Daily Papers

Fine-grained visual representations are essential for medical image analysis, particularly when diagnostically relevant evidence is subtle and spatially localized. Modern transformer-based medical vision encoders must therefore learn patch-level representations that are both clinically meaningful and spatially consistent. Without these properties, large vision-language models (LVLMs) operate on an ambiguous visual foundation, limiting their ability to generate clinically reliable and spatially grounded responses. However, existing training strategies for medical vision encoders rarely achieve both objectives. Image-text alignment provides clinically meaningful supervision primarily at the image level, leaving the spatial localization of diagnostic evidence weakly constrained. In contrast, self-supervised learning promotes spatial consistency but lacks the semantic supervision needed to distinguish visually similar yet clinically distinct regions. To address this gap, we present LoFi, a medical vision foundation model built on location-aware fine-grained representation learning. LoFi trains a vision encoder with a lightweight large language model under grounding and grounded captioning objectives. Because these objectives require predicting location from clinical text and vice versa, spatial consistency emerges without any explicit patch-level regularization. To enable training at scale, we construct MedG, a large-scale medical grounding dataset of 4.48M image-text-box triplets curated from 84 datasets spanning 7 modalities. Across phrase grounding, visual question answering, and region-based organ classification under perturbations, LoFi consistently outperforms general-purpose and medical vision foundation models as well as state-of-the-art LVLMs. Code is available at https://github.com/myeongkyunkang/lofi-medg.

Organ segmentation is a fundamental task in medical imaging since it is useful for many clinical automation pipelines. However, some tasks do not require full segmentation. Instead, a classifier can identify the selected organ without segmenting the entire volume. In this study, we demonstrate a classifier based method to obtain organ labels in real time by using a large context size with a sparse data sampling strategy. Although our method operates as an independent classifier at query locations, it can generate full segmentations by querying grid locations at any resolution, offering faster performance than segmentation algorithms. We compared our method with existing segmentation techniques, demonstrating its superior runtime potential for practical applications in medical imaging.

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 organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via P{-}ConvNet and nearest neighbor fusion. Then we describe a regional ConvNet (R_1{-}ConvNet) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked R_2{-}ConvNet leveraging the joint space of CT intensities and the P{-}ConvNet dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6pm6.3% in training and 71.8pm10.7% in testing.

A CT examination captures multiple organs, but many biomedical questions concern abnormalities, prognosis, or longitudinal change in a specific organ. These questions require a separate representation for each organ within the same CT volume. Existing CT foundation models commonly produce a single volume-level representation, while recent anatomy-aware methods either encode pre-separated organ volumes or explicitly disentangle images into organ token groups. The former may remove clinically relevant surrounding context, while the latter does not condition a shared encoder on a selected organ before its features are formed. We introduce OrganLens for organ-specific representation learning through self-supervision. An organ identity conditions a shared CT encoder, while organ-specific distillation and anatomy-mask supervision shape features for anatomy-weighted pooling into organ-specific representations. At inference, the shared model produces 11 organ-specific representations without external segmentation masks. We evaluate OrganLens on CT-RATE, RAD-ChestCT, INSPECT, and NLST across diverse acquisitions and downstream evaluations. Relative to CT-pretrained DINOv2, heart representations raise CT-RATE cardiomegaly AUROC from 0.910 to 0.953, while lung representations improve the Harrell C-index for NLST lung-cancer mortality by 14.2\%. The global representation reaches INSPECT Recall@10 of 33.09\% and 32.04\% for text-to-image and image-to-text retrieval, respectively. Across organ-related tasks, anatomically matched representations provide stronger task-relevant signal, while the global representation retains broad utility. OrganLens offers a scalable approach to organ-specific CT representation learning with a shared encoder. More broadly, it provides the medical research community with a reusable framework for studying organ-specific disease across cohorts and clinical endpoints.

Multi-organ segmentation in medical imaging remains challenging due to large anatomical variability, complex inter-organ dependencies, and diverse organ scales and shapes. Conventional encoder-decoder architectures often struggle to capture both fine-grained local details and long-range context, which are crucial for accurate delineation - especially for small or deformable organs. To address these limitations, we propose MD-RWKV-UNet, a dynamic encoder network that enables scale-aware representation and spatially adaptive context modeling. At its core is the MD-RWKV block, a dual-path module that integrates deformable spatial shifts with the Receptance Weighted Key Value mechanism, allowing the receptive field to adapt dynamically to local structural cues. We further incorporate Selective Kernel Attention to enable adaptive selection of convolutional kernels with varying receptive fields, enhancing multi-scale interaction and improving robustness to organ size and shape variation. In parallel, a cross-stage dual-attention fusion strategy aggregates multi-level features across the encoder, preserving low-level structure while enhancing semantic consistency. Unlike methods that stack static convolutions or rely heavily on global attention, our approach provides a lightweight yet expressive solution for dynamic organ modeling. Experiments on Synapse and ACDC demonstrate state-of-the-art performance, particularly in boundary precision and small-organ segmentation.

Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To mitigate the limitations, we present AMOS, a large-scale, diverse, clinical dataset for abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease patients, each with voxel-level annotations of 15 abdominal organs, providing challenging examples and test-bed for studying robust segmentation algorithms under diverse targets and scenarios. We further benchmark several state-of-the-art medical segmentation models to evaluate the status of the existing methods on this new challenging dataset. We have made our datasets, benchmark servers, and baselines publicly available, and hope to inspire future research. Information can be found at https://amos22.grand-challenge.org.

Accurately segmenting different organs from medical images is a critical prerequisite for computer-assisted diagnosis and intervention planning. This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases. Our study introduces a novel technique integrating momentum within residual blocks for enhanced training dynamics in medical image analysis. We applied our method in two distinct tasks: segmenting liver, lung, & colon data and classifying abdominal pelvic CT and MRI scans. The proposed approach has shown promising results, outperforming state-of-the-art methods on publicly available benchmarking datasets. For instance, in the lung segmentation dataset, our approach yielded significant enhancements over the TransNetR model, including a 5.72% increase in dice score, a 5.04% improvement in mean Intersection over Union (mIoU), an 8.02% improvement in recall, and a 4.42% improvement in precision. Hence, incorporating momentum led to state-of-the-art performance in both segmentation and classification tasks, representing a significant advancement in the field of medical imaging.

Foundation models have recently achieved impressive success in computational pathology, demonstrating strong generalization across diverse histopathology tasks. However, existing models overlook the heterogeneous and non-uniform organization of pathological regions of interest (ROIs) because they rely on natural image backbones not tailored for tissue morphology. Consequently, they often fail to capture the coherent tissue architecture beyond isolated patches, limiting interpretability and clinical relevance. To address these challenges, we present Cross-modal Adaptive Region Encoder (CARE), a foundation model for pathology that automatically partitions WSIs into several morphologically relevant regions. Specifically, CARE employs a two-stage pretraining strategy: (1) a self-supervised unimodal pretraining stage that learns morphological representations from 34,277 whole-slide images (WSIs) without segmentation annotations, and (2) a cross-modal alignment stage that leverages RNA and protein profiles to refine the construction and representation of adaptive regions. This molecular guidance enables CARE to identify biologically relevant patterns and generate irregular yet coherent tissue regions, selecting the most representative area as ROI. CARE supports a broad range of pathology-related tasks, using either the ROI feature or the slide-level feature obtained by aggregating adaptive regions. Based on only one-tenth of the pretraining data typically used by mainstream foundation models, CARE achieves superior average performance across 33 downstream benchmarks, including morphological classification, molecular prediction, and survival analysis, and outperforms other foundation model baselines overall.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Autonomous surgical procedures, in particular minimal invasive surgeries, are the next frontier for Artificial Intelligence research. However, the existing challenges include precise identification of the human anatomy and the surgical settings, and modeling the environment for training of an autonomous agent. To address the identification of human anatomy and the surgical settings, we propose a deep learning based semantic segmentation algorithm to identify and label the tissues and organs in the endoscopic video feed of the human torso region. We present an annotated dataset, m2caiSeg, created from endoscopic video feeds of real-world surgical procedures. Overall, the data consists of 307 images, each of which is annotated for the organs and different surgical instruments present in the scene. We propose and train a deep convolutional neural network for the semantic segmentation task. To cater for the low quantity of annotated data, we use unsupervised pre-training and data augmentation. The trained model is evaluated on an independent test set of the proposed dataset. We obtained a F1 score of 0.33 while using all the labeled categories for the semantic segmentation task. Secondly, we labeled all instruments into an 'Instruments' superclass to evaluate the model's performance on discerning the various organs and obtained a F1 score of 0.57. We propose a new dataset and a deep learning method for pixel level identification of various organs and instruments in a endoscopic surgical scene. Surgical scene understanding is one of the first steps towards automating surgical procedures.

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.

Background: We evaluate SAM 2 for surgical scene understanding by examining its semantic segmentation capabilities for organs/tissues both in zero-shot scenarios and after fine-tuning. Methods: We utilized five public datasets to evaluate and fine-tune SAM 2 for segmenting anatomical tissues in surgical videos/images. Fine-tuning was applied to the image encoder and mask decoder. We limited training subsets from 50 to 400 samples per class to better model real-world constraints with data acquisition. The impact of dataset size on fine-tuning performance was evaluated with weighted mean Dice coefficient (WMDC), and the results were also compared against previously reported state-of-the-art (SOTA) results. Results: SurgiSAM 2, a fine-tuned SAM 2 model, demonstrated significant improvements in segmentation performance, achieving a 17.9% relative WMDC gain compared to the baseline SAM 2. Increasing prompt points from 1 to 10 and training data scale from 50/class to 400/class enhanced performance; the best WMDC of 0.92 on the validation subset was achieved with 10 prompt points and 400 samples per class. On the test subset, this model outperformed prior SOTA methods in 24/30 (80%) of the classes with a WMDC of 0.91 using 10-point prompts. Notably, SurgiSAM 2 generalized effectively to unseen organ classes, achieving SOTA on 7/9 (77.8%) of them. Conclusion: SAM 2 achieves remarkable zero-shot and fine-tuned performance for surgical scene segmentation, surpassing prior SOTA models across several organ classes of diverse datasets. This suggests immense potential for enabling automated/semi-automated annotation pipelines, thereby decreasing the burden of annotations facilitating several surgical applications.

Efficiently quantifying renal structures can provide distinct spatial context and facilitate biomarker discovery for kidney morphology. However, the development and evaluation of the transformer model to segment the renal cortex, medulla, and collecting system remains challenging due to data inefficiency. Inspired by the hierarchical structures in vision transformer, we propose a novel method using a 3D block aggregation transformer for segmenting kidney components on contrast-enhanced CT scans. We construct the first cohort of renal substructures segmentation dataset with 116 subjects under institutional review board (IRB) approval. Our method yields the state-of-the-art performance (Dice of 0.8467) against the baseline approach of 0.8308 with the data-efficient design. The Pearson R achieves 0.9891 between the proposed method and manual standards and indicates the strong correlation and reproducibility for volumetric analysis. We extend the proposed method to the public KiTS dataset, the method leads to improved accuracy compared to transformer-based approaches. We show that the 3D block aggregation transformer can achieve local communication between sequence representations without modifying self-attention, and it can serve as an accurate and efficient quantification tool for characterizing renal structures.

Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realizes global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissue structures. To address such challenges and inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting of multiple modalities, anatomies, and a wide range of tissue classes, including 133 structures in the brain, 14 organs in the abdomen, 4 hierarchical components in the kidneys, inter-connected kidney tumors and brain tumors. We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in a single network, outperforming prior state-of-the-art method SLANT27 ensembled with 27 networks.

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

Advancing AI in computational pathology requires large, high-quality, and diverse datasets, yet existing public datasets are often limited in organ diversity, class coverage, or annotation quality. To bridge this gap, we introduce SPIDER (Supervised Pathology Image-DEscription Repository), the largest publicly available patch-level dataset covering multiple organ types, including Skin, Colorectal, and Thorax, with comprehensive class coverage for each organ. SPIDER provides high-quality annotations verified by expert pathologists and includes surrounding context patches, which enhance classification performance by providing spatial context. Alongside the dataset, we present baseline models trained on SPIDER using the Hibou-L foundation model as a feature extractor combined with an attention-based classification head. The models achieve state-of-the-art performance across multiple tissue categories and serve as strong benchmarks for future digital pathology research. Beyond patch classification, the model enables rapid identification of significant areas, quantitative tissue metrics, and establishes a foundation for multimodal approaches. Both the dataset and trained models are publicly available to advance research, reproducibility, and AI-driven pathology development. Access them at: https://github.com/HistAI/SPIDER

The objective of Radiology Report Generation (RRG) is to automatically generate coherent textual analyses of diseases based on radiological images, thereby alleviating the workload of radiologists. Current AI-based methods for RRG primarily focus on modifications to the encoder-decoder model architecture. To advance these approaches, this paper introduces an Organ-Regional Information Driven (ORID) framework which can effectively integrate multi-modal information and reduce the influence of noise from unrelated organs. Specifically, based on the LLaVA-Med, we first construct an RRG-related instruction dataset to improve organ-regional diagnosis description ability and get the LLaVA-Med-RRG. After that, we propose an organ-based cross-modal fusion module to effectively combine the information from the organ-regional diagnosis description and radiology image. To further reduce the influence of noise from unrelated organs on the radiology report generation, we introduce an organ importance coefficient analysis module, which leverages Graph Neural Network (GNN) to examine the interconnections of the cross-modal information of each organ region. Extensive experiments an1d comparisons with state-of-the-art methods across various evaluation metrics demonstrate the superior performance of our proposed method.

Despite the recent successes of deep learning, such models are still far from some human abilities like learning from few examples, reasoning and explaining decisions. In this paper, we focus on organ annotation in medical images and we introduce a reasoning framework that is based on learning fuzzy relations on a small dataset for generating explanations. Given a catalogue of relations, it efficiently induces the most relevant relations and combines them for building constraints in order to both solve the organ annotation task and generate explanations. We test our approach on a publicly available dataset of medical images where several organs are already segmented. A demonstration of our model is proposed with an example of explained annotations. It was trained on a small training set containing as few as a couple of examples.

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.

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.

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.

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

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.

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

Liver Cirrhosis plays a critical role in the prognosis of chronic liver disease. Early detection and timely intervention are critical in significantly reducing mortality rates. However, the intricate anatomical architecture and diverse pathological changes of liver tissue complicate the accurate detection and characterization of lesions in clinical settings. Existing methods underutilize the spatial anatomical details in volumetric MRI data, thereby hindering their clinical effectiveness and explainability. To address this challenge, we introduce a novel Mamba-based network, SRMA-Mamba, designed to model the spatial relationships within the complex anatomical structures of MRI volumes. By integrating the Spatial Anatomy-Based Mamba module (SABMamba), SRMA-Mamba performs selective Mamba scans within liver cirrhotic tissues and combines anatomical information from the sagittal, coronal, and axial planes to construct a global spatial context representation, enabling efficient volumetric segmentation of pathological liver structures. Furthermore, we introduce the Spatial Reverse Attention module (SRMA), designed to progressively refine cirrhotic details in the segmentation map, utilizing both the coarse segmentation map and hierarchical encoding features. Extensive experiments demonstrate that SRMA-Mamba surpasses state-of-the-art methods, delivering exceptional performance in 3D pathological liver segmentation. Our code is available for public: https://github.com/JunZengz/SRMA-Mamba.

With the significantly increasing incidence and prevalence of abdominal diseases, there is a need to embrace greater use of new innovations and technology for the diagnosis and treatment of patients. Although deep-learning methods have notably been developed to assist radiologists in diagnosing abdominal diseases, existing models have the restricted ability to segment common lesions in the abdomen due to missing annotations for typical abdominal pathologies in their training datasets. To address the limitation, we introduce MSWAL, the first 3D Multi-class Segmentation of the Whole Abdominal Lesions dataset, which broadens the coverage of various common lesion types, such as gallstones, kidney stones, liver tumors, kidney tumors, pancreatic cancer, liver cysts, and kidney cysts. With CT scans collected from 694 patients (191,417 slices) of different genders across various scanning phases, MSWAL demonstrates strong robustness and generalizability. The transfer learning experiment from MSWAL to two public datasets, LiTS and KiTS, effectively demonstrates consistent improvements, with Dice Similarity Coefficient (DSC) increase of 3.00% for liver tumors and 0.89% for kidney tumors, demonstrating that the comprehensive annotations and diverse lesion types in MSWAL facilitate effective learning across different domains and data distributions. Furthermore, we propose Inception nnU-Net, a novel segmentation framework that effectively integrates an Inception module with the nnU-Net architecture to extract information from different receptive fields, achieving significant enhancement in both voxel-level DSC and region-level F1 compared to the cutting-edge public algorithms on MSWAL. Our dataset will be released after being accepted, and the code is publicly released at https://github.com/tiuxuxsh76075/MSWAL-.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

The high cure rate of cancer is inextricably linked to physicians' accuracy in diagnosis and treatment, therefore a model that can accomplish high-precision tumor segmentation has become a necessity in many applications of the medical industry. It can effectively lower the rate of misdiagnosis while considerably lessening the burden on clinicians. However, fully automated target organ segmentation is problematic due to the irregular stereo structure of 3D volume organs. As a basic model for this class of real applications, U-Net excels. It can learn certain global and local features, but still lacks the capacity to grasp spatial long-range relationships and contextual information at multiple scales. This paper proposes a tumor segmentation model MPU-Net for patient volume CT images, which is inspired by Transformer with a global attention mechanism. By combining image serialization with the Position Attention Module, the model attempts to comprehend deeper contextual dependencies and accomplish precise positioning. Each layer of the decoder is also equipped with a multi-scale module and a cross-attention mechanism. The capability of feature extraction and integration at different levels has been enhanced, and the hybrid loss function developed in this study can better exploit high-resolution characteristic information. Moreover, the suggested architecture is tested and evaluated on the Liver Tumor Segmentation Challenge 2017 (LiTS 2017) dataset. Compared with the benchmark model U-Net, MPU-Net shows excellent segmentation results. The dice, accuracy, precision, specificity, IOU, and MCC metrics for the best model segmentation results are 92.17%, 99.08%, 91.91%, 99.52%, 85.91%, and 91.74%, respectively. Outstanding indicators in various aspects illustrate the exceptional performance of this framework in automatic medical image segmentation.

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600K objects for segmentation and 440K patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900K and 2.1 million nuclei, glands and lumina, respectively and make the results available to the community for downstream analysis.

The in-vivo identification of the kidney stone types during an ureteroscopy would be a major medical advance in urology, as it could reduce the time of the tedious renal calculi extraction process, while diminishing infection risks. Furthermore, such an automated procedure would make possible to prescribe anti-recurrence treatments immediately. Nowadays, only few experienced urologists are able to recognize the kidney stone types in the images of the videos displayed on a screen during the endoscopy. Thus, several deep learning (DL) models have recently been proposed to automatically recognize the kidney stone types using ureteroscopic images. However, these DL models are of black box nature whicl limits their applicability in clinical settings. This contribution proposes a case-based reasoning DL model which uses prototypical parts (PPs) and generates local and global descriptors. The PPs encode for each class (i.e., kidney stone type) visual feature information (hue, saturation, intensity and textures) similar to that used by biologists. The PPs are optimally generated due a new loss function used during the model training. Moreover, the local and global descriptors of PPs allow to explain the decisions ("what" information, "where in the images") in an understandable way for biologists and urologists. The proposed DL model has been tested on a database including images of the six most widespread kidney stone types. The overall average classification accuracy was 90.37. When comparing this results with that of the eight other DL models of the kidney stone state-of-the-art, it can be seen that the valuable gain in explanability was not reached at the expense of accuracy which was even slightly increased with respect to that (88.2) of the best method of the literature. These promising and interpretable results also encourage urologists to put their trust in AI-based solutions.

Learning anatomical segmentation from heterogeneous labels in multi-center datasets is a common situation encountered in clinical scenarios, where certain anatomical structures are only annotated in images coming from particular medical centers, but not in the full database. Here we first show how state-of-the-art pixel-level segmentation models fail in naively learning this task due to domain memorization issues and conflicting labels. We then propose to adopt HybridGNet, a landmark-based segmentation model which learns the available anatomical structures using graph-based representations. By analyzing the latent space learned by both models, we show that HybridGNet naturally learns more domain-invariant feature representations, and provide empirical evidence in the context of chest X-ray multiclass segmentation. We hope these insights will shed light on the training of deep learning models with heterogeneous labels from public and multi-center datasets.

Accurate delineation of pathological lungs from computed tomography (CT) images remains mostly unsolved because available methods fail to provide a reliable generic solution due to high variability of abnormality appearance. Local descriptor-based classification methods have shown to work well in annotating pathologies; however, these methods are usually computationally intensive which restricts their widespread use in real-time or near-real-time clinical applications. In this paper, we present a novel approach for fast, accurate, reliable segmentation of pathological lungs from CT scans by combining region-based segmentation method with local descriptor classification that is performed on an optimized sampling grid. Our method works in two stages; during stage one, we adapted the fuzzy connectedness (FC) image segmentation algorithm to perform initial lung parenchyma extraction. In the second stage, texture-based local descriptors are utilized to segment abnormal imaging patterns using a near optimal keypoint analysis by employing centroid of supervoxel as grid points. The quantitative results show that our pathological lung segmentation method is fast, robust, and improves on current standards and has potential to enhance the performance of routine clinical tasks.

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

Accurate and generalizable object segmentation in ultrasound imaging remains a significant challenge due to anatomical variability, diverse imaging protocols, and limited annotated data. In this study, we propose a prompt-driven vision-language model (VLM) that integrates Grounding DINO with SAM2 to enable object segmentation across multiple ultrasound organs. A total of 18 public ultrasound datasets, encompassing the breast, thyroid, liver, prostate, kidney, and paraspinal muscle, were utilized. These datasets were divided into 15 for fine-tuning and validation of Grounding DINO using Low Rank Adaptation (LoRA) to the ultrasound domain, and 3 were held out entirely for testing to evaluate performance in unseen distributions. Comprehensive experiments demonstrate that our approach outperforms state-of-the-art segmentation methods, including UniverSeg, MedSAM, MedCLIP-SAM, BiomedParse, and SAMUS on most seen datasets while maintaining strong performance on unseen datasets without additional fine-tuning. These results underscore the promise of VLMs in scalable and robust ultrasound image analysis, reducing dependence on large, organ-specific annotated datasets. We will publish our code on code.sonography.ai after acceptance.

Rich and accurate medical image segmentation is poised to underpin the next generation of AI-defined clinical practice by delineating critical anatomy for pre-operative planning, guiding real-time intra-operative navigation, and supporting precise post-operative assessment. However, commonly used learning methods for medical and surgical imaging segmentation tasks penalise all errors equivalently and thus fail to exploit any inter-class semantics in the labels space. This becomes particularly problematic as the cardinality and richness of labels increases to include subtly different classes. In this work, we propose two tree-based semantic loss functions which take advantage of a hierarchical organisation of the labels. We further incorporate our losses in a recently proposed approach for training with sparse, background-free annotations to extend the applicability of our proposed losses. Extensive experiments are reported on two medical and surgical image segmentation tasks, namely head MRI for whole brain parcellation (WBP) with full supervision and neurosurgical hyperspectral imaging (HSI) for scene understanding with sparse annotations. Results demonstrate that our proposed method reaches state-of-the-art performance in both cases.

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.

Convolutional Neural Networks (CNNs) and Transformers have been the most popular architectures for biomedical image segmentation, but both of them have limited ability to handle long-range dependencies because of inherent locality or computational complexity. To address this challenge, we introduce U-Mamba, a general-purpose network for biomedical image segmentation. Inspired by the State Space Sequence Models (SSMs), a new family of deep sequence models known for their strong capability in handling long sequences, we design a hybrid CNN-SSM block that integrates the local feature extraction power of convolutional layers with the abilities of SSMs for capturing the long-range dependency. Moreover, U-Mamba enjoys a self-configuring mechanism, allowing it to automatically adapt to various datasets without manual intervention. We conduct extensive experiments on four diverse tasks, including the 3D abdominal organ segmentation in CT and MR images, instrument segmentation in endoscopy images, and cell segmentation in microscopy images. The results reveal that U-Mamba outperforms state-of-the-art CNN-based and Transformer-based segmentation networks across all tasks. This opens new avenues for efficient long-range dependency modeling in biomedical image analysis. The code, models, and data are publicly available at https://wanglab.ai/u-mamba.html.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

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.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

Accurate segmentation of anatomical structures in ultrasound (US) images, particularly small ones, is challenging due to noise and variability in imaging conditions (e.g., probe position, patient anatomy, tissue characteristics and pathology). To address this, we introduce Segment Anything Small (SAS), a simple yet effective scale- and texture-aware data augmentation technique designed to enhance the performance of deep learning models for segmenting small anatomical structures in ultrasound images. SAS employs a dual transformation strategy: (1) simulating diverse organ scales by resizing and embedding organ thumbnails into a black background, and (2) injecting noise into regions of interest to simulate varying tissue textures. These transformations generate realistic and diverse training data without introducing hallucinations or artifacts, improving the model's robustness to noise and variability. We fine-tuned a promptable foundation model on a controlled organ-specific medical imaging dataset and evaluated its performance on one internal and five external datasets. Experimental results demonstrate significant improvements in segmentation performance, with Dice score gains of up to 0.35 and an average improvement of 0.16 [95% CI 0.132,0.188]. Additionally, our iterative point prompts provide precise control and adaptive refinement, achieving performance comparable to bounding box prompts with just two points. SAS enhances model robustness and generalizability across diverse anatomical structures and imaging conditions, particularly for small structures, without compromising the accuracy of larger ones. By offering a computationally efficient solution that eliminates the need for extensive human labeling efforts, SAS emerges as a powerful tool for advancing medical image analysis, particularly in resource-constrained settings.

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.

Size measurements of tumor manifestations on follow-up CT examinations are crucial for evaluating treatment outcomes in cancer patients. Efficient lesion segmentation can speed up these radiological workflows. While numerous benchmarks and challenges address lesion segmentation in specific organs like the liver, kidneys, and lungs, the larger variety of lesion types encountered in clinical practice demands a more universal approach. To address this gap, we introduced the ULS23 benchmark for 3D universal lesion segmentation in chest-abdomen-pelvis CT examinations. The ULS23 training dataset contains 38,693 lesions across this region, including challenging pancreatic, colon and bone lesions. For evaluation purposes, we curated a dataset comprising 775 lesions from 284 patients. Each of these lesions was identified as a target lesion in a clinical context, ensuring diversity and clinical relevance within this dataset. The ULS23 benchmark is publicly accessible via uls23.grand-challenge.org, enabling researchers worldwide to assess the performance of their segmentation methods. Furthermore, we have developed and publicly released our baseline semi-supervised 3D lesion segmentation model. This model achieved an average Dice coefficient of 0.703 pm 0.240 on the challenge test set. We invite ongoing submissions to advance the development of future ULS models.

Multi-organ segmentation is a critical yet challenging task due to complex anatomical backgrounds, blurred boundaries, and diverse morphologies. This study introduces the Gradient-aware Adaptive Momentum Evolution Deep Snake (GAMED-Snake) model, which establishes a novel paradigm for contour-based segmentation by integrating gradient-based learning with adaptive momentum evolution mechanisms. The GAMED-Snake model incorporates three major innovations: First, the Distance Energy Map Prior (DEMP) generates a pixel-level force field that effectively attracts contour points towards the true boundaries, even in scenarios with complex backgrounds and blurred edges. Second, the Differential Convolution Inception Module (DCIM) precisely extracts comprehensive energy gradients, significantly enhancing segmentation accuracy. Third, the Adaptive Momentum Evolution Mechanism (AMEM) employs cross-attention to establish dynamic features across different iterations of evolution, enabling precise boundary alignment for diverse morphologies. Experimental results on four challenging multi-organ segmentation datasets demonstrate that GAMED-Snake improves the mDice metric by approximately 2% compared to state-of-the-art methods. Code will be available at https://github.com/SYSUzrc/GAMED-Snake.

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.

Despite that the segment anything model (SAM) achieved impressive results on general-purpose semantic segmentation with strong generalization ability on daily images, its demonstrated performance on medical image segmentation is less precise and not stable, especially when dealing with tumor segmentation tasks that involve objects of small sizes, irregular shapes, and low contrast. Notably, the original SAM architecture is designed for 2D natural images, therefore would not be able to extract the 3D spatial information from volumetric medical data effectively. In this paper, we propose a novel adaptation method for transferring SAM from 2D to 3D for promptable medical image segmentation. Through a holistically designed scheme for architecture modification, we transfer the SAM to support volumetric inputs while retaining the majority of its pre-trained parameters for reuse. The fine-tuning process is conducted in a parameter-efficient manner, wherein most of the pre-trained parameters remain frozen, and only a few lightweight spatial adapters are introduced and tuned. Regardless of the domain gap between natural and medical data and the disparity in the spatial arrangement between 2D and 3D, the transformer trained on natural images can effectively capture the spatial patterns present in volumetric medical images with only lightweight adaptations. We conduct experiments on four open-source tumor segmentation datasets, and with a single click prompt, our model can outperform domain state-of-the-art medical image segmentation models on 3 out of 4 tasks, specifically by 8.25%, 29.87%, and 10.11% for kidney tumor, pancreas tumor, colon cancer segmentation, and achieve similar performance for liver tumor segmentation. We also compare our adaptation method with existing popular adapters, and observed significant performance improvement on most datasets.

Multi-class tissue-type classification of colorectal cancer (CRC) histopathologic images is a significant step in the development of downstream machine learning models for diagnosis and treatment planning. However, existing public CRC datasets often lack morphologic diversity, suffer from class imbalance, and contain low-quality image tiles, limiting model performance and generalizability. To address these issues, we introduce STARC-9 (STAnford coloRectal Cancer), a large-scale dataset for multi-class tissue classification. STARC-9 contains 630,000 hematoxylin and eosin-stained image tiles uniformly sampled across nine clinically relevant tissue classes (70,000 tiles per class) from 200 CRC patients at the Stanford University School of Medicine. The dataset was built using a novel framework, DeepCluster++, designed to ensure intra-class diversity and reduce manual curation. First, an encoder from a histopathology-specific autoencoder extracts feature vectors from tiles within each whole-slide image. Then, K-means clustering groups morphologically similar tiles, followed by equal-frequency binning to sample diverse morphologic patterns within each class. The selected tiles are subsequently verified by expert gastrointestinal pathologists to ensure accuracy. This semi-automated process significantly reduces manual effort while producing high-quality, diverse tiles. To evaluate STARC-9, we benchmarked convolutional neural networks, transformers, and pathology-specific foundation models on multi-class CRC tissue classification and segmentation tasks, showing superior generalizability compared to models trained on existing datasets. Although we demonstrate the utility of DeepCluster++ on CRC as a pilot use-case, it is a flexible framework that can be used for constructing high-quality datasets from large WSI repositories across a wide range of cancer and non-cancer applications.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole.

Purpose: This paper proposes a new network framework called EAR-U-Net, which leverages EfficientNetB4, attention gate, and residual learning techniques to achieve automatic and accurate liver segmentation. Methods: The proposed method is based on the U-Net framework. First, we use EfficientNetB4 as the encoder to extract more feature information during the encoding stage. Then, an attention gate is introduced in the skip connection to eliminate irrelevant regions and highlight features of a specific segmentation task. Finally, to alleviate the problem of gradient vanishment, we replace the traditional convolution of the decoder with a residual block to improve the segmentation accuracy. Results: We verified the proposed method on the LiTS17 and SLiver07 datasets and compared it with classical networks such as FCN, U-Net, Attention U-Net, and Attention Res-U-Net. In the Sliver07 evaluation, the proposed method achieved the best segmentation performance on all five standard metrics. Meanwhile, in the LiTS17 assessment, the best performance is obtained except for a slight inferior on RVD. Moreover, we also participated in the MICCIA-LiTS17 challenge, and the Dice per case score was 0.952. Conclusion: The proposed method's qualitative and quantitative results demonstrated its applicability in liver segmentation and proved its good prospect in computer-assisted liver segmentation.

Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work in cancer grading has focused mainly on classifying pre-defined regions of interest (ROIs), or relied on large amounts of fine-grained labels. In this paper, we propose a two-stage attention-based multiple instance learning model for slide-level cancer grading and weakly-supervised ROI detection and demonstrate its use in prostate cancer. Compared with existing Gleason classification models, our model goes a step further by utilizing visualized saliency maps to select informative tiles for fine-grained grade classification. The model was primarily developed on a large-scale whole slide dataset consisting of 3,521 prostate biopsy slides with only slide-level labels from 718 patients. The model achieved state-of-the-art performance for prostate cancer grading with an accuracy of 85.11\% for classifying benign, low-grade (Gleason grade 3+3 or 3+4), and high-grade (Gleason grade 4+3 or higher) slides on an independent test set.

Accurate recognition of anatomical structures is essential for safe and effective minimally invasive surgery (MIS), yet it remains underexplored in surgical computer vision due to limited annotated data and methods tailored primarily to natural scenes. In this work, we present a combined dataset and model framework to advance anatomy-aware perception in MIS. First, we introduce ATLAS-120k, a large-scale clip-level semantic segmentation dataset comprising over 120,000 annotated frames from 100 surgical videos spanning 14 procedures and multiple modalities, including laparoscopic and robot-assisted surgery. The dataset captures substantial procedural variability and was created using a scalable annotation pipeline that integrates expert manual labeling, automated propagation, iterative refinement, and surgeon verification to ensure high-quality annotations. Second, we propose ATLAS (Anatomy Recognition with Context Learning using Foundation Representations), a video semantic segmentation model specifically designed for surgical anatomy recognition. Unlike conventional approaches that emphasize object tracking, ATLAS leverages foundation-model embeddings together with lightweight temporal reasoning to incorporate contextual cues such as procedure type, surgical phase, and short-term visual memory. This design enables temporally consistent and accurate predictions while maintaining real-time feasibility. Together, the dataset and model establish a practical foundation for robust surgical scene understanding and support the development of clinically applicable guidance systems for minimally invasive surgery. The models, dataset annotations and annotation platform are publicly available at: https://github.com/TimJaspers0801/ATLAS.

The convolutional neural network-based methods have become more and more popular for medical image segmentation due to their outstanding performance. However, they struggle with capturing long-range dependencies, which are essential for accurately modeling global contextual correlations. Thanks to the ability to model long-range dependencies by expanding the receptive field, the transformer-based methods have gained prominence. Inspired by this, we propose an advanced 2D feature extraction method by combining the convolutional neural network and Transformer architectures. More specifically, we introduce a parallelized encoder structure, where one branch uses ResNet to extract local information from images, while the other branch uses Transformer to extract global information. Furthermore, we integrate pyramid structures into the Transformer to extract global information at varying resolutions, especially in intensive prediction tasks. To efficiently utilize the different information in the parallelized encoder at the decoder stage, we use a channel attention module to merge the features of the encoder and propagate them through skip connections and bottlenecks. Intensive numerical experiments are performed on both aortic vessel tree, cardiac, and multi-organ datasets. By comparing with state-of-the-art medical image segmentation methods, our method is shown with better segmentation accuracy, especially on small organs. The code is publicly available on https://github.com/HongkunSun/ParaTransCNN.

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

Creating a large-scale dataset of abnormality annotation on medical images is a labor-intensive and costly task. Leveraging weak supervision from readily available data such as radiology reports can compensate lack of large-scale data for anomaly detection methods. However, most of the current methods only use image-level pathological observations, failing to utilize the relevant anatomy mentions in reports. Furthermore, Natural Language Processing (NLP)-mined weak labels are noisy due to label sparsity and linguistic ambiguity. We propose an Anatomy-Guided chest X-ray Network (AGXNet) to address these issues of weak annotation. Our framework consists of a cascade of two networks, one responsible for identifying anatomical abnormalities and the second responsible for pathological observations. The critical component in our framework is an anatomy-guided attention module that aids the downstream observation network in focusing on the relevant anatomical regions generated by the anatomy network. We use Positive Unlabeled (PU) learning to account for the fact that lack of mention does not necessarily mean a negative label. Our quantitative and qualitative results on the MIMIC-CXR dataset demonstrate the effectiveness of AGXNet in disease and anatomical abnormality localization. Experiments on the NIH Chest X-ray dataset show that the learned feature representations are transferable and can achieve the state-of-the-art performances in disease classification and competitive disease localization results. Our code is available at https://github.com/batmanlab/AGXNet

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.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

Pathological diagnosis remains the definitive standard for identifying tumors. The rise of multimodal large models has simplified the process of integrating image analysis with textual descriptions. Despite this advancement, the substantial costs associated with training and deploying these complex multimodal models, together with a scarcity of high-quality training datasets, create a significant divide between cutting-edge technology and its application in the clinical setting. We had meticulously compiled a dataset of approximately 45,000 cases, covering over 6 different tasks, including the classification of organ tissues, generating pathology report descriptions, and addressing pathology-related questions and answers. We have fine-tuned multimodal large models, specifically LLaVA, Qwen-VL, InternLM, with this dataset to enhance instruction-based performance. We conducted a qualitative assessment of the capabilities of the base model and the fine-tuned model in performing image captioning and classification tasks on the specific dataset. The evaluation results demonstrate that the fine-tuned model exhibits proficiency in addressing typical pathological questions. We hope that by making both our models and datasets publicly available, they can be valuable to the medical and research communities.

Vision-specific concepts such as "region" have played a key role in extending general machine learning frameworks to tasks like object detection. Given the success of region-based detectors for supervised learning and the progress of intra-image methods for contrastive learning, we explore the use of regions for reconstructive pre-training. Starting from Masked Autoencoding (MAE) both as a baseline and an inspiration, we propose a parallel pre-text task tailored to address the one-to-many mapping between images and regions. Since such regions can be generated in an unsupervised way, our approach (R-MAE) inherits the wide applicability from MAE, while being more "region-aware". We conduct thorough analyses during the development of R-MAE, and converge on a variant that is both effective and efficient (1.3% overhead over MAE). Moreover, it shows consistent quantitative improvements when generalized to various pre-training data and downstream detection and segmentation benchmarks. Finally, we provide extensive qualitative visualizations to enhance the understanding of R-MAE's behaviour and potential. Code will be made available at https://github.com/facebookresearch/r-mae.

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

Few-shot medical image segmentation (FS-MIS) aims to segment novel regions of interest (ROIs) from a few annotated support examples. Despite rapid progress, existing FS-MIS solutions span diverse paradigms but are evaluated under inconsistent settings, leaving their relative effectiveness unclear. We introduce FAME, a unified benchmark for evaluating FS-MIS solutions, covering specialists, SAM-based methods, CLIP-based methods, and MLLM-based methods. FAME contains 14,958 test samples across 7 anatomical sites, 9 imaging modalities, and 14 ROI categories, and evaluates models under zero-shot and ten-shot settings with additional assessment of target-absence recognition and generalization under covariate and semantic shifts. Our evaluation reveals several findings. First, effective few-shot segmentation depends on how models exploit support examples: direct visual adaptation generally outperforms prompt-based strategies. Second, increasing support examples improves performance only when models can effectively utilize them. Third, semantic transfer remains substantially more challenging than imaging-domain adaptation, and strong localization ability does not necessarily imply reliable target-absence recognition. We hope FAME provides a comprehensive understanding of current FS-MIS solutions and facilitates the development of more effective and reliable few-shot medical segmentation methods.

Vision-grounded medical report generation aims to produce clinically accurate descriptions of medical images, anchored in explicit visual evidence to improve interpretability and facilitate integration into clinical workflows. However, existing methods often rely on separately trained detection modules that require extensive expert annotations, introducing high labeling costs and limiting generalizability due to pathology distribution bias across datasets. To address these challenges, we propose Self-Supervised Anatomical Consistency Learning (SS-ACL) -- a novel and annotation-free framework that aligns generated reports with corresponding anatomical regions using simple textual prompts. SS-ACL constructs a hierarchical anatomical graph inspired by the invariant top-down inclusion structure of human anatomy, organizing entities by spatial location. It recursively reconstructs fine-grained anatomical regions to enforce intra-sample spatial alignment, inherently guiding attention maps toward visually relevant areas prompted by text. To further enhance inter-sample semantic alignment for abnormality recognition, SS-ACL introduces a region-level contrastive learning based on anatomical consistency. These aligned embeddings serve as priors for report generation, enabling attention maps to provide interpretable visual evidence. Extensive experiments demonstrate that SS-ACL, without relying on expert annotations, (i) generates accurate and visually grounded reports -- outperforming state-of-the-art methods by 10\% in lexical accuracy and 25\% in clinical efficacy, and (ii) achieves competitive performance on various downstream visual tasks, surpassing current leading visual foundation models by 8\% in zero-shot visual grounding.

Accurate disease interpretation from radiology remains challenging due to imaging heterogeneity. Achieving expert-level diagnostic decisions requires integration of subtle image features with clinical knowledge. Yet major vision-language models (VLMs) treat images as holistic entities and overlook fine-grained image details that are vital for disease diagnosis. Clinicians analyze images by utilizing their prior medical knowledge and identify anatomical structures as important region of interests (ROIs). Inspired from this human-centric workflow, we introduce Anatomy-VLM, a fine-grained, vision-language model that incorporates multi-scale information. First, we design a model encoder to localize key anatomical features from entire medical images. Second, these regions are enriched with structured knowledge for contextually-aware interpretation. Finally, the model encoder aligns multi-scale medical information to generate clinically-interpretable disease prediction. Anatomy-VLM achieves outstanding performance on both in- and out-of-distribution datasets. We also validate the performance of Anatomy-VLM on downstream image segmentation tasks, suggesting that its fine-grained alignment captures anatomical and pathology-related knowledge. Furthermore, the Anatomy-VLM's encoder facilitates zero-shot anatomy-wise interpretation, providing its strong expert-level clinical interpretation capabilities.

Respiratory motion and the associated deformations of abdominal organs and tumors are essential information in clinical applications. However, inter- and intra-patient multi-organ deformations are complex and have not been statistically formulated, whereas single organ deformations have been widely studied. In this paper, we introduce a multi-organ deformation library and its application to deformation reconstruction based on the shape features of multiple abdominal organs. Statistical multi-organ motion/deformation models of the stomach, liver, left and right kidneys, and duodenum were generated by shape matching their region labels defined on four-dimensional computed tomography images. A total of 250 volumes were measured from 25 pancreatic cancer patients. This paper also proposes a per-region-based deformation learning using the reproducing kernel to predict the displacement of pancreatic cancer for adaptive radiotherapy. The experimental results show that the proposed concept estimates deformations better than general per-patient-based learning models and achieves a clinically acceptable estimation error with a mean distance of 1.2 pm 0.7 mm and a Hausdorff distance of 4.2 pm 2.3 mm throughout the respiratory motion.

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.

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.

Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input for a second FCN. The second FCN solely segments lesions within the predicted liver ROIs of step 1. CFCN models were trained on an abdominal CT dataset comprising 100 hepatic tumor volumes. Validations on further datasets show that CFCN-based semantic liver and lesion segmentation achieves Dice scores over 94% for liver with computation times below 100s per volume. We further experimentally demonstrate the robustness of the proposed method on an 38 MRI liver tumor volumes and the public 3DIRCAD dataset.

Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We formulate the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge and 3DIRCADb Dataset. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model.

Promptable segmentation foundation models such as SAM3 have demonstrated strong generalization capabilities through interactive and concept-based prompting. However, their direct applicability to medical image segmentation remains limited by severe domain shifts, the absence of privileged spatial prompts, and the need to reason over complex anatomical and volumetric structures. Here we present Medical SAM3, a foundation model for universal prompt-driven medical image segmentation, obtained by fully fine-tuning SAM3 on large-scale, heterogeneous 2D and 3D medical imaging datasets with paired segmentation masks and text prompts. Through a systematic analysis of vanilla SAM3, we observe that its performance degrades substantially on medical data, with its apparent competitiveness largely relying on strong geometric priors such as ground-truth-derived bounding boxes. These findings motivate full model adaptation beyond prompt engineering alone. By fine-tuning SAM3's model parameters on 33 datasets spanning 10 medical imaging modalities, Medical SAM3 acquires robust domain-specific representations while preserving prompt-driven flexibility. Extensive experiments across organs, imaging modalities, and dimensionalities demonstrate consistent and significant performance gains, particularly in challenging scenarios characterized by semantic ambiguity, complex morphology, and long-range 3D context. Our results establish Medical SAM3 as a universal, text-guided segmentation foundation model for medical imaging and highlight the importance of holistic model adaptation for achieving robust prompt-driven segmentation under severe domain shift. Code and model will be made available at https://github.com/AIM-Research-Lab/Medical-SAM3.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.

The morphometry of a kidney tumor revealed by contrast-enhanced Computed Tomography (CT) imaging is an important factor in clinical decision making surrounding the lesion's diagnosis and treatment. Quantitative study of the relationship between kidney tumor morphology and clinical outcomes is difficult due to data scarcity and the laborious nature of manually quantifying imaging predictors. Automatic semantic segmentation of kidneys and kidney tumors is a promising tool towards automatically quantifying a wide array of morphometric features, but no sizeable annotated dataset is currently available to train models for this task. We present the KiTS19 challenge dataset: A collection of multi-phase CT imaging, segmentation masks, and comprehensive clinical outcomes for 300 patients who underwent nephrectomy for kidney tumors at our center between 2010 and 2018. 210 (70%) of these patients were selected at random as the training set for the 2019 MICCAI KiTS Kidney Tumor Segmentation Challenge and have been released publicly. With the presence of clinical context and surgical outcomes, this data can serve not only for benchmarking semantic segmentation models, but also for developing and studying biomarkers which make use of the imaging and semantic segmentation masks.

Tissue segmentation is a routine preprocessing step to reduce the computational cost of whole slide image (WSI) analysis by excluding background regions. Traditional image processing techniques are commonly used for tissue segmentation, but often require manual adjustments to parameter values for atypical cases, fail to exclude all slide and scanning artifacts from the background, and are unable to segment adipose tissue. Pen marking artifacts in particular can be a potential source of bias for subsequent analyses if not removed. In addition, several applications require the separation of individual cross-sections, which can be challenging due to tissue fragmentation and adjacent positioning. To address these problems, we develop a convolutional neural network for tissue and pen marking segmentation using a dataset of 200 H&E stained WSIs. For separating tissue cross-sections, we propose a novel post-processing method based on clustering predicted centroid locations of the cross-sections in a 2D histogram. On an independent test set, the model achieved a mean Dice score of 0.981pm0.033 for tissue segmentation and a mean Dice score of 0.912pm0.090 for pen marking segmentation. The mean absolute difference between the number of annotated and separated cross-sections was 0.075pm0.350. Our results demonstrate that the proposed model can accurately segment H&E stained tissue cross-sections and pen markings in WSIs while being robust to many common slide and scanning artifacts. The model with trained model parameters and post-processing method are made publicly available as a Python package called SlideSegmenter.

Several medical Multimodal Large Languange Models (MLLMs) have been developed to address tasks involving visual images with textual instructions across various medical modalities, achieving impressive results. Most current medical generalist models are region-agnostic, treating the entire image as a holistic representation. However, they struggle to identify which specific regions they are focusing on when generating a sentence. To mimic the behavior of doctors, who typically begin by reviewing the entire image before concentrating on specific regions for a thorough evaluation, we aim to enhance the capability of medical MLLMs in understanding anatomical regions within entire medical scans. To achieve it, we first formulate Region-Centric tasks and construct a large-scale dataset, MedRegInstruct, to incorporate regional information into training. Combining our collected dataset with other medical multimodal corpora for training, we propose a Region-Aware medical MLLM, MedRegA, which is the first bilingual generalist medical AI system to simultaneously handle image-level and region-level medical vision-language tasks across a broad range of modalities. Our MedRegA not only enables three region-centric tasks, but also achieves the best performance for visual question answering, report generation and medical image classification over 8 modalities, showcasing significant versatility. Experiments demonstrate that our model can not only accomplish powerful performance across various medical vision-language tasks in bilingual settings, but also recognize and detect structures in multimodal medical scans, boosting the interpretability and user interactivity of medical MLLMs. Our project page is https://medrega.github.io.

Deep learning classifiers face significant challenges when dealing with heterogeneous multi-modal and multi-organ biomedical datasets. The low-level feature distinguishability limited to imaging-modality hinders the classifiers' ability to learn high-level semantic relationships, resulting in sub-optimal performance. To address this issue, image augmentation strategies are employed as regularization techniques. While additive noise input during network training is a well-established augmentation as regularization method, modern pipelines often favor more robust techniques such as dropout and weight decay. This preference stems from the observation that combining these established techniques with noise input can adversely affect model performance. In this study, we propose a novel pretraining pipeline that learns to generate conditional noise mask specifically tailored to improve performance on multi-modal and multi-organ datasets. As a reinforcement learning algorithm, our approach employs a dual-component system comprising a very light-weight policy network that learns to sample conditional noise using a differentiable beta distribution as well as a classifier network. The policy network is trained using the reinforce algorithm to generate image-specific noise masks that regularize the classifier during pretraining. A key aspect is that the policy network's role is limited to obtaining an intermediate (or heated) model before fine-tuning. During inference, the policy network is omitted, allowing direct comparison between the baseline and noise-regularized models. We conducted experiments and related analyses on RadImageNet datasets. Results demonstrate that fine-tuning the intermediate models consistently outperforms conventional training algorithms on both classification and generalization to unseen concept tasks.

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

Self-Supervised Learning (SSL) has demonstrated promising results in 3D medical image analysis. However, the lack of high-level semantics in pre-training still heavily hinders the performance of downstream tasks. We observe that 3D medical images contain relatively consistent contextual position information, i.e., consistent geometric relations between different organs, which leads to a potential way for us to learn consistent semantic representations in pre-training. In this paper, we propose a simple-yet-effective Volume Contrast (VoCo) framework to leverage the contextual position priors for pre-training. Specifically, we first generate a group of base crops from different regions while enforcing feature discrepancy among them, where we employ them as class assignments of different regions. Then, we randomly crop sub-volumes and predict them belonging to which class (located at which region) by contrasting their similarity to different base crops, which can be seen as predicting contextual positions of different sub-volumes. Through this pretext task, VoCo implicitly encodes the contextual position priors into model representations without the guidance of annotations, enabling us to effectively improve the performance of downstream tasks that require high-level semantics. Extensive experimental results on six downstream tasks demonstrate the superior effectiveness of VoCo. Code will be available at https://github.com/Luffy03/VoCo.

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.

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

The medical imaging community generates a wealth of datasets, many of which are openly accessible and annotated for specific diseases and tasks such as multi-organ or lesion segmentation. Current practices continue to limit model training and supervised pre-training to one or a few similar datasets, neglecting the synergistic potential of other available annotated data. We propose MultiTalent, a method that leverages multiple CT datasets with diverse and conflicting class definitions to train a single model for a comprehensive structure segmentation. Our results demonstrate improved segmentation performance compared to previous related approaches, systematically, also compared to single dataset training using state-of-the-art methods, especially for lesion segmentation and other challenging structures. We show that MultiTalent also represents a powerful foundation model that offers a superior pre-training for various segmentation tasks compared to commonly used supervised or unsupervised pre-training baselines. Our findings offer a new direction for the medical imaging community to effectively utilize the wealth of available data for improved segmentation performance. The code and model weights will be published here: [tba]

Unified Medical Image Segmentation (UMIS) is critical for comprehensive anatomical assessment but faces challenges due to multi-scale structural heterogeneity. Conventional pixel-based approaches, lacking object-level anatomical insight and inter-organ relational modeling, struggle with morphological complexity and feature conflicts, limiting their efficacy in UMIS. We propose Mamba Snake, a novel deep snake framework enhanced by state space modeling for UMIS. Mamba Snake frames multi-contour evolution as a hierarchical state space atlas, effectively modeling macroscopic inter-organ topological relationships and microscopic contour refinements. We introduce a snake-specific vision state space module, the Mamba Evolution Block (MEB), which leverages effective spatiotemporal information aggregation for adaptive refinement of complex morphologies. Energy map shape priors further ensure robust long-range contour evolution in heterogeneous data. Additionally, a dual-classification synergy mechanism is incorporated to concurrently optimize detection and segmentation, mitigating under-segmentation of microstructures in UMIS. Extensive evaluations across five clinical datasets reveal Mamba Snake's superior performance, with an average Dice improvement of 3\% over state-of-the-art methods.

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 several surgical instrument segmentation 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. Code is available at https://github.com/franciszzj/TP-SIS.

Efficiently capturing multi-scale information and building long-range dependencies among pixels are essential for medical image segmentation because of the various sizes and shapes of the lesion regions or organs. In this paper, we present Multi-scale Cross-axis Attention (MCA) to solve the above challenging issues based on the efficient axial attention. Instead of simply connecting axial attention along the horizontal and vertical directions sequentially, we propose to calculate dual cross attentions between two parallel axial attentions to capture global information better. To process the significant variations of lesion regions or organs in individual sizes and shapes, we also use multiple convolutions of strip-shape kernels with different kernel sizes in each axial attention path to improve the efficiency of the proposed MCA in encoding spatial information. We build the proposed MCA upon the MSCAN backbone, yielding our network, termed MCANet. Our MCANet with only 4M+ parameters performs even better than most previous works with heavy backbones (e.g., Swin Transformer) on four challenging tasks, including skin lesion segmentation, nuclei segmentation, abdominal multi-organ segmentation, and polyp segmentation. Code is available at https://github.com/haoshao-nku/medical_seg.

Precise lesion resection depends on accurately identifying fine-grained anatomical structures. While many coarse-grained segmentation (CGS) methods have been successful in large-scale segmentation (e.g., organs), they fall short in clinical scenarios requiring fine-grained segmentation (FGS), which remains challenging due to frequent individual variations in small-scale anatomical structures. Although recent Mamba-based models have advanced medical image segmentation, they often rely on fixed manually-defined scanning orders, which limit their adaptability to individual variations in FGS. To address this, we propose ASM-UNet, a novel Mamba-based architecture for FGS. It introduces adaptive scan scores to dynamically guide the scanning order, generated by combining group-level commonalities and individual-level variations. Experiments on two public datasets (ACDC and Synapse) and a newly proposed challenging biliary tract FGS dataset, namely BTMS, demonstrate that ASM-UNet achieves superior performance in both CGS and FGS tasks. Our code and dataset are available at https://github.com/YqunYang/ASM-UNet.

Surgical instrument segmentation under Federated Learning (FL) is a promising direction, which enables multiple surgical sites to collaboratively train the model without centralizing datasets. However, there exist very limited FL works in surgical data science, and FL methods for other modalities do not consider inherent characteristics in surgical domain: i) different scenarios show diverse anatomical backgrounds while highly similar instrument representation; ii) there exist surgical simulators which promote large-scale synthetic data generation with minimal efforts. In this paper, we propose a novel Personalized FL scheme, Spatio-Temporal Representation Decoupling and Enhancement (FedST), which wisely leverages surgical domain knowledge during both local-site and global-server training to boost segmentation. Concretely, our model embraces a Representation Separation and Cooperation (RSC) mechanism in local-site training, which decouples the query embedding layer to be trained privately, to encode respective backgrounds. Meanwhile, other parameters are optimized globally to capture the consistent representations of instruments, including the temporal layer to capture similar motion patterns. A textual-guided channel selection is further designed to highlight site-specific features, facilitating model adapta tion to each site. Moreover, in global-server training, we propose Synthesis-based Explicit Representation Quantification (SERQ), which defines an explicit representation target based on synthetic data to synchronize the model convergence during fusion for improving model generalization.

Self-supervised learning (SSL) has recently achieved promising performance for 3D medical image analysis tasks. Most current methods follow existing SSL paradigm originally designed for photographic or natural images, which cannot explicitly and thoroughly exploit the intrinsic similar anatomical structures across varying medical images. This may in fact degrade the quality of learned deep representations by maximizing the similarity among features containing spatial misalignment information and different anatomical semantics. In this work, we propose a new self-supervised learning framework, namely Alice, that explicitly fulfills Anatomical invariance modeling and semantic alignment via elaborately combining discriminative and generative objectives. Alice introduces a new contrastive learning strategy which encourages the similarity between views that are diversely mined but with consistent high-level semantics, in order to learn invariant anatomical features. Moreover, we design a conditional anatomical feature alignment module to complement corrupted embeddings with globally matched semantics and inter-patch topology information, conditioned by the distribution of local image content, which permits to create better contrastive pairs. Our extensive quantitative experiments on three 3D medical image analysis tasks demonstrate and validate the performance superiority of Alice, surpassing the previous best SSL counterpart methods and showing promising ability for united representation learning. Codes are available at https://github.com/alibaba-damo-academy/alice.

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

Accurate semantic segmentation for histopathology image is crucial for quantitative tissue analysis and downstream clinical modeling. Recent segmentation foundation models have improved generalization through large-scale pretraining, yet remain poorly aligned with pathology because they treat segmentation as a static visual prediction task. Here we present VISTA-PATH, an interactive, class-aware pathology segmentation foundation model designed to resolve heterogeneous structures, incorporate expert feedback, and produce pixel-level segmentation that are directly meaningful for clinical interpretation. VISTA-PATH jointly conditions segmentation on visual context, semantic tissue descriptions, and optional expert-provided spatial prompts, enabling precise multi-class segmentation across heterogeneous pathology images. To support this paradigm, we curate VISTA-PATH Data, a large-scale pathology segmentation corpus comprising over 1.6 million image-mask-text triplets spanning 9 organs and 93 tissue classes. Across extensive held-out and external benchmarks, VISTA-PATH consistently outperforms existing segmentation foundation models. Importantly, VISTA-PATH supports dynamic human-in-the-loop refinement by propagating sparse, patch-level bounding-box annotation feedback into whole-slide segmentation. Finally, we show that the high-fidelity, class-aware segmentation produced by VISTA-PATH is a preferred model for computational pathology. It improve tissue microenvironment analysis through proposed Tumor Interaction Score (TIS), which exhibits strong and significant associations with patient survival. Together, these results establish VISTA-PATH as a foundation model that elevates pathology image segmentation from a static prediction to an interactive and clinically grounded representation for digital pathology. Source code and demo can be found at https://github.com/zhihuanglab/VISTA-PATH.

The emerging area of computational pathology (CPath) is ripe ground for the application of deep learning (DL) methods to healthcare due to the sheer volume of raw pixel data in whole-slide images (WSIs) of cancerous tissue slides. However, it is imperative for the DL algorithms relying on nuclei-level details to be able to cope with data from `the clinical wild', which tends to be quite challenging. We study, and extend recently released PanNuke dataset consisting of ~200,000 nuclei categorized into 5 clinically important classes for the challenging tasks of segmenting and classifying nuclei in WSIs. Previous pan-cancer datasets consisted of only up to 9 different tissues and up to 21,000 unlabeled nuclei and just over 24,000 labeled nuclei with segmentation masks. PanNuke consists of 19 different tissue types that have been semi-automatically annotated and quality controlled by clinical pathologists, leading to a dataset with statistics similar to the clinical wild and with minimal selection bias. We study the performance of segmentation and classification models when applied to the proposed dataset and demonstrate the application of models trained on PanNuke to whole-slide images. We provide comprehensive statistics about the dataset and outline recommendations and research directions to address the limitations of existing DL tools when applied to real-world CPath applications.

Learning visual representations is foundational for a broad spectrum of downstream tasks. Although recent vision-language contrastive models, such as CLIP and SigLIP, have achieved impressive zero-shot performance via large-scale vision-language alignment, their reliance on global representations constrains their effectiveness for dense prediction tasks, such as grounding, OCR, and segmentation. To address this gap, we introduce Region-Aware Cluster Discrimination (RICE), a novel method that enhances region-level visual and OCR capabilities. We first construct a billion-scale candidate region dataset and propose a Region Transformer layer to extract rich regional semantics. We further design a unified region cluster discrimination loss that jointly supports object and OCR learning within a single classification framework, enabling efficient and scalable distributed training on large-scale data. Extensive experiments show that RICE consistently outperforms previous methods on tasks, including segmentation, dense detection, and visual perception for Multimodal Large Language Models (MLLMs). The pre-trained models have been released at https://github.com/deepglint/MVT.

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation.

With the growing volume of CT examinations, there is an increasing demand for automated tools such as organ segmentation, abnormality detection, and report generation to support radiologists in managing their clinical workload. Multi-label classification of 3D Chest CT scans remains a critical yet challenging problem due to the complex spatial relationships inherent in volumetric data and the wide variability of abnormalities. Existing methods based on 3D convolutional neural networks struggle to capture long-range dependencies, while Vision Transformers often require extensive pre-training on large-scale, domain-specific datasets to perform competitively. In this work of academic research, we propose a 2.5D alternative by introducing a new graph-based framework that represents 3D CT volumes as structured graphs, where axial slice triplets serve as nodes processed through spectral graph convolution, enabling the model to reason over inter-slice dependencies while maintaining complexity compatible with clinical deployment. Our method, trained and evaluated on 3 datasets from independent institutions, achieves strong cross-dataset generalization, and shows competitive performance compared to state-of-the-art visual encoders. We further conduct comprehensive ablation studies to evaluate the impact of various aggregation strategies, edge-weighting schemes, and graph connectivity patterns. Additionally, we demonstrate the broader applicability of our approach through transfer experiments on automated radiology report generation and abdominal CT data.

Segmentation of anatomical structures and pathological regions in medical images is essential for modern clinical diagnosis, disease research, and treatment planning. While significant advancements have been made in deep learning-based segmentation techniques, many of these methods still suffer from limitations in data efficiency, generalizability, and interactivity. As a result, developing precise segmentation methods that require fewer labeled datasets remains a critical challenge in medical image analysis. Recently, the introduction of foundation models like CLIP and Segment-Anything-Model (SAM), with robust cross-domain representations, has paved the way for interactive and universal image segmentation. However, further exploration of these models for data-efficient segmentation in medical imaging is still needed and highly relevant. In this paper, we introduce MedCLIP-SAMv2, a novel framework that integrates the CLIP and SAM models to perform segmentation on clinical scans using text prompts, in both zero-shot and weakly supervised settings. Our approach includes fine-tuning the BiomedCLIP model with a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss, and leveraging the Multi-modal Information Bottleneck (M2IB) to create visual prompts for generating segmentation masks from SAM in the zero-shot setting. We also investigate using zero-shot segmentation labels within a weakly supervised paradigm to enhance segmentation quality further. Extensive testing across four diverse segmentation tasks and medical imaging modalities (breast tumor ultrasound, brain tumor MRI, lung X-ray, and lung CT) demonstrates the high accuracy of our proposed framework. Our code is available at https://github.com/HealthX-Lab/MedCLIP-SAMv2.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

Vision foundation models (FMs) are accelerating the development of digital pathology algorithms and transforming biomedical research. These models learn, in a self-supervised manner, to represent histological features in highly heterogeneous tiles extracted from whole-slide images (WSIs) of real-world patient samples. The performance of these FMs is significantly influenced by the size, diversity, and balance of the pre-training data. However, data selection has been primarily guided by expert knowledge at the WSI level, focusing on factors such as disease classification and tissue types, while largely overlooking the granular details available at the tile level. In this paper, we investigate the potential of unsupervised automatic data curation at the tile-level, taking into account 350 million tiles. Specifically, we apply hierarchical clustering trees to pre-extracted tile embeddings, allowing us to sample balanced datasets uniformly across the embedding space of the pretrained FM. We further identify these datasets are subject to a trade-off between size and balance, potentially compromising the quality of representations learned by FMs, and propose tailored batch sampling strategies to mitigate this effect. We demonstrate the effectiveness of our method through improved performance on a diverse range of clinically relevant downstream tasks.

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.

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.

Humans can develop internal world models that encode common sense knowledge, telling them how the world works and predicting the consequences of their actions. This concept has emerged as a promising direction for establishing general-purpose machine-learning models in recent preliminary works, e.g., for visual representation learning. In this paper, we present CheXWorld, the first effort towards a self-supervised world model for radiographic images. Specifically, our work develops a unified framework that simultaneously models three aspects of medical knowledge essential for qualified radiologists, including 1) local anatomical structures describing the fine-grained characteristics of local tissues (e.g., architectures, shapes, and textures); 2) global anatomical layouts describing the global organization of the human body (e.g., layouts of organs and skeletons); and 3) domain variations that encourage CheXWorld to model the transitions across different appearance domains of radiographs (e.g., varying clarity, contrast, and exposure caused by collecting radiographs from different hospitals, devices, or patients). Empirically, we design tailored qualitative and quantitative analyses, revealing that CheXWorld successfully captures these three dimensions of medical knowledge. Furthermore, transfer learning experiments across eight medical image classification and segmentation benchmarks showcase that CheXWorld significantly outperforms existing SSL methods and large-scale medical foundation models. Code & pre-trained models are available at https://github.com/LeapLabTHU/CheXWorld.

Semi-supervised learning relaxes the need of large pixel-wise labeled datasets for image segmentation by leveraging unlabeled data. A prominent way to exploit unlabeled data is to regularize model predictions. Since the predictions of unlabeled data can be unreliable, uncertainty-aware schemes are typically employed to gradually learn from meaningful and reliable predictions. Uncertainty estimation methods, however, rely on multiple inferences from the model predictions that must be computed for each training step, which is computationally expensive. Moreover, these uncertainty maps capture pixel-wise disparities and do not consider global information. This work proposes a novel method to estimate segmentation uncertainty by leveraging global information from the segmentation masks. More precisely, an anatomically-aware representation is first learnt to model the available segmentation masks. The learnt representation thereupon maps the prediction of a new segmentation into an anatomically-plausible segmentation. The deviation from the plausible segmentation aids in estimating the underlying pixel-level uncertainty in order to further guide the segmentation network. The proposed method consequently estimates the uncertainty using a single inference from our representation, thereby reducing the total computation. We evaluate our method on two publicly available segmentation datasets of left atria in cardiac MRIs and of multiple organs in abdominal CTs. Our anatomically-aware method improves the segmentation accuracy over the state-of-the-art semi-supervised methods in terms of two commonly used evaluation metrics.

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.

The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

In this paper, we present a practical approach to improve anatomical shape accuracy in whole-body medical segmentation. Our analysis shows that a shape-focused toolkit can enhance segmentation performance by over 8%, without the need for model re-training or fine-tuning. In comparison, modifications to model architecture typically lead to marginal gains of less than 3%. Motivated by this observation, we introduce ShapeKit, a flexible and easy-to-integrate toolkit designed to refine anatomical shapes. This work highlights the underappreciated value of shape-based tools and calls attention to their potential impact within the medical segmentation community.

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.

Self-supervised learning (SSL) approaches have recently shown substantial success in learning visual representations from unannotated images. Compared with photographic images, medical images acquired with the same imaging protocol exhibit high consistency in anatomy. To exploit this anatomical consistency, this paper introduces a novel SSL approach, called PEAC (patch embedding of anatomical consistency), for medical image analysis. Specifically, in this paper, we propose to learn global and local consistencies via stable grid-based matching, transfer pre-trained PEAC models to diverse downstream tasks, and extensively demonstrate that (1) PEAC achieves significantly better performance than the existing state-of-the-art fully/self-supervised methods, and (2) PEAC captures the anatomical structure consistency across views of the same patient and across patients of different genders, weights, and healthy statuses, which enhances the interpretability of our method for medical image analysis.

Medical image segmentation faces challenges due to variations in anatomical structures. While convolutional neural networks (CNNs) effectively capture local features, they struggle with modeling long-range dependencies. Transformers mitigate this issue with self-attention mechanisms but lack the ability to preserve local contextual information. State-of-the-art models primarily follow an encoder-decoder architecture, achieving notable success. However, two key limitations remain: (1) Shallow layers, which are closer to the input, capture fine-grained details but suffer from information loss as data propagates through deeper layers. (2) Inefficient integration of local details and global context between the encoder and decoder stages. To address these challenges, we propose the MACMD-based decoder, which enhances attention mechanisms and facilitates channel mixing between encoder and decoder stages via skip connections. This design leverages hierarchical dilated convolutions, attention-driven modulation, and a cross channel-mixing module to capture long-range dependencies while preserving local contextual details, essential for precise medical image segmentation. We evaluated our approach using multiple transformer encoders on both binary and multi-organ segmentation tasks. The results demonstrate that our method outperforms state-of-the-art approaches in terms of Dice score and computational efficiency, highlighting its effectiveness in achieving accurate and robust segmentation performance. The code available at https://github.com/lalitmaurya47/MACMD

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/.

The Segment Anything Model (SAM) has garnered significant attention for its versatile segmentation abilities and intuitive prompt-based interface. However, its application in medical imaging presents challenges, requiring either substantial training costs and extensive medical datasets for full model fine-tuning or high-quality prompts for optimal performance. This paper introduces H-SAM: a prompt-free adaptation of SAM tailored for efficient fine-tuning of medical images via a two-stage hierarchical decoding procedure. In the initial stage, H-SAM employs SAM's original decoder to generate a prior probabilistic mask, guiding a more intricate decoding process in the second stage. Specifically, we propose two key designs: 1) A class-balanced, mask-guided self-attention mechanism addressing the unbalanced label distribution, enhancing image embedding; 2) A learnable mask cross-attention mechanism spatially modulating the interplay among different image regions based on the prior mask. Moreover, the inclusion of a hierarchical pixel decoder in H-SAM enhances its proficiency in capturing fine-grained and localized details. This approach enables SAM to effectively integrate learned medical priors, facilitating enhanced adaptation for medical image segmentation with limited samples. Our H-SAM demonstrates a 4.78% improvement in average Dice compared to existing prompt-free SAM variants for multi-organ segmentation using only 10% of 2D slices. Notably, without using any unlabeled data, H-SAM even outperforms state-of-the-art semi-supervised models relying on extensive unlabeled training data across various medical datasets. Our code is available at https://github.com/Cccccczh404/H-SAM.

We create a framework for bootstrapping visual representation learning from a primitive visual grouping capability. We operationalize grouping via a contour detector that partitions an image into regions, followed by merging of those regions into a tree hierarchy. A small supervised dataset suffices for training this grouping primitive. Across a large unlabeled dataset, we apply this learned primitive to automatically predict hierarchical region structure. These predictions serve as guidance for self-supervised contrastive feature learning: we task a deep network with producing per-pixel embeddings whose pairwise distances respect the region hierarchy. Experiments demonstrate that our approach can serve as state-of-the-art generic pre-training, benefiting downstream tasks. We additionally explore applications to semantic region search and video-based object instance tracking.

Large medical imaging datasets can be cheaply and quickly annotated with low-confidence, weak labels (e.g., radiological scores). Access to high-confidence labels, such as histology-based diagnoses, is rare and costly. Pretraining strategies, like contrastive learning (CL) methods, can leverage unlabeled or weakly-annotated datasets. These methods typically require large batch sizes, which poses a difficulty in the case of large 3D images at full resolution, due to limited GPU memory. Nevertheless, volumetric positional information about the spatial context of each 2D slice can be very important for some medical applications. In this work, we propose an efficient weakly-supervised positional (WSP) contrastive learning strategy where we integrate both the spatial context of each 2D slice and a weak label via a generic kernel-based loss function. We illustrate our method on cirrhosis prediction using a large volume of weakly-labeled images, namely radiological low-confidence annotations, and small strongly-labeled (i.e., high-confidence) datasets. The proposed model improves the classification AUC by 5% with respect to a baseline model on our internal dataset, and by 26% on the public LIHC dataset from the Cancer Genome Atlas. The code is available at: https://github.com/Guerbet-AI/wsp-contrastive.

Due to the inherent flexibility of prompting, foundation models have emerged as the predominant force in the fields of natural language processing and computer vision. The recent introduction of the Segment Anything Model (SAM) signifies a noteworthy expansion of the prompt-driven paradigm into the domain of image segmentation, thereby introducing a plethora of previously unexplored capabilities. However, the viability of its application to medical image segmentation remains uncertain, given the substantial distinctions between natural and medical images. In this work, we provide a comprehensive overview of recent endeavors aimed at extending the efficacy of SAM to medical image segmentation tasks, encompassing both empirical benchmarking and methodological adaptations. Additionally, we explore potential avenues for future research directions in SAM's role within medical image segmentation. While direct application of SAM to medical image segmentation does not yield satisfactory performance on multi-modal and multi-target medical datasets so far, numerous insights gleaned from these efforts serve as valuable guidance for shaping the trajectory of foundational models in the realm of medical image analysis. To support ongoing research endeavors, we maintain an active repository that contains an up-to-date paper list and a succinct summary of open-source projects at https://github.com/YichiZhang98/SAM4MIS.

Purpose: This study investigated how nodule segmentation and surrounding peritumoral regions influence radionics-based lung cancer classification. Methods: Using 3D CT scans with bounding box annotated nodules, we generated 3D segmentations using four techniques: Otsu, Fuzzy C-Means (FCM), Gaussian Mixture Model (GMM), and K-Nearest Neighbors (KNN). Radiomics features were extracted using the PyRadiomics library, and multiple machine-learning-based classifiers, including Random Forest, Logistic Regression, and KNN, were employed to classify nodules as cancerous or non-cancerous. The best-performing segmentation and model were further analyzed by expanding the initial nodule segmentation into the peritumoral region (2, 4, 6, 8, 10, and 12 mm) to understand the influence of the surrounding area on classification. Additionally, we compared our results to deep learning-based feature extractors Foundation Model for Cancer Biomarkers (FMCB) and other state-of-the-art baseline models. Results: Incorporating peritumoral regions significantly enhanced performance, with the best result obtained at 8 mm expansion (AUC = 0.78). Compared to image-based deep learning models, such as FMCB (AUC = 0.71) and ResNet50-SWS++ (AUC = 0.71), our radiomics-based approach demonstrated superior classification accuracy. Conclusion: The study highlights the importance of peritumoral expansion in improving lung cancer classification using radiomics. These findings can inform the development of more robust AI-driven diagnostic tools.

Nuclear segmentation, classification and quantification within Haematoxylin & Eosin stained histology images enables the extraction of interpretable cell-based features that can be used in downstream explainable models in computational pathology (CPath). However, automatic recognition of different nuclei is faced with a major challenge in that there are several different types of nuclei, some of them exhibiting large intraclass variability. In this work, we propose an approach that combine Separable-HoverNet and Instance-YOLOv5 to indentify colon nuclei small and unbalanced. Our approach can achieve mPQ+ 0.389 on the Segmentation and Classification-Preliminary Test Dataset and r2 0.599 on the Cellular Composition-Preliminary Test Dataset on ISBI 2022 CoNIC Challenge.

Medical image segmentation using deep learning (DL) has enabled the development of automated analysis pipelines for large-scale population studies. However, state-of-the-art DL methods are prone to hallucinations, which can result in anatomically implausible segmentations. With manual correction impractical at scale, automated quality control (QC) techniques have to address the challenge. While promising, existing QC methods are organ-specific, limiting their generalizability and usability beyond their original intended task. To overcome this limitation, we propose no-new Quality Control (nnQC), a robust QC framework based on a diffusion-generative paradigm that self-adapts to any input organ dataset. Central to nnQC is a novel Team of Experts (ToE) architecture, where two specialized experts independently encode 3D spatial awareness, represented by the relative spatial position of an axial slice, and anatomical information derived from visual features from the original image. A weighted conditional module dynamically combines the pair of independent embeddings, or opinions to condition the sampling mechanism within a diffusion process, enabling the generation of a spatially aware pseudo-ground truth for predicting QC scores. Within its framework, nnQC integrates fingerprint adaptation to ensure adaptability across organs, datasets, and imaging modalities. We evaluated nnQC on seven organs using twelve publicly available datasets. Our results demonstrate that nnQC consistently outperforms state-of-the-art methods across all experiments, including cases where segmentation masks are highly degraded or completely missing, confirming its versatility and effectiveness across different organs.

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.

Fully convolutional neural networks (F-CNNs) have set the state-of-the-art in image segmentation for a plethora of applications. Architectural innovations within F-CNNs have mainly focused on improving spatial encoding or network connectivity to aid gradient flow. In this paper, we explore an alternate direction of recalibrating the feature maps adaptively, to boost meaningful features, while suppressing weak ones. We draw inspiration from the recently proposed squeeze & excitation (SE) module for channel recalibration of feature maps for image classification. Towards this end, we introduce three variants of SE modules for image segmentation, (i) squeezing spatially and exciting channel-wise (cSE), (ii) squeezing channel-wise and exciting spatially (sSE) and (iii) concurrent spatial and channel squeeze & excitation (scSE). We effectively incorporate these SE modules within three different state-of-the-art F-CNNs (DenseNet, SD-Net, U-Net) and observe consistent improvement of performance across all architectures, while minimally effecting model complexity. Evaluations are performed on two challenging applications: whole brain segmentation on MRI scans (Multi-Atlas Labelling Challenge Dataset) and organ segmentation on whole body contrast enhanced CT scans (Visceral Dataset).

Segmenting and recognizing diverse object parts is crucial in computer vision and robotics. Despite significant progress in object segmentation, part-level segmentation remains underexplored due to complex boundaries and scarce annotated data. To address this, we propose a novel Weakly-supervised Part Segmentation (WPS) setting and an approach called WPS-SAM, built on the large-scale pre-trained vision foundation model, Segment Anything Model (SAM). WPS-SAM is an end-to-end framework designed to extract prompt tokens directly from images and perform pixel-level segmentation of part regions. During its training phase, it only uses weakly supervised labels in the form of bounding boxes or points. Extensive experiments demonstrate that, through exploiting the rich knowledge embedded in pre-trained foundation models, WPS-SAM outperforms other segmentation models trained with pixel-level strong annotations. Specifically, WPS-SAM achieves 68.93% mIOU and 79.53% mACC on the PartImageNet dataset, surpassing state-of-the-art fully supervised methods by approximately 4% in terms of mIOU.

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.