Furthermore, the lack of a standardize benchmark strategy makes difficult to compare existing methods in a uniform way. In order to overcome these issues we set up the Retinal Fundus Glaucoma Challenge, REFUGE (https://refuge.grand-challenge.org), held in conjunction with MICCAI 2018. The challenge consisted of two primary tasks, namely optic disc/cup segmentation and glaucoma classification. As part of REFUGE, we have publicly released a data set of 1200 fundus images with ground truth segmentations and clinical glaucoma labels, currently the largest existing one. We have also built an evaluation framework to ease and ensure fairness in the comparison of different models, encouraging the development of novel techniques in the field. 12 teams qualified and participated in the online challenge. This paper summarizes their methods and analyzes their corresponding results. In particular, we observed that two of the top-ranked teams outperformed two human experts in the glaucoma classification task. Furthermore, the segmentation results were in general consistent with the ground truth annotations, with complementary outcomes that can be further exploited by ensembling the results.

Airway segmentation on CT scans is critical for pulmonary disease diagnosis and endobronchial navigation. Manual extraction of airway requires strenuous efforts due to the complicated structure and various appearance of airway. For automatic airway extraction, convolutional neural networks (CNNs) based methods have recently become the state-of-the-art approach. However, there still remains a challenge for CNNs to perceive the tree-like pattern and comprehend the connectivity of airway. To address this, we propose a voxel-connectivity aware approach named AirwayNet for accurate airway segmentation. By connectivity modeling, conventional binary segmentation task is transformed into 26 tasks of connectivity prediction. Thus, our AirwayNet learns both airway structure and relationship between neighboring voxels. To take advantage of context knowledge, lung distance map and voxel coordinates are fed into AirwayNet as additional semantic information. Compared to existing approaches, AirwayNet achieved superior performance, demonstrating the effectiveness of the network's awareness of voxel connectivity.

In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {https://github.com/ChengyinLee/MulModSeg_2024{link}}.

Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.

In this paper, we present PRISM, a Promptable and Robust Interactive Segmentation Model, aiming for precise segmentation of 3D medical images. PRISM accepts various visual inputs, including points, boxes, and scribbles as sparse prompts, as well as masks as dense prompts. Specifically, PRISM is designed with four principles to achieve robustness: (1) Iterative learning. The model produces segmentations by using visual prompts from previous iterations to achieve progressive improvement. (2) Confidence learning. PRISM employs multiple segmentation heads per input image, each generating a continuous map and a confidence score to optimize predictions. (3) Corrective learning. Following each segmentation iteration, PRISM employs a shallow corrective refinement network to reassign mislabeled voxels. (4) Hybrid design. PRISM integrates hybrid encoders to better capture both the local and global information. Comprehensive validation of PRISM is conducted using four public datasets for tumor segmentation in the colon, pancreas, liver, and kidney, highlighting challenges caused by anatomical variations and ambiguous boundaries in accurate tumor identification. Compared to state-of-the-art methods, both with and without prompt engineering, PRISM significantly improves performance, achieving results that are close to human levels. The code is publicly available at https://github.com/MedICL-VU/PRISM.

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

Medical image segmentation has recently demonstrated impressive progress with deep neural networks, yet the heterogeneous modalities and scarcity of mask annotations limit the development of segmentation models on unannotated modalities. This paper investigates a new paradigm for leveraging generative models in medical applications: controllably synthesizing data for unannotated modalities, without requiring registered data pairs. Specifically, we make the following contributions in this paper: (i) we collect and curate a large-scale radiology image-text dataset, MedGen-1M, comprising modality labels, attributes, region, and organ information, along with a subset of organ mask annotations, to support research in controllable medical image generation; (ii) we propose a diffusion-based data engine, termed MRGen, which enables generation conditioned on text prompts and masks, synthesizing MR images for diverse modalities lacking mask annotations, to train segmentation models on unannotated modalities; (iii) we conduct extensive experiments across various modalities, illustrating that our data engine can effectively synthesize training samples and extend MRI segmentation towards unannotated modalities.

In the domain of medical imaging, many supervised learning based methods for segmentation face several challenges such as high variability in annotations from multiple experts, paucity of labelled data and class imbalanced datasets. These issues may result in segmentations that lack the requisite precision for clinical analysis and can be misleadingly overconfident without associated uncertainty quantification. We propose the PULASki for biomedical image segmentation that accurately captures variability in expert annotations, even in small datasets. Our approach makes use of an improved loss function based on statistical distances in a conditional variational autoencoder structure (Probabilistic UNet), which improves learning of the conditional decoder compared to the standard cross-entropy particularly in class imbalanced problems. We analyse our method for two structurally different segmentation tasks (intracranial vessel and multiple sclerosis (MS) lesion) and compare our results to four well-established baselines in terms of quantitative metrics and qualitative output. Empirical results demonstrate the PULASKi method outperforms all baselines at the 5\% significance level. The generated segmentations are shown to be much more anatomically plausible than in the 2D case, particularly for the vessel task. Our method can also be applied to a wide range of multi-label segmentation tasks and and is useful for downstream tasks such as hemodynamic modelling (computational fluid dynamics and data assimilation), clinical decision making, and treatment planning.

We propose Segment Any Mesh, a novel zero-shot mesh part segmentation method that overcomes the limitations of shape analysis-based, learning-based, and contemporary approaches. Our approach operates in two phases: multimodal rendering and 2D-to-3D lifting. In the first phase, multiview renders of the mesh are individually processed through Segment Anything to generate 2D masks. These masks are then lifted into a mesh part segmentation by associating masks that refer to the same mesh part across the multiview renders. We find that applying Segment Anything to multimodal feature renders of normals and shape diameter scalars achieves better results than using only untextured renders of meshes. By building our method on top of Segment Anything, we seamlessly inherit any future improvements made to 2D segmentation. We compare our method with a robust, well-evaluated shape analysis method, Shape Diameter Function, and show that our method is comparable to or exceeds its performance. Since current benchmarks contain limited object diversity, we also curate and release a dataset of generated meshes and use it to demonstrate our method's improved generalization over Shape Diameter Function via human evaluation. We release the code and dataset at https://github.com/gtangg12/samesh

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.

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.

Purpose: Foundation models, trained on multitudes of public datasets, often require additional fine-tuning or re-prompting mechanisms to be applied to visually distinct target domains such as surgical videos. Further, without domain knowledge, they cannot model the specific semantics of the target domain. Hence, when applied to surgical video segmentation, they fail to generalise to sections where previously tracked objects leave the scene or new objects enter. Methods: We propose SASVi, a novel re-prompting mechanism based on a frame-wise Mask R-CNN Overseer model, which is trained on a minimal amount of scarcely available annotations for the target domain. This model automatically re-prompts the foundation model SAM2 when the scene constellation changes, allowing for temporally smooth and complete segmentation of full surgical videos. Results: Re-prompting based on our Overseer model significantly improves the temporal consistency of surgical video segmentation compared to similar prompting techniques and especially frame-wise segmentation, which neglects temporal information, by at least 1.5%. Our proposed approach allows us to successfully deploy SAM2 to surgical videos, which we quantitatively and qualitatively demonstrate for three different cholecystectomy and cataract surgery datasets. Conclusion: SASVi can serve as a new baseline for smooth and temporally consistent segmentation of surgical videos with scarcely available annotation data. Our method allows us to leverage scarce annotations and obtain complete annotations for full videos of the large-scale counterpart datasets. We make those annotations publicly available, providing extensive annotation data for the future development of surgical data science models.

Rotoscoping, the detailed delineation of scene elements through a video shot, is a painstaking task of tremendous importance in professional post-production pipelines. While pixel-wise segmentation techniques can help for this task, professional rotoscoping tools rely on parametric curves that offer the artists a much better interactive control on the definition, editing and manipulation of the segments of interest. Sticking to this prevalent rotoscoping paradigm, we propose a novel framework to capture and track the visual aspect of an arbitrary object in a scene, given a first closed outline of this object. This model combines a collection of local foreground/background appearance models spread along the outline, a global appearance model of the enclosed object and a set of distinctive foreground landmarks. The structure of this rich appearance model allows simple initialization, efficient iterative optimization with exact minimization at each step, and on-line adaptation in videos. We demonstrate qualitatively and quantitatively the merit of this framework through comparisons with tools based on either dynamic segmentation with a closed curve or pixel-wise binary labelling.

Accurate segmentation of regions of interest in biomedical images holds substantial value in image analysis. Although several foundation models for biomedical segmentation have currently achieved excellent performance on certain datasets, they typically demonstrate sub-optimal performance on unseen domain data. We owe the deficiency to lack of vision-language knowledge before segmentation. Multimodal Large Language Models (MLLMs) bring outstanding understanding and reasoning capabilities to multimodal tasks, which inspires us to leverage MLLMs to inject Vision-Language Knowledge (VLK), thereby enabling vision models to demonstrate superior generalization capabilities on cross-domain datasets. In this paper, we propose using MLLMs to guide SAM in learning microscopy crose-domain data, unifying Segment Anything in Microscopy, named uLLSAM. Specifically, we propose the Vision-Language Semantic Alignment (VLSA) module, which injects VLK into Segment Anything Model (SAM). We find that after SAM receives global VLK prompts, its performance improves significantly, but there are deficiencies in boundary contour perception. Therefore, we further propose Semantic Boundary Regularization (SBR) to prompt SAM. Our method achieves performance improvements of 7.71% in Dice and 12.10% in SA across 9 in-domain microscopy datasets, achieving state-of-the-art performance. Our method also demonstrates improvements of 6.79% in Dice and 10.08% in SA across 10 out-ofdomain datasets, exhibiting strong generalization capabilities. Code is available at https://github.com/ieellee/uLLSAM.

We present MeshSegmenter, a simple yet effective framework designed for zero-shot 3D semantic segmentation. This model successfully extends the powerful capabilities of 2D segmentation models to 3D meshes, delivering accurate 3D segmentation across diverse meshes and segment descriptions. Specifically, our model leverages the Segment Anything Model (SAM) model to segment the target regions from images rendered from the 3D shape. In light of the importance of the texture for segmentation, we also leverage the pretrained stable diffusion model to generate images with textures from 3D shape, and leverage SAM to segment the target regions from images with textures. Textures supplement the shape for segmentation and facilitate accurate 3D segmentation even in geometrically non-prominent areas, such as segmenting a car door within a car mesh. To achieve the 3D segments, we render 2D images from different views and conduct segmentation for both textured and untextured images. Lastly, we develop a multi-view revoting scheme that integrates 2D segmentation results and confidence scores from various views onto the 3D mesh, ensuring the 3D consistency of segmentation results and eliminating inaccuracies from specific perspectives. Through these innovations, MeshSegmenter offers stable and reliable 3D segmentation results both quantitatively and qualitatively, highlighting its potential as a transformative tool in the field of 3D zero-shot segmentation. The code is available at https://github.com/zimingzhong/MeshSegmenter.

Current 3D scene segmentation methods are heavily dependent on manually annotated 3D training datasets. Such manual annotations are labor-intensive, and often lack fine-grained details. Importantly, models trained on this data typically struggle to recognize object classes beyond the annotated classes, i.e., they do not generalize well to unseen domains and require additional domain-specific annotations. In contrast, 2D foundation models demonstrate strong generalization and impressive zero-shot abilities, inspiring us to incorporate these characteristics from 2D models into 3D models. Therefore, we explore the use of image segmentation foundation models to automatically generate training labels for 3D segmentation. We propose Segment3D, a method for class-agnostic 3D scene segmentation that produces high-quality 3D segmentation masks. It improves over existing 3D segmentation models (especially on fine-grained masks), and enables easily adding new training data to further boost the segmentation performance -- all without the need for manual training labels.

Medical image segmentation poses challenges due to domain gaps, data modality variations, and dependency on domain knowledge or experts, especially for low- and middle-income countries (LMICs). Whereas for humans, given a few exemplars (with corresponding labels), we are able to segment different medical images even without exten-sive domain-specific clinical training. In addition, current SAM-based medical segmentation models use fine-grained visual prompts, such as the bounding rectangle generated from manually annotated target segmentation mask, as the bounding box (bbox) prompt during the testing phase. However, in actual clinical scenarios, no such precise prior knowledge is available. Our experimental results also reveal that previous models nearly fail to predict when given coarser bbox prompts. Considering these issues, in this paper, we introduce a domain-aware selective adaptation approach to adapt the general knowledge learned from a large model trained with natural images to the corresponding medical domains/modalities, with access to only a few (e.g. less than 5) exemplars. Our method mitigates the aforementioned limitations, providing an efficient and LMICs-friendly solution. Extensive experimental analysis showcases the effectiveness of our approach, offering potential advancements in healthcare diagnostics and clinical applications in LMICs.

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

Considering the increased workload in pathology laboratories today, automated tools such as artificial intelligence models can help pathologists with their tasks and ease the workload. In this paper, we are proposing a segmentation model (DRU-Net) that can provide a delineation of human non-small cell lung carcinomas and an augmentation method that can improve classification results. The proposed model is a fused combination of truncated pre-trained DenseNet201 and ResNet101V2 as a patch-wise classifier followed by a lightweight U-Net as a refinement model. We have used two datasets (Norwegian Lung Cancer Biobank and Haukeland University Hospital lung cancer cohort) to create our proposed model. The DRU-Net model achieves an average of 0.91 Dice similarity coefficient. The proposed spatial augmentation method (multi-lens distortion) improved the network performance by 3%. Our findings show that choosing image patches that specifically include regions of interest leads to better results for the patch-wise classifier compared to other sampling methods. The qualitative analysis showed that the DRU-Net model is generally successful in detecting the tumor. On the test set, some of the cases showed areas of false positive and false negative segmentation in the periphery, particularly in tumors with inflammatory and reactive changes.

Accurate medical image segmentation is critical for early medical diagnosis. Most existing methods are based on U-shape structure and use element-wise addition or concatenation to fuse different level features progressively in decoder. However, both the two operations easily generate plenty of redundant information, which will weaken the complementarity between different level features, resulting in inaccurate localization and blurred edges of lesions. To address this challenge, we propose a general multi-scale in multi-scale subtraction network (M^{2}SNet) to finish diverse segmentation from medical image. Specifically, we first design a basic subtraction unit (SU) to produce the difference features between adjacent levels in encoder. Next, we expand the single-scale SU to the intra-layer multi-scale SU, which can provide the decoder with both pixel-level and structure-level difference information. Then, we pyramidally equip the multi-scale SUs at different levels with varying receptive fields, thereby achieving the inter-layer multi-scale feature aggregation and obtaining rich multi-scale difference information. In addition, we build a training-free network ``LossNet'' to comprehensively supervise the task-aware features from bottom layer to top layer, which drives our multi-scale subtraction network to capture the detailed and structural cues simultaneously. Without bells and whistles, our method performs favorably against most state-of-the-art methods under different evaluation metrics on eleven datasets of four different medical image segmentation tasks of diverse image modalities, including color colonoscopy imaging, ultrasound imaging, computed tomography (CT), and optical coherence tomography (OCT). The source code can be available at https://github.com/Xiaoqi-Zhao-DLUT/MSNet.

Recently, the emergence of diffusion models has opened up new opportunities for single-view reconstruction. However, all the existing methods represent the target object as a closed mesh devoid of any structural information, thus neglecting the part-based structure, which is crucial for many downstream applications, of the reconstructed shape. Moreover, the generated meshes usually suffer from large noises, unsmooth surfaces, and blurry textures, making it challenging to obtain satisfactory part segments using 3D segmentation techniques. In this paper, we present Part123, a novel framework for part-aware 3D reconstruction from a single-view image. We first use diffusion models to generate multiview-consistent images from a given image, and then leverage Segment Anything Model (SAM), which demonstrates powerful generalization ability on arbitrary objects, to generate multiview segmentation masks. To effectively incorporate 2D part-based information into 3D reconstruction and handle inconsistency, we introduce contrastive learning into a neural rendering framework to learn a part-aware feature space based on the multiview segmentation masks. A clustering-based algorithm is also developed to automatically derive 3D part segmentation results from the reconstructed models. Experiments show that our method can generate 3D models with high-quality segmented parts on various objects. Compared to existing unstructured reconstruction methods, the part-aware 3D models from our method benefit some important applications, including feature-preserving reconstruction, primitive fitting, and 3D shape editing.

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.

Data diversity and volume are crucial to the success of training deep learning models, while in the medical imaging field, the difficulty and cost of data collection and annotation are especially huge. Specifically in robotic surgery, data scarcity and imbalance have heavily affected the model accuracy and limited the design and deployment of deep learning-based surgical applications such as surgical instrument segmentation. Considering this, we rethink the surgical instrument segmentation task and propose a one-to-many data generation solution that gets rid of the complicated and expensive process of data collection and annotation from robotic surgery. In our method, we only utilize a single surgical background tissue image and a few open-source instrument images as the seed images and apply multiple augmentations and blending techniques to synthesize amounts of image variations. In addition, we also introduce the chained augmentation mixing during training to further enhance the data diversities. The proposed approach is evaluated on the real datasets of the EndoVis-2018 and EndoVis-2017 surgical scene segmentation. Our empirical analysis suggests that without the high cost of data collection and annotation, we can achieve decent surgical instrument segmentation performance. Moreover, we also observe that our method can deal with novel instrument prediction in the deployment domain. We hope our inspiring results will encourage researchers to emphasize data-centric methods to overcome demanding deep learning limitations besides data shortage, such as class imbalance, domain adaptation, and incremental learning. Our code is available at https://github.com/lofrienger/Single_SurgicalScene_For_Segmentation.

Early tumor detection save lives. Each year, more than 300 million computed tomography (CT) scans are performed worldwide, offering a vast opportunity for effective cancer screening. However, detecting small or early-stage tumors on these CT scans remains challenging, even for experts. Artificial intelligence (AI) models can assist by highlighting suspicious regions, but training such models typically requires extensive tumor masks--detailed, voxel-wise outlines of tumors manually drawn by radiologists. Drawing these masks is costly, requiring years of effort and millions of dollars. In contrast, nearly every CT scan in clinical practice is already accompanied by medical reports describing the tumor's size, number, appearance, and sometimes, pathology results--information that is rich, abundant, and often underutilized for AI training. We introduce R-Super, which trains AI to segment tumors that match their descriptions in medical reports. This approach scales AI training with large collections of readily available medical reports, substantially reducing the need for manually drawn tumor masks. When trained on 101,654 reports, AI models achieved performance comparable to those trained on 723 masks. Combining reports and masks further improved sensitivity by +13% and specificity by +8%, surpassing radiologists in detecting five of the seven tumor types. Notably, R-Super enabled segmentation of tumors in the spleen, gallbladder, prostate, bladder, uterus, and esophagus, for which no public masks or AI models previously existed. This study challenges the long-held belief that large-scale, labor-intensive tumor mask creation is indispensable, establishing a scalable and accessible path toward early detection across diverse tumor types. We plan to release our trained models, code, and dataset at https://github.com/MrGiovanni/R-Super

In this study, we present seg2med, an advanced medical image synthesis framework that uses Denoising Diffusion Probabilistic Models (DDPM) to generate high-quality synthetic medical images conditioned on anatomical masks from TotalSegmentator. The framework synthesizes CT and MR images from segmentation masks derived from real patient data and XCAT digital phantoms, achieving a Structural Similarity Index Measure (SSIM) of 0.94 +/- 0.02 for CT and 0.89 +/- 0.04 for MR images compared to ground-truth images of real patients. It also achieves a Feature Similarity Index Measure (FSIM) of 0.78 +/- 0.04 for CT images from XCAT. The generative quality is further supported by a Fr\'echet Inception Distance (FID) of 3.62 for CT image generation. Additionally, seg2med can generate paired CT and MR images with consistent anatomical structures and convert images between CT and MR modalities, achieving SSIM values of 0.91 +/- 0.03 for MR-to-CT and 0.77 +/- 0.04 for CT-to-MR conversion. Despite the limitations of incomplete anatomical details in segmentation masks, the framework shows strong performance in cross-modality synthesis and multimodal imaging. seg2med also demonstrates high anatomical fidelity in CT synthesis, achieving a mean Dice coefficient greater than 0.90 for 11 abdominal organs and greater than 0.80 for 34 organs out of 59 in 58 test cases. The highest Dice of 0.96 +/- 0.01 was recorded for the right scapula. Leveraging the TotalSegmentator toolkit, seg2med enables segmentation mask generation across diverse datasets, supporting applications in clinical imaging, data augmentation, multimodal synthesis, and diagnostic algorithm development.

The Segment Anything Model 2 (SAM 2) is the latest generation foundation model for image and video segmentation. Trained on the expansive Segment Anything Video (SA-V) dataset, which comprises 35.5 million masks across 50.9K videos, SAM 2 advances its predecessor's capabilities by supporting zero-shot segmentation through various prompts (e.g., points, boxes, and masks). Its robust zero-shot performance and efficient memory usage make SAM 2 particularly appealing for surgical tool segmentation in videos, especially given the scarcity of labeled data and the diversity of surgical procedures. In this study, we evaluate the zero-shot video segmentation performance of the SAM 2 model across different types of surgeries, including endoscopy and microscopy. We also assess its performance on videos featuring single and multiple tools of varying lengths to demonstrate SAM 2's applicability and effectiveness in the surgical domain. We found that: 1) SAM 2 demonstrates a strong capability for segmenting various surgical videos; 2) When new tools enter the scene, additional prompts are necessary to maintain segmentation accuracy; and 3) Specific challenges inherent to surgical videos can impact the robustness of SAM 2.

Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use of volumetric information, 3D CNNs are widely used. However, 3D CNNs suffer from higher inference time and computation cost, which hinders their further clinical applications. Additionally, with the increased number of parameters, the risk of overfitting is higher, especially for medical images where data and annotations are expensive to acquire. To issue this problem, many 2.5D segmentation methods have been proposed to make use of volumetric spatial information with less computation cost. Despite these works lead to improvements on a variety of segmentation tasks, to the best of our knowledge, there has not previously been a large-scale empirical comparison of these methods. In this paper, we aim to present a review of the latest developments of 2.5D methods for volumetric medical image segmentation. Additionally, to compare the performance and effectiveness of these methods, we provide an empirical study of these methods on three representative segmentation tasks involving different modalities and targets. Our experimental results highlight that 3D CNNs may not always be the best choice. Despite all these 2.5D methods can bring performance gains to 2D baseline, not all the methods hold the benefits on different datasets. We hope the results and conclusions of our study will prove useful for the community on exploring and developing efficient volumetric medical image segmentation methods.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Conventional medical image segmentation methods have been found inadequate in facilitating physicians with the identification of specific lesions for diagnosis and treatment. Given the utility of text as an instructional format, we introduce a novel task termed Medical Image Referring Segmentation (MIRS), which requires segmenting specified lesions in images based on the given language expressions. Due to the varying object scales in medical images, MIRS demands robust vision-language modeling and comprehensive multi-scale interaction for precise localization and segmentation under linguistic guidance. However, existing medical image segmentation methods fall short in meeting these demands, resulting in insufficient segmentation accuracy. In response, we propose an approach named Language-guided Scale-aware MedSegmentor (LSMS), incorporating two appealing designs: (1)~a Scale-aware Vision-Language Attention module that leverages diverse convolutional kernels to acquire rich visual knowledge and interact closely with linguistic features, thereby enhancing lesion localization capability; (2)~a Full-Scale Decoder that globally models multi-modal features across various scales, capturing complementary information between scales to accurately outline lesion boundaries. Addressing the lack of suitable datasets for MIRS, we constructed a vision-language medical dataset called Reference Hepatic Lesion Segmentation (RefHL-Seg). This dataset comprises 2,283 abdominal CT slices from 231 cases, with corresponding textual annotations and segmentation masks for various liver lesions in images. We validated the performance of LSMS for MIRS and conventional medical image segmentation tasks across various datasets. Our LSMS consistently outperforms on all datasets with lower computational costs. The code and datasets will be released.

Open-vocabulary 3D instance segmentation transcends traditional closed-vocabulary methods by enabling the identification of both previously seen and unseen objects in real-world scenarios. It leverages a dual-modality approach, utilizing both 3D point clouds and 2D multi-view images to generate class-agnostic object mask proposals. Previous efforts predominantly focused on enhancing 3D mask proposal models; consequently, the information that could come from 2D association to 3D was not fully exploited. This bias towards 3D data, while effective for familiar indoor objects, limits the system's adaptability to new and varied object types, where 2D models offer greater utility. Addressing this gap, we introduce Zero-Shot Dual-Path Integration Framework that equally values the contributions of both 3D and 2D modalities. Our framework comprises three components: 3D pathway, 2D pathway, and Dual-Path Integration. 3D pathway generates spatially accurate class-agnostic mask proposals of common indoor objects from 3D point cloud data using a pre-trained 3D model, while 2D pathway utilizes pre-trained open-vocabulary instance segmentation model to identify a diverse array of object proposals from multi-view RGB-D images. In Dual-Path Integration, our Conditional Integration process, which operates in two stages, filters and merges the proposals from both pathways adaptively. This process harmonizes output proposals to enhance segmentation capabilities. Our framework, utilizing pre-trained models in a zero-shot manner, is model-agnostic and demonstrates superior performance on both seen and unseen data, as evidenced by comprehensive evaluations on the ScanNet200 and qualitative results on ARKitScenes datasets.

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

Segmenting biomarkers in medical images is crucial for various biotech applications. Despite advances, Transformer and CNN based methods often struggle with variations in staining and morphology, limiting feature extraction. In medical image segmentation, where datasets often have limited sample availability, recent state-of-the-art (SOTA) methods achieve higher accuracy by leveraging pre-trained encoders, whereas end-to-end methods tend to underperform. This is due to challenges in effectively transferring rich multiscale features from encoders to decoders, as well as limitations in decoder efficiency. To address these issues, we propose an architecture that captures multi-scale local and global contextual information and a novel decoder design, which effectively integrates features from the encoder, emphasizes important channels and regions, and reconstructs spatial dimensions to enhance segmentation accuracy. Our method, compatible with various encoders, outperforms SOTA methods, as demonstrated by experiments on four datasets and ablation studies. Specifically, our method achieves absolute performance gains of 2.76% on MoNuSeg, 3.12% on DSB, 2.87% on Electron Microscopy, and 4.03% on TNBC datasets compared to existing SOTA methods. Code: https://github.com/saadwazir/MCADS-Decoder

Recent works on click-based interactive segmentation have demonstrated state-of-the-art results by using various inference-time optimization schemes. These methods are considerably more computationally expensive compared to feedforward approaches, as they require performing backward passes through a network during inference and are hard to deploy on mobile frameworks that usually support only forward passes. In this paper, we extensively evaluate various design choices for interactive segmentation and discover that new state-of-the-art results can be obtained without any additional optimization schemes. Thus, we propose a simple feedforward model for click-based interactive segmentation that employs the segmentation masks from previous steps. It allows not only to segment an entirely new object, but also to start with an external mask and correct it. When analyzing the performance of models trained on different datasets, we observe that the choice of a training dataset greatly impacts the quality of interactive segmentation. We find that the models trained on a combination of COCO and LVIS with diverse and high-quality annotations show performance superior to all existing models. The code and trained models are available at https://github.com/saic-vul/ritm_interactive_segmentation.

Tumor segmentation in CT scans is key for diagnosis, surgery, and prognosis, yet segmentation masks are scarce because their creation requires time and expertise. Public abdominal CT datasets have from dozens to a couple thousand tumor masks, but hospitals have hundreds of thousands of tumor CTs with radiology reports. Thus, leveraging reports to improve segmentation is key for scaling. In this paper, we propose a report-supervision loss (R-Super) that converts radiology reports into voxel-wise supervision for tumor segmentation AI. We created a dataset with 6,718 CT-Report pairs (from the UCSF Hospital), and merged it with public CT-Mask datasets (from AbdomenAtlas 2.0). We used our R-Super to train with these masks and reports, and strongly improved tumor segmentation in internal and external validation--F1 Score increased by up to 16% with respect to training with masks only. By leveraging readily available radiology reports to supplement scarce segmentation masks, R-Super strongly improves AI performance both when very few training masks are available (e.g., 50), and when many masks were available (e.g., 1.7K). Project: https://github.com/MrGiovanni/R-Super

Semantic medical 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 medical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive. In this paper, we present ScribblePrompt, an interactive segmentation framework for medical imaging that enables human annotators to segment unseen structures using scribbles, clicks, and bounding boxes. Scribbles are an intuitive and effective form of user interaction for complex tasks, however most existing methods focus on click-based interactions. We introduce algorithms for simulating realistic scribbles that enable training models that are amenable to multiple types of interaction. To achieve generalization to new tasks, we train on a diverse collection of 65 open-access biomedical datasets -- using both real and synthetic labels. We test ScribblePrompt on multiple network architectures and unseen datasets, and demonstrate that it can be used in real-time on a single CPU. We evaluate ScribblePrompt using manually-collected scribbles, simulated interactions, and a user study. ScribblePrompt outperforms existing methods in all our evaluations. In the user study, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to existing methods. We showcase ScribblePrompt in an online demo and provide code at https://scribbleprompt.csail.mit.edu

Tuberculosis (TB) is a chronic lung disease that occurs due to bacterial infection and is one of the top 10 leading causes of death. Accurate and early detection of TB is very important, otherwise, it could be life-threatening. In this work, we have detected TB reliably from the chest X-ray images using image pre-processing, data augmentation, image segmentation, and deep-learning classification techniques. Several public databases were used to create a database of 700 TB infected and 3500 normal chest X-ray images for this study. Nine different deep CNNs (ResNet18, ResNet50, ResNet101, ChexNet, InceptionV3, Vgg19, DenseNet201, SqueezeNet, and MobileNet), which were used for transfer learning from their pre-trained initial weights and trained, validated and tested for classifying TB and non-TB normal cases. Three different experiments were carried out in this work: segmentation of X-ray images using two different U-net models, classification using X-ray images, and segmented lung images. The accuracy, precision, sensitivity, F1-score, specificity in the detection of tuberculosis using X-ray images were 97.07 %, 97.34 %, 97.07 %, 97.14 % and 97.36 % respectively. However, segmented lungs for the classification outperformed than whole X-ray image-based classification and accuracy, precision, sensitivity, F1-score, specificity were 99.9 %, 99.91 %, 99.9 %, 99.9 %, and 99.52 % respectively. The paper also used a visualization technique to confirm that CNN learns dominantly from the segmented lung regions results in higher detection accuracy. The proposed method with state-of-the-art performance can be useful in the computer-aided faster diagnosis of tuberculosis.

Medical image segmentation is a critical task in clinical workflows, particularly for the detection and delineation of pathological regions. While convolutional architectures like U-Net have become standard for such tasks, their limited receptive field restricts global context modeling. Recent efforts integrating transformers have addressed this, but often result in deep, computationally expensive models unsuitable for real-time use. In this work, we present a novel end-to-end lightweight architecture designed specifically for real-time binary medical image segmentation. Our model combines a Swin Transformer-like encoder with a U-Net-like decoder, connected via skip pathways to preserve spatial detail while capturing contextual information. Unlike existing designs such as Swin Transformer or U-Net, our architecture is significantly shallower and competitively efficient. To improve the encoder's ability to learn meaningful features without relying on large amounts of labeled data, we first train it using Barlow Twins, a self-supervised learning method that helps the model focus on important patterns by reducing unnecessary repetition in the learned features. After this pretraining, we fine-tune the entire model for our specific task. Experiments on benchmark binary segmentation tasks demonstrate that our model achieves competitive accuracy with substantially reduced parameter count and faster inference, positioning it as a practical alternative for deployment in real-time and resource-limited clinical environments. The code for our method is available at Github repository: https://github.com/mkianih/Barlow-Swin.

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://www.pami.sjtu.edu.cn/News/56

Accurate medical image segmentation is crucial for precise anatomical delineation. Deep learning models like U-Net have shown great success but depend heavily on large datasets and struggle with domain shifts, complex structures, and limited training samples. Recent studies have explored diffusion models for segmentation by iteratively refining masks. However, these methods still retain the conventional image-to-mask mapping, making them highly sensitive to input data, which hampers stability and generalization. In contrast, we introduce DiffAtlas, a novel generative framework that models both images and masks through diffusion during training, effectively ``GenAI-fying'' atlas-based segmentation. During testing, the model is guided to generate a specific target image-mask pair, from which the corresponding mask is obtained. DiffAtlas retains the robustness of the atlas paradigm while overcoming its scalability and domain-specific limitations. Extensive experiments on CT and MRI across same-domain, cross-modality, varying-domain, and different data-scale settings using the MMWHS and TotalSegmentator datasets demonstrate that our approach outperforms existing methods, particularly in limited-data and zero-shot modality segmentation. Code is available at https://github.com/M3DV/DiffAtlas.

Despite that deep learning has achieved state-of-the-art performance for medical image segmentation, its success relies on a large set of manually annotated images for training that are expensive to acquire. In this paper, we propose an annotation-efficient learning framework for segmentation tasks that avoids annotations of training images, where we use an improved Cycle-Consistent Generative Adversarial Network (GAN) to learn from a set of unpaired medical images and auxiliary masks obtained either from a shape model or public datasets. We first use the GAN to generate pseudo labels for our training images under the implicit high-level shape constraint represented by a Variational Auto-encoder (VAE)-based discriminator with the help of the auxiliary masks, and build a Discriminator-guided Generator Channel Calibration (DGCC) module which employs our discriminator's feedback to calibrate the generator for better pseudo labels. To learn from the pseudo labels that are noisy, we further introduce a noise-robust iterative learning method using noise-weighted Dice loss. We validated our framework with two situations: objects with a simple shape model like optic disc in fundus images and fetal head in ultrasound images, and complex structures like lung in X-Ray images and liver in CT images. Experimental results demonstrated that 1) Our VAE-based discriminator and DGCC module help to obtain high-quality pseudo labels. 2) Our proposed noise-robust learning method can effectively overcome the effect of noisy pseudo labels. 3) The segmentation performance of our method without using annotations of training images is close or even comparable to that of learning from human annotations.

Medical image segmentation is a key task in the imaging workflow, influencing many image-based decisions. Traditional, fully-supervised segmentation models rely on large amounts of labeled training data, typically obtained through manual annotation, which can be an expensive, time-consuming, and error-prone process. This signals a need for accurate, automatic, and annotation-efficient methods of training these models. We propose ADA-SAM (automated, domain-specific, and adaptive segment anything model), a novel multitask learning framework for medical image segmentation that leverages class activation maps from an auxiliary classifier to guide the predictions of the semi-supervised segmentation branch, which is based on the Segment Anything (SAM) framework. Additionally, our ADA-SAM model employs a novel gradient feedback mechanism to create a learnable connection between the segmentation and classification branches by using the segmentation gradients to guide and improve the classification predictions. We validate ADA-SAM on real-world clinical data collected during rehabilitation trials, and demonstrate that our proposed method outperforms both fully-supervised and semi-supervised baselines by double digits in limited label settings. Our code is available at: https://github.com/tbwa233/ADA-SAM.

We propose a simple three-stage approach to segment unseen objects in RGB images using their CAD models. Leveraging recent powerful foundation models, DINOv2 and Segment Anything, we create descriptors and generate proposals, including binary masks for a given input RGB image. By matching proposals with reference descriptors created from CAD models, we achieve precise object ID assignment along with modal masks. We experimentally demonstrate that our method achieves state-of-the-art results in CAD-based novel object segmentation, surpassing existing approaches on the seven core datasets of the BOP challenge by 19.8\% AP using the same BOP evaluation protocol. Our source code is available at https://github.com/nv-nguyen/cnos.

Recent advances in methods focused on the grounding problem have resulted in techniques that can be used to construct a symbolic language associated with a specific domain. Inspired by how humans communicate complex ideas through language, we developed a generalized Symbolic Semantic (S^2) framework for interpretable segmentation. Unlike adversarial models (e.g., GANs), we explicitly model cooperation between two agents, a Sender and a Receiver, that must cooperate to achieve a common goal. The Sender receives information from a high layer of a segmentation network and generates a symbolic sentence derived from a categorical distribution. The Receiver obtains the symbolic sentences and co-generates the segmentation mask. In order for the model to converge, the Sender and Receiver must learn to communicate using a private language. We apply our architecture to segment tumors in the TCGA dataset. A UNet-like architecture is used to generate input to the Sender network which produces a symbolic sentence, and a Receiver network co-generates the segmentation mask based on the sentence. Our Segmentation framework achieved similar or better performance compared with state-of-the-art segmentation methods. In addition, our results suggest direct interpretation of the symbolic sentences to discriminate between normal and tumor tissue, tumor morphology, and other image characteristics.

With the development of Deep Neural Networks (DNNs), many efforts have been made to handle medical image segmentation. Traditional methods such as nnUNet train specific segmentation models on the individual datasets. Plenty of recent methods have been proposed to adapt the foundational Segment Anything Model (SAM) to medical image segmentation. However, they still focus on discrete representations to generate pixel-wise predictions, which are spatially inflexible and scale poorly to higher resolution. In contrast, implicit methods learn continuous representations for segmentation, which is crucial for medical image segmentation. In this paper, we propose I-MedSAM, which leverages the benefits of both continuous representations and SAM, to obtain better cross-domain ability and accurate boundary delineation. Since medical image segmentation needs to predict detailed segmentation boundaries, we designed a novel adapter to enhance the SAM features with high-frequency information during Parameter-Efficient Fine-Tuning (PEFT). To convert the SAM features and coordinates into continuous segmentation output, we utilize Implicit Neural Representation (INR) to learn an implicit segmentation decoder. We also propose an uncertainty-guided sampling strategy for efficient learning of INR. Extensive evaluations on 2D medical image segmentation tasks have shown that our proposed method with only 1.6M trainable parameters outperforms existing methods including discrete and implicit methods. The code will be available at: https://github.com/ucwxb/I-MedSAM.

Deep learning (DL) has become the dominant approach for medical image segmentation, yet ensuring the reliability and clinical applicability of these models requires addressing key challenges such as annotation variability, calibration, and uncertainty estimation. This is why we created the Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS), which highlights the critical role of multiple annotators in establishing a more comprehensive ground truth, emphasizing that segmentation is inherently subjective and that leveraging inter-annotator variability is essential for robust model evaluation. Seven teams participated in the challenge, submitting a variety of DL models evaluated using metrics such as Dice Similarity Coefficient (DSC), Expected Calibration Error (ECE), and Continuous Ranked Probability Score (CRPS). By incorporating consensus and dissensus ground truth, we assess how DL models handle uncertainty and whether their confidence estimates align with true segmentation performance. Our findings reinforce the importance of well-calibrated models, as better calibration is strongly correlated with the quality of the results. Furthermore, we demonstrate that segmentation models trained on diverse datasets and enriched with pre-trained knowledge exhibit greater robustness, particularly in cases deviating from standard anatomical structures. Notably, the best-performing models achieved high DSC and well-calibrated uncertainty estimates. This work underscores the need for multi-annotator ground truth, thorough calibration assessments, and uncertainty-aware evaluations to develop trustworthy and clinically reliable DL-based medical image segmentation models.

Medical imaging is crucial for diagnosing a patient's health condition, and accurate segmentation of these images is essential for isolating regions of interest to ensure precise diagnosis and treatment planning. Existing methods primarily rely on bounding boxes or point-based prompts, while few have explored text-related prompts, despite clinicians often describing their observations and instructions in natural language. To address this gap, we first propose a RAG-based free-form text prompt generator, that leverages the domain corpus to generate diverse and realistic descriptions. Then, we introduce FLanS, a novel medical image segmentation model that handles various free-form text prompts, including professional anatomy-informed queries, anatomy-agnostic position-driven queries, and anatomy-agnostic size-driven queries. Additionally, our model also incorporates a symmetry-aware canonicalization module to ensure consistent, accurate segmentations across varying scan orientations and reduce confusion between the anatomical position of an organ and its appearance in the scan. FLanS is trained on a large-scale dataset of over 100k medical images from 7 public datasets. Comprehensive experiments demonstrate the model's superior language understanding and segmentation precision, along with a deep comprehension of the relationship between them, outperforming SOTA baselines on both in-domain and out-of-domain datasets.

Implicit neural fields have made remarkable progress in reconstructing 3D surfaces from multiple images; however, they encounter challenges when it comes to separating individual objects within a scene. Previous work has attempted to tackle this problem by introducing a framework to train separate signed distance fields (SDFs) simultaneously for each of N objects and using a regularization term to prevent objects from overlapping. However, all of these methods require segmentation masks to be provided, which are not always readily available. We introduce our method, ObjectCarver, to tackle the problem of object separation from just click input in a single view. Given posed multi-view images and a set of user-input clicks to prompt segmentation of the individual objects, our method decomposes the scene into separate objects and reconstructs a high-quality 3D surface for each one. We introduce a loss function that prevents floaters and avoids inappropriate carving-out due to occlusion. In addition, we introduce a novel scene initialization method that significantly speeds up the process while preserving geometric details compared to previous approaches. Despite requiring neither ground truth masks nor monocular cues, our method outperforms baselines both qualitatively and quantitatively. In addition, we introduce a new benchmark dataset for evaluation.

Accurate retinal vessel (RV) segmentation is a crucial step in the quantitative assessment of retinal vasculature, which is needed for the early detection of retinal diseases and other conditions. Numerous studies have been conducted to tackle the problem of segmenting vessels automatically using a pixel-wise classification approach. The common practice of creating ground truth labels is to categorize pixels as foreground and background. This approach is, however, biased, and it ignores the uncertainty of a human annotator when it comes to annotating e.g. thin vessels. In this work, we propose a simple and effective method that casts the RV segmentation task as an image-level regression. For this purpose, we first introduce a novel Segmentation Annotation Uncertainty-Aware (SAUNA) transform, which adds pixel uncertainty to the ground truth using the pixel's closeness to the annotation boundary and vessel thickness. To train our model with soft labels, we generalize the earlier proposed Jaccard metric loss to arbitrary hypercubes for soft Jaccard index (Intersection-over-Union) optimization. Additionally, we employ a stable version of the Focal-L1 loss for pixel-wise regression. We conduct thorough experiments and compare our method to a diverse set of baselines across 5 retinal image datasets. Our empirical results indicate that the integration of the SAUNA transform and these segmentation losses led to significant performance boosts for different segmentation models. Particularly, our methodology enables UNet-like architectures to substantially outperform computational-intensive baselines. Our implementation is available at https://github.com/Oulu-IMEDS/SAUNA.

We present ReXGroundingCT, the first publicly available dataset to link free-text radiology findings with pixel-level segmentations in 3D chest CT scans that is manually annotated. While prior datasets have relied on structured labels or predefined categories, ReXGroundingCT captures the full expressiveness of clinical language represented in free text and grounds it to spatially localized 3D segmentation annotations in volumetric imaging. This addresses a critical gap in medical AI: the ability to connect complex, descriptive text, such as "3 mm nodule in the left lower lobe", to its precise anatomical location in three-dimensional space, a capability essential for grounded radiology report generation systems. The dataset comprises 3,142 non-contrast chest CT scans paired with standardized radiology reports from the CT-RATE dataset. Using a systematic three-stage pipeline, GPT-4 was used to extract positive lung and pleural findings, which were then manually segmented by expert annotators. A total of 8,028 findings across 16,301 entities were annotated, with quality control performed by board-certified radiologists. Approximately 79% of findings are focal abnormalities, while 21% are non-focal. The training set includes up to three representative segmentations per finding, while the validation and test sets contain exhaustive labels for each finding entity. ReXGroundingCT establishes a new benchmark for developing and evaluating sentence-level grounding and free-text medical segmentation models in chest CT. The dataset can be accessed at https://huggingface.co/datasets/rajpurkarlab/ReXGroundingCT.

Image segmentation remains a pivotal component in medical image analysis, aiding in the extraction of critical information for precise diagnostic practices. With the advent of deep learning, automated image segmentation methods have risen to prominence, showcasing exceptional proficiency in processing medical imagery. Motivated by the Segment Anything Model (SAM)-a foundational model renowned for its remarkable precision and robust generalization capabilities in segmenting 2D natural images-we introduce SAM3D, an innovative adaptation tailored for 3D volumetric medical image analysis. Unlike current SAM-based methods that segment volumetric data by converting the volume into separate 2D slices for individual analysis, our SAM3D model processes the entire 3D volume image in a unified approach. Extensive experiments are conducted on multiple medical image datasets to demonstrate that our network attains competitive results compared with other state-of-the-art methods in 3D medical segmentation tasks while being significantly efficient in terms of parameters. Code and checkpoints are available at https://github.com/UARK-AICV/SAM3D.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Biomedical image analysis is fundamental for biomedical discovery in cell biology, pathology, radiology, and many other biomedical domains. Holistic image analysis comprises interdependent subtasks such as segmentation, detection, and recognition of relevant objects. Here, we propose BiomedParse, a biomedical foundation model for imaging parsing that can jointly conduct segmentation, detection, and recognition for 82 object types across 9 imaging modalities. Through joint learning, we can improve accuracy for individual tasks and enable novel applications such as segmenting all relevant objects in an image through a text prompt, rather than requiring users to laboriously specify the bounding box for each object. We leveraged readily available natural-language labels or descriptions accompanying those datasets and use GPT-4 to harmonize the noisy, unstructured text information with established biomedical object ontologies. We created a large dataset comprising over six million triples of image, segmentation mask, and textual description. On image segmentation, we showed that BiomedParse is broadly applicable, outperforming state-of-the-art methods on 102,855 test image-mask-label triples across 9 imaging modalities (everything). On object detection, which aims to locate a specific object of interest, BiomedParse again attained state-of-the-art performance, especially on objects with irregular shapes (everywhere). On object recognition, which aims to identify all objects in a given image along with their semantic types, we showed that BiomedParse can simultaneously segment and label all biomedical objects in an image (all at once). In summary, BiomedParse is an all-in-one tool for biomedical image analysis by jointly solving segmentation, detection, and recognition for all major biomedical image modalities, paving the path for efficient and accurate image-based biomedical discovery.

Model-based reconstruction employing the time separation technique (TST) was found to improve dynamic perfusion imaging of the liver using C-arm cone-beam computed tomography (CBCT). To apply TST using prior knowledge extracted from CT perfusion data, the liver should be accurately segmented from the CT scans. Reconstructions of primary and model-based CBCT data need to be segmented for proper visualisation and interpretation of perfusion maps. This research proposes Turbolift learning, which trains a modified version of the multi-scale Attention UNet on different liver segmentation tasks serially, following the order of the trainings CT, CBCT, CBCT TST - making the previous trainings act as pre-training stages for the subsequent ones - addressing the problem of limited number of datasets for training. For the final task of liver segmentation from CBCT TST, the proposed method achieved an overall Dice scores of 0.874pm0.031 and 0.905pm0.007 in 6-fold and 4-fold cross-validation experiments, respectively - securing statistically significant improvements over the model, which was trained only for that task. Experiments revealed that Turbolift not only improves the overall performance of the model but also makes it robust against artefacts originating from the embolisation materials and truncation artefacts. Additionally, in-depth analyses confirmed the order of the segmentation tasks. This paper shows the potential of segmenting the liver from CT, CBCT, and CBCT TST, learning from the available limited training data, which can possibly be used in the future for the visualisation and evaluation of the perfusion maps for the treatment evaluation of liver diseases.

Acquiring and annotating sufficient labeled data is crucial in developing accurate and robust learning-based models, but obtaining such data can be challenging in many medical image segmentation tasks. One promising solution is to synthesize realistic data with ground-truth mask annotations. However, no prior studies have explored generating complete 3D volumetric images with masks. In this paper, we present MedGen3D, a deep generative framework that can generate paired 3D medical images and masks. First, we represent the 3D medical data as 2D sequences and propose the Multi-Condition Diffusion Probabilistic Model (MC-DPM) to generate multi-label mask sequences adhering to anatomical geometry. Then, we use an image sequence generator and semantic diffusion refiner conditioned on the generated mask sequences to produce realistic 3D medical images that align with the generated masks. Our proposed framework guarantees accurate alignment between synthetic images and segmentation maps. Experiments on 3D thoracic CT and brain MRI datasets show that our synthetic data is both diverse and faithful to the original data, and demonstrate the benefits for downstream segmentation tasks. We anticipate that MedGen3D's ability to synthesize paired 3D medical images and masks will prove valuable in training deep learning models for medical imaging tasks.

An increasing number of public datasets have shown a marked impact on automated organ segmentation and tumor detection. However, due to the small size and partially labeled problem of each dataset, as well as a limited investigation of diverse types of tumors, the resulting models are often limited to segmenting specific organs/tumors and ignore the semantics of anatomical structures, nor can they be extended to novel domains. To address these issues, we propose the CLIP-Driven Universal Model, which incorporates text embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models. This CLIP-based label encoding captures anatomical relationships, enabling the model to learn a structured feature embedding and segment 25 organs and 6 types of tumors. The proposed model is developed from an assembly of 14 datasets, using a total of 3,410 CT scans for training and then evaluated on 6,162 external CT scans from 3 additional datasets. We rank first on the Medical Segmentation Decathlon (MSD) public leaderboard and achieve state-of-the-art results on Beyond The Cranial Vault (BTCV). Additionally, the Universal Model is computationally more efficient (6x faster) compared with dataset-specific models, generalized better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks.

Automatic polyp segmentation has proven to be immensely helpful for endoscopy procedures, reducing the missing rate of adenoma detection for endoscopists while increasing efficiency. However, classifying a polyp as being neoplasm or not and segmenting it at the pixel level is still a challenging task for doctors to perform in a limited time. In this work, we propose a fine-grained formulation for the polyp segmentation problem. Our formulation aims to not only segment polyp regions, but also identify those at high risk of malignancy with high accuracy. In addition, we present a UNet-based neural network architecture called NeoUNet, along with a hybrid loss function to solve this problem. Experiments show highly competitive results for NeoUNet on our benchmark dataset compared to existing polyp segmentation models.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

This work explores the use of computer vision for image segmentation and classification of medical fluid samples in transparent containers (for example, tubes, syringes, infusion bags). Handling fluids such as infusion fluids, blood, and urine samples is a significant part of the work carried out in medical labs and hospitals. The ability to accurately identify and segment the liquids and the vessels that contain them from images can help in automating such processes. Modern computer vision typically involves training deep neural nets on large datasets of annotated images. This work presents a new dataset containing 1,300 annotated images of medical samples involving vessels containing liquids and solid material. The images are annotated with the type of liquid (e.g., blood, urine), the phase of the material (e.g., liquid, solid, foam, suspension), the type of vessel (e.g., syringe, tube, cup, infusion bottle/bag), and the properties of the vessel (transparent, opaque). In addition, vessel parts such as corks, labels, spikes, and valves are annotated. Relations and hierarchies between vessels and materials are also annotated, such as which vessel contains which material or which vessels are linked or contain each other. Three neural networks are trained on the dataset: One network learns to detect vessels, a second net detects the materials and parts inside each vessel, and a third net identifies relationships and connectivity between vessels.

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

Medical image segmentation is fundamental for biomedical discovery. Existing methods lack generalizability and demand extensive, time-consuming manual annotation for new clinical application. Here, we propose MedSAM-3, a text promptable medical segmentation model for medical image and video segmentation. By fine-tuning the Segment Anything Model (SAM) 3 architecture on medical images paired with semantic conceptual labels, our MedSAM-3 enables medical Promptable Concept Segmentation (PCS), allowing precise targeting of anatomical structures via open-vocabulary text descriptions rather than solely geometric prompts. We further introduce the MedSAM-3 Agent, a framework that integrates Multimodal Large Language Models (MLLMs) to perform complex reasoning and iterative refinement in an agent-in-the-loop workflow. Comprehensive experiments across diverse medical imaging modalities, including X-ray, MRI, Ultrasound, CT, and video, demonstrate that our approach significantly outperforms existing specialist and foundation models. We will release our code and model at https://github.com/Joey-S-Liu/MedSAM3.

The task of localizing and categorizing objects in medical images often remains formulated as a semantic segmentation problem. This approach, however, only indirectly solves the coarse localization task by predicting pixel-level scores, requiring ad-hoc heuristics when mapping back to object-level scores. State-of-the-art object detectors on the other hand, allow for individual object scoring in an end-to-end fashion, while ironically trading in the ability to exploit the full pixel-wise supervision signal. This can be particularly disadvantageous in the setting of medical image analysis, where data sets are notoriously small. In this paper, we propose Retina U-Net, a simple architecture, which naturally fuses the Retina Net one-stage detector with the U-Net architecture widely used for semantic segmentation in medical images. The proposed architecture recaptures discarded supervision signals by complementing object detection with an auxiliary task in the form of semantic segmentation without introducing the additional complexity of previously proposed two-stage detectors. We evaluate the importance of full segmentation supervision on two medical data sets, provide an in-depth analysis on a series of toy experiments and show how the corresponding performance gain grows in the limit of small data sets. Retina U-Net yields strong detection performance only reached by its more complex two-staged counterparts. Our framework including all methods implemented for operation on 2D and 3D images is available at github.com/pfjaeger/medicaldetectiontoolkit.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

The recently introduced Segment Anything Model (SAM) combines a clever architecture and large quantities of training data to obtain remarkable image segmentation capabilities. However, it fails to reproduce such results for Out-Of-Distribution (OOD) domains such as medical images. Moreover, while SAM is conditioned on either a mask or a set of points, it may be desirable to have a fully automatic solution. In this work, we replace SAM's conditioning with an encoder that operates on the same input image. By adding this encoder and without further fine-tuning SAM, we obtain state-of-the-art results on multiple medical images and video benchmarks. This new encoder is trained via gradients provided by a frozen SAM. For inspecting the knowledge within it, and providing a lightweight segmentation solution, we also learn to decode it into a mask by a shallow deconvolution network.

While deep learning models have become the predominant method for medical image segmentation, they are typically not capable of generalizing to unseen segmentation tasks involving new anatomies, image modalities, or labels. Given a new segmentation task, researchers generally have to train or fine-tune models, which is time-consuming and poses a substantial barrier for clinical researchers, who often lack the resources and expertise to train neural networks. We present UniverSeg, a method for solving unseen medical segmentation tasks without additional training. Given a query image and example set of image-label pairs that define a new segmentation task, UniverSeg employs a new Cross-Block mechanism to produce accurate segmentation maps without the need for additional training. To achieve generalization to new tasks, we have gathered and standardized a collection of 53 open-access medical segmentation datasets with over 22,000 scans, which we refer to as MegaMedical. We used this collection to train UniverSeg on a diverse set of anatomies and imaging modalities. We demonstrate that UniverSeg substantially outperforms several related methods on unseen tasks, and thoroughly analyze and draw insights about important aspects of the proposed system. The UniverSeg source code and model weights are freely available at https://universeg.csail.mit.edu

Recent advancements in prompt-based medical image segmentation have enabled clinicians to identify tumors using simple input like bounding boxes or text prompts. However, existing methods face challenges when doctors need to interact through natural language or when position reasoning is required - understanding spatial relationships between anatomical structures and pathologies. We present PRS-Med, a framework that integrates vision-language models with segmentation capabilities to generate both accurate segmentation masks and corresponding spatial reasoning outputs. Additionally, we introduce the MMRS dataset (Multimodal Medical in Positional Reasoning Segmentation), which provides diverse, spatially-grounded question-answer pairs to address the lack of position reasoning data in medical imaging. PRS-Med demonstrates superior performance across six imaging modalities (CT, MRI, X-ray, ultrasound, endoscopy, RGB), significantly outperforming state-of-the-art methods in both segmentation accuracy and position reasoning. Our approach enables intuitive doctor-system interaction through natural language, facilitating more efficient diagnoses. Our dataset pipeline, model, and codebase will be released to foster further research in spatially-aware multimodal reasoning for medical applications.

Recent advances in zero-shot referring image segmentation (RIS), driven by models such as the Segment Anything Model (SAM) and CLIP, have made substantial progress in aligning visual and textual information. Despite these successes, the extraction of precise and high-quality mask region representations remains a critical challenge, limiting the full potential of RIS tasks. In this paper, we introduce a training-free, hybrid global-local feature extraction approach that integrates detailed mask-specific features with contextual information from the surrounding area, enhancing mask region representation. To further strengthen alignment between mask regions and referring expressions, we propose a spatial guidance augmentation strategy that improves spatial coherence, which is essential for accurately localizing described areas. By incorporating multiple spatial cues, this approach facilitates more robust and precise referring segmentation. Extensive experiments on standard RIS benchmarks demonstrate that our method significantly outperforms existing zero-shot RIS models, achieving substantial performance gains. We believe our approach advances RIS tasks and establishes a versatile framework for region-text alignment, offering broader implications for cross-modal understanding and interaction. Code is available at https://github.com/fhgyuanshen/HybridGL .

Accurate analysis and modeling of renal functions require a precise segmentation of the renal blood vessels. Micro-CT scans provide image data at higher resolutions, making more small vessels near the renal cortex visible. Although deep-learning-based methods have shown state-of-the-art performance in automatic blood vessel segmentations, they require a large amount of labeled training data. However, voxel-wise labeling in micro-CT scans is extremely time-consuming given the huge volume sizes. To mitigate the problem, we simulate synthetic renal vascular trees physiologically while generating corresponding scans of the simulated trees by training a generative model on unlabeled scans. This enables the generative model to learn the mapping implicitly without the need for explicit functions to emulate the image acquisition process. We further propose an additional segmentation branch over the generative model trained on the generated scans. We demonstrate that the model can directly segment blood vessels on real scans and validate our method on both 3D micro-CT scans of rat kidneys and a proof-of-concept experiment on 2D retinal images. Code and 3D results are available at https://github.com/miccai2023anony/RenalVesselSeg

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu

Pixel-wise image segmentation is a highly demanding task in medical-image analysis. In practice, it is difficult to find annotated medical images with corresponding segmentation masks. In this paper, we present Kvasir-SEG: an open-access dataset of gastrointestinal polyp images and corresponding segmentation masks, manually annotated by a medical doctor and then verified by an experienced gastroenterologist. Moreover, we also generated the bounding boxes of the polyp regions with the help of segmentation masks. We demonstrate the use of our dataset with a traditional segmentation approach and a modern deep-learning based Convolutional Neural Network (CNN) approach. The dataset will be of value for researchers to reproduce results and compare methods. By adding segmentation masks to the Kvasir dataset, which only provide frame-wise annotations, we enable multimedia and computer vision researchers to contribute in the field of polyp segmentation and automatic analysis of colonoscopy images.

Interactive Medical Image Segmentation (IMIS) has long been constrained by the limited availability of large-scale, diverse, and densely annotated datasets, which hinders model generalization and consistent evaluation across different models. In this paper, we introduce the IMed-361M benchmark dataset, a significant advancement in general IMIS research. First, we collect and standardize over 6.4 million medical images and their corresponding ground truth masks from multiple data sources. Then, leveraging the strong object recognition capabilities of a vision foundational model, we automatically generated dense interactive masks for each image and ensured their quality through rigorous quality control and granularity management. Unlike previous datasets, which are limited by specific modalities or sparse annotations, IMed-361M spans 14 modalities and 204 segmentation targets, totaling 361 million masks-an average of 56 masks per image. Finally, we developed an IMIS baseline network on this dataset that supports high-quality mask generation through interactive inputs, including clicks, bounding boxes, text prompts, and their combinations. We evaluate its performance on medical image segmentation tasks from multiple perspectives, demonstrating superior accuracy and scalability compared to existing interactive segmentation models. To facilitate research on foundational models in medical computer vision, we release the IMed-361M and model at https://github.com/uni-medical/IMIS-Bench.

Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (e.g., foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.

Uncertainty estimation is essential for the safe clinical deployment of medical image segmentation systems, enabling the identification of unreliable predictions and supporting human oversight. While prior work has largely focused on pixel-level uncertainty, landmark-based segmentation offers inherent topological guarantees yet remains underexplored from an uncertainty perspective. In this work, we study uncertainty estimation for anatomical landmark-based segmentation on chest X-rays. Inspired by hybrid neural network architectures that combine standard image convolutional encoders with graph-based generative decoders, and leveraging their variational latent space, we derive two complementary measures: (i) latent uncertainty, captured directly from the learned distribution parameters, and (ii) predictive uncertainty, obtained by generating multiple stochastic output predictions from latent samples. Through controlled corruption experiments we show that both uncertainty measures increase with perturbation severity, reflecting both global and local degradation. We demonstrate that these uncertainty signals can identify unreliable predictions by comparing with manual ground-truth, and support out-of-distribution detection on the CheXmask dataset. More importantly, we release CheXmask-U (huggingface.co/datasets/mcosarinsky/CheXmask-U), a large scale dataset of 657,566 chest X-ray landmark segmentations with per-node uncertainty estimates, enabling researchers to account for spatial variations in segmentation quality when using these anatomical masks. Our findings establish uncertainty estimation as a promising direction to enhance robustness and safe deployment of landmark-based anatomical segmentation methods in chest X-ray. A fully working interactive demo of the method is available at huggingface.co/spaces/matiasky/CheXmask-U and the source code at github.com/mcosarinsky/CheXmask-U.

Medical image segmentation and video object segmentation are essential for diagnosing and analyzing diseases by identifying and measuring biological structures. Recent advances in natural domain have been driven by foundation models like the Segment Anything Model 2 (SAM 2). To explore the performance of SAM 2 in biomedical applications, we designed two evaluation pipelines for single-frame image segmentation and multi-frame video segmentation with varied prompt designs, revealing SAM 2's limitations in medical contexts. Consequently, we developed BioSAM 2, an enhanced foundation model optimized for biomedical data based on SAM 2. Our experiments show that BioSAM 2 not only surpasses the performance of existing state-of-the-art foundation models but also matches or even exceeds specialist models, demonstrating its efficacy and potential in the medical domain.

Recent advances in large vision-language models (LVLMs) have demonstrated strong performance on general-purpose medical tasks. However, their effectiveness in specialized domains such as dentistry remains underexplored. In particular, panoramic X-rays, a widely used imaging modality in oral radiology, pose interpretative challenges due to dense anatomical structures and subtle pathological cues, which are not captured by existing medical benchmarks or instruction datasets. To this end, we introduce MMOral, the first large-scale multimodal instruction dataset and benchmark tailored for panoramic X-ray interpretation. MMOral consists of 20,563 annotated images paired with 1.3 million instruction-following instances across diverse task types, including attribute extraction, report generation, visual question answering, and image-grounded dialogue. In addition, we present MMOral-Bench, a comprehensive evaluation suite covering five key diagnostic dimensions in dentistry. We evaluate 64 LVLMs on MMOral-Bench and find that even the best-performing model, i.e., GPT-4o, only achieves 41.45% accuracy, revealing significant limitations of current models in this domain. To promote the progress of this specific domain, we also propose OralGPT, which conducts supervised fine-tuning (SFT) upon Qwen2.5-VL-7B with our meticulously curated MMOral instruction dataset. Remarkably, a single epoch of SFT yields substantial performance enhancements for LVLMs, e.g., OralGPT demonstrates a 24.73% improvement. Both MMOral and OralGPT hold significant potential as a critical foundation for intelligent dentistry and enable more clinically impactful multimodal AI systems in the dental field. The dataset, model, benchmark, and evaluation suite are available at https://github.com/isbrycee/OralGPT.

The field of medical image segmentation is hindered by the scarcity of large, publicly available annotated datasets. Not all datasets are made public for privacy reasons, and creating annotations for a large dataset is time-consuming and expensive, as it requires specialized expertise to accurately identify regions of interest (ROIs) within the images. To address these challenges, we evaluate the performance of the Segment Anything Model (SAM) as an annotation tool for medical data by using it to produce so-called "pseudo labels" on the Medical Segmentation Decathlon (MSD) computed tomography (CT) tasks. The pseudo labels are then used in place of ground truth labels to train a UNet model in a weakly-supervised manner. We experiment with different prompt types on SAM and find that the bounding box prompt is a simple yet effective method for generating pseudo labels. This method allows us to develop a weakly-supervised model that performs comparably to a fully supervised model.

Recently, the Segment Anything Model (SAM) has demonstrated promising segmentation capabilities in a variety of downstream segmentation tasks. However in the context of universal medical image segmentation there exists a notable performance discrepancy when directly applying SAM due to the domain gap between natural and 2D/3D medical data. In this work, we propose a dual-branch adapted SAM framework, named DB-SAM, that strives to effectively bridge this domain gap. Our dual-branch adapted SAM contains two branches in parallel: a ViT branch and a convolution branch. The ViT branch incorporates a learnable channel attention block after each frozen attention block, which captures domain-specific local features. On the other hand, the convolution branch employs a light-weight convolutional block to extract domain-specific shallow features from the input medical image. To perform cross-branch feature fusion, we design a bilateral cross-attention block and a ViT convolution fusion block, which dynamically combine diverse information of two branches for mask decoder. Extensive experiments on large-scale medical image dataset with various 3D and 2D medical segmentation tasks reveal the merits of our proposed contributions. On 21 3D medical image segmentation tasks, our proposed DB-SAM achieves an absolute gain of 8.8%, compared to a recent medical SAM adapter in the literature. The code and model are available at https://github.com/AlfredQin/DB-SAM.

The Segment Anything Model (SAM) has recently gained popularity in the field of image segmentation due to its impressive capabilities in various segmentation tasks and its prompt-based interface. However, recent studies and individual experiments have shown that SAM underperforms in medical image segmentation, since the lack of the medical specific knowledge. This raises the question of how to enhance SAM's segmentation capability for medical images. In this paper, instead of fine-tuning the SAM model, we propose the Medical SAM Adapter (Med-SA), which incorporates domain-specific medical knowledge into the segmentation model using a light yet effective adaptation technique. In Med-SA, we propose Space-Depth Transpose (SD-Trans) to adapt 2D SAM to 3D medical images and Hyper-Prompting Adapter (HyP-Adpt) to achieve prompt-conditioned adaptation. We conduct comprehensive evaluation experiments on 17 medical image segmentation tasks across various image modalities. Med-SA outperforms several state-of-the-art (SOTA) medical image segmentation methods, while updating only 2\% of the parameters. Our code is released at https://github.com/KidsWithTokens/Medical-SAM-Adapter.

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

Existing methodologies in open vocabulary 3D semantic segmentation primarily concentrate on establishing a unified feature space encompassing 3D, 2D, and textual modalities. Nevertheless, traditional techniques such as global feature alignment or vision-language model distillation tend to impose only approximate correspondence, struggling notably with delineating fine-grained segmentation boundaries. To address this gap, we propose a more meticulous mask-level alignment between 3D features and the 2D-text embedding space through a cross-modal mask reasoning framework, XMask3D. In our approach, we developed a mask generator based on the denoising UNet from a pre-trained diffusion model, leveraging its capability for precise textual control over dense pixel representations and enhancing the open-world adaptability of the generated masks. We further integrate 3D global features as implicit conditions into the pre-trained 2D denoising UNet, enabling the generation of segmentation masks with additional 3D geometry awareness. Subsequently, the generated 2D masks are employed to align mask-level 3D representations with the vision-language feature space, thereby augmenting the open vocabulary capability of 3D geometry embeddings. Finally, we fuse complementary 2D and 3D mask features, resulting in competitive performance across multiple benchmarks for 3D open vocabulary semantic segmentation. Code is available at https://github.com/wangzy22/XMask3D.

Interactive segmentation has recently attracted attention for specialized tasks where expert input is required to further enhance the segmentation performance. In this work, we propose a novel interactive segmentation framework, where user clicks are dynamically adapted in size based on the current segmentation mask. The clicked regions form a weight map and are fed to a deep neural network as a novel weighted loss function. To evaluate our loss function, an interactive U-Net (IU-Net) model which applies both foreground and background user clicks as the main method of interaction is employed. We train and validate on the BCV dataset, while testing on spleen and colon cancer CT images from the MSD dataset to improve the overall segmentation accuracy in comparison to the standard U-Net using our weighted loss function. Applying dynamic user click sizes increases the overall accuracy by 5.60% and 10.39% respectively by utilizing only a single user interaction.