Daily Papers

Few-shot semantic segmentation (FSS) methods have shown great promise in handling data-scarce scenarios, particularly in medical image segmentation tasks. However, most existing FSS architectures lack sufficient interpretability and fail to fully incorporate the underlying physical structures of semantic regions. To address these issues, in this paper, we propose a novel deep unfolding network, called the Learned Mumford-Shah Network (LMS-Net), for the FSS task. Specifically, motivated by the effectiveness of pixel-to-prototype comparison in prototypical FSS methods and the capability of deep priors to model complex spatial structures, we leverage our learned Mumford-Shah model (LMS model) as a mathematical foundation to integrate these insights into a unified framework. By reformulating the LMS model into prototype update and mask update tasks, we propose an alternating optimization algorithm to solve it efficiently. Further, the iterative steps of this algorithm are unfolded into corresponding network modules, resulting in LMS-Net with clear interpretability. Comprehensive experiments on three publicly available medical segmentation datasets verify the effectiveness of our method, demonstrating superior accuracy and robustness in handling complex structures and adapting to challenging segmentation scenarios. These results highlight the potential of LMS-Net to advance FSS in medical imaging applications. Our code will be available at: https://github.com/SDZhang01/LMSNet

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

Large-scale models pre-trained on large-scale datasets have profoundly advanced the development of deep learning. However, the state-of-the-art models for medical image segmentation are still small-scale, with their parameters only in the tens of millions. Further scaling them up to higher orders of magnitude is rarely explored. An overarching goal of exploring large-scale models is to train them on large-scale medical segmentation datasets for better transfer capacities. In this work, we design a series of Scalable and Transferable U-Net (STU-Net) models, with parameter sizes ranging from 14 million to 1.4 billion. Notably, the 1.4B STU-Net is the largest medical image segmentation model to date. Our STU-Net is based on nnU-Net framework due to its popularity and impressive performance. We first refine the default convolutional blocks in nnU-Net to make them scalable. Then, we empirically evaluate different scaling combinations of network depth and width, discovering that it is optimal to scale model depth and width together. We train our scalable STU-Net models on a large-scale TotalSegmentator dataset and find that increasing model size brings a stronger performance gain. This observation reveals that a large model is promising in medical image segmentation. Furthermore, we evaluate the transferability of our model on 14 downstream datasets for direct inference and 3 datasets for further fine-tuning, covering various modalities and segmentation targets. We observe good performance of our pre-trained model in both direct inference and fine-tuning. The code and pre-trained models are available at https://github.com/Ziyan-Huang/STU-Net.

Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, and quantitative and qualitative results. Our code is publicly available at: https://github.com/amirhossein-kz/HiFormer

U-shaped networks and its variants have demonstrated exceptional results for medical image segmentation. In this paper, we propose a novel dual self-distillation (DSD) framework in U-shaped networks for volumetric medical image segmentation. DSD distills knowledge from the ground-truth segmentation labels to the decoder layers. Additionally, DSD also distills knowledge from the deepest decoder and encoder layer to the shallower decoder and encoder layers respectively of a single U-shaped network. DSD is a general training strategy that could be attached to the backbone architecture of any U-shaped network to further improve its segmentation performance. We attached DSD on several state-of-the-art U-shaped backbones, and extensive experiments on various public 3D medical image segmentation datasets (cardiac substructure, brain tumor and Hippocampus) demonstrated significant improvement over the same backbones without DSD. On average, after attaching DSD to the U-shaped backbones, we observed an increase of 2.82\%, 4.53\% and 1.3\% in Dice similarity score, a decrease of 7.15 mm, 6.48 mm and 0.76 mm in the Hausdorff distance, for cardiac substructure, brain tumor and Hippocampus segmentation, respectively. These improvements were achieved with negligible increase in the number of trainable parameters and training time. Our proposed DSD framework also led to significant qualitative improvements for cardiac substructure, brain tumor and Hippocampus segmentation over the U-shaped backbones. The source code is publicly available at https://github.com/soumbane/DualSelfDistillation.

Diffusion models have been used extensively for high quality image and video generation tasks. In this paper, we propose a novel conditional diffusion model with spatial attention and latent embedding (cDAL) for medical image segmentation. In cDAL, a convolutional neural network (CNN) based discriminator is used at every time-step of the diffusion process to distinguish between the generated labels and the real ones. A spatial attention map is computed based on the features learned by the discriminator to help cDAL generate more accurate segmentation of discriminative regions in an input image. Additionally, we incorporated a random latent embedding into each layer of our model to significantly reduce the number of training and sampling time-steps, thereby making it much faster than other diffusion models for image segmentation. We applied cDAL on 3 publicly available medical image segmentation datasets (MoNuSeg, Chest X-ray and Hippocampus) and observed significant qualitative and quantitative improvements with higher Dice scores and mIoU over the state-of-the-art algorithms. The source code is publicly available at https://github.com/Hejrati/cDAL/.

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.

Self-Supervised Learning (SSL) presents an exciting opportunity to unlock the potential of vast, untapped clinical datasets, for various downstream applications that suffer from the scarcity of labeled data. While SSL has revolutionized fields like natural language processing and computer vision, its adoption in 3D medical image computing has been limited by three key pitfalls: Small pre-training dataset sizes, architectures inadequate for 3D medical image analysis, and insufficient evaluation practices. In this paper, we address these issues by i) leveraging a large-scale dataset of 39k 3D brain MRI volumes and ii) using a Residual Encoder U-Net architecture within the state-of-the-art nnU-Net framework. iii) A robust development framework, incorporating 5 development and 8 testing brain MRI segmentation datasets, allowed performance-driven design decisions to optimize the simple concept of Masked Auto Encoders (MAEs) for 3D CNNs. The resulting model not only surpasses previous SSL methods but also outperforms the strong nnU-Net baseline by an average of approximately 3 Dice points setting a new state-of-the-art. Our code and models are made available here.

Recent advances in deep learning-based medical image segmentation studies achieve nearly human-level performance in fully supervised manner. However, acquiring pixel-level expert annotations is extremely expensive and laborious in medical imaging fields. Unsupervised domain adaptation (UDA) can alleviate this problem, which makes it possible to use annotated data in one imaging modality to train a network that can successfully perform segmentation on target imaging modality with no labels. In this work, we propose SDC-UDA, a simple yet effective volumetric UDA framework for slice-direction continuous cross-modality medical image segmentation which combines intra- and inter-slice self-attentive image translation, uncertainty-constrained pseudo-label refinement, and volumetric self-training. Our method is distinguished from previous methods on UDA for medical image segmentation in that it can obtain continuous segmentation in the slice direction, thereby ensuring higher accuracy and potential in clinical practice. We validate SDC-UDA with multiple publicly available cross-modality medical image segmentation datasets and achieve state-of-the-art segmentation performance, not to mention the superior slice-direction continuity of prediction compared to previous studies.

Foundation models pre-trained on large-scale natural image datasets offer a powerful paradigm for medical image segmentation. However, effectively transferring their learned representations for precise clinical applications remains a challenge. In this work, we propose Dino U-Net, a novel encoder-decoder architecture designed to exploit the high-fidelity dense features of the DINOv3 vision foundation model. Our architecture introduces an encoder built upon a frozen DINOv3 backbone, which employs a specialized adapter to fuse the model's rich semantic features with low-level spatial details. To preserve the quality of these representations during dimensionality reduction, we design a new fidelity-aware projection module (FAPM) that effectively refines and projects the features for the decoder. We conducted extensive experiments on seven diverse public medical image segmentation datasets. Our results show that Dino U-Net achieves state-of-the-art performance, consistently outperforming previous methods across various imaging modalities. Our framework proves to be highly scalable, with segmentation accuracy consistently improving as the backbone model size increases up to the 7-billion-parameter variant. The findings demonstrate that leveraging the superior, dense-pretrained features from a general-purpose foundation model provides a highly effective and parameter-efficient approach to advance the accuracy of medical image segmentation. The code is available at https://github.com/yifangao112/DinoUNet.

In semi-supervised medical image segmentation, there exist empirical mismatch problems between labeled and unlabeled data distribution. The knowledge learned from the labeled data may be largely discarded if treating labeled and unlabeled data separately or in an inconsistent manner. We propose a straightforward method for alleviating the problem - copy-pasting labeled and unlabeled data bidirectionally, in a simple Mean Teacher architecture. The method encourages unlabeled data to learn comprehensive common semantics from the labeled data in both inward and outward directions. More importantly, the consistent learning procedure for labeled and unlabeled data can largely reduce the empirical distribution gap. In detail, we copy-paste a random crop from a labeled image (foreground) onto an unlabeled image (background) and an unlabeled image (foreground) onto a labeled image (background), respectively. The two mixed images are fed into a Student network and supervised by the mixed supervisory signals of pseudo-labels and ground-truth. We reveal that the simple mechanism of copy-pasting bidirectionally between labeled and unlabeled data is good enough and the experiments show solid gains (e.g., over 21% Dice improvement on ACDC dataset with 5% labeled data) compared with other state-of-the-arts on various semi-supervised medical image segmentation datasets. Code is available at https://github.com/DeepMed-Lab-ECNU/BCP}.

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

Collecting pixel-level labels for medical datasets can be a laborious and expensive process, and enhancing segmentation performance with a scarcity of labeled data is a crucial challenge. This work introduces AugPaint, a data augmentation framework that utilizes inpainting to generate image-label pairs from limited labeled data. AugPaint leverages latent diffusion models, known for their ability to generate high-quality in-domain images with low overhead, and adapts the sampling process for the inpainting task without need for retraining. Specifically, given a pair of image and label mask, we crop the area labeled with the foreground and condition on it during reversed denoising process for every noise level. Masked background area would gradually be filled in, and all generated images are paired with the label mask. This approach ensures the accuracy of match between synthetic images and label masks, setting it apart from existing dataset generation methods. The generated images serve as valuable supervision for training downstream segmentation models, effectively addressing the challenge of limited annotations. We conducted extensive evaluations of our data augmentation method on four public medical image segmentation datasets, including CT, MRI, and skin imaging. Results across all datasets demonstrate that AugPaint outperforms state-of-the-art label-efficient methodologies, significantly improving segmentation performance.

Medical image segmentation is a cornerstone of modern clinical diagnostics. While Vision Transformers that leverage shifted window-based self-attention have established new benchmarks in this field, they are often hampered by a critical limitation: their localized attention mechanism struggles to effectively fuse local details with global context. This deficiency is particularly detrimental to challenging tasks such as the segmentation of microtumors and miniature organs, where both fine-grained boundary definition and broad contextual understanding are paramount. To address this gap, we propose HBFormer, a novel Hybrid-Bridge Transformer architecture. The 'Hybrid' design of HBFormer synergizes a classic U-shaped encoder-decoder framework with a powerful Swin Transformer backbone for robust hierarchical feature extraction. The core innovation lies in its 'Bridge' mechanism, a sophisticated nexus for multi-scale feature integration. This bridge is architecturally embodied by our novel Multi-Scale Feature Fusion (MFF) decoder. Departing from conventional symmetric designs, the MFF decoder is engineered to fuse multi-scale features from the encoder with global contextual information. It achieves this through a synergistic combination of channel and spatial attention modules, which are constructed from a series of dilated and depth-wise convolutions. These components work in concert to create a powerful feature bridge that explicitly captures long-range dependencies and refines object boundaries with exceptional precision. Comprehensive experiments on challenging medical image segmentation datasets, including multi-organ, liver tumor, and bladder tumor benchmarks, demonstrate that HBFormer achieves state-of-the-art results, showcasing its outstanding capabilities in microtumor and miniature organ segmentation. Code and models are available at: https://github.com/lzeeorno/HBFormer.

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

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.

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

Fairness in artificial intelligence models has gained significantly more attention in recent years, especially in the area of medicine, as fairness in medical models is critical to people's well-being and lives. High-quality medical fairness datasets are needed to promote fairness learning research. Existing medical fairness datasets are all for classification tasks, and no fairness datasets are available for medical segmentation, while medical segmentation is an equally important clinical task as classifications, which can provide detailed spatial information on organ abnormalities ready to be assessed by clinicians. In this paper, we propose the first fairness dataset for medical segmentation named Harvard-FairSeg with 10,000 subject samples. In addition, we propose a fair error-bound scaling approach to reweight the loss function with the upper error-bound in each identity group, using the segment anything model (SAM). We anticipate that the segmentation performance equity can be improved by explicitly tackling the hard cases with high training errors in each identity group. To facilitate fair comparisons, we utilize a novel equity-scaled segmentation performance metric to compare segmentation metrics in the context of fairness, such as the equity-scaled Dice coefficient. Through comprehensive experiments, we demonstrate that our fair error-bound scaling approach either has superior or comparable fairness performance to the state-of-the-art fairness learning models. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-fairseg10k.

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.

Image translation across domains for unpaired datasets has gained interest and great improvement lately. In medical imaging, there are multiple imaging modalities, with very different characteristics. Our goal is to use cross-modality adaptation between CT and MRI whole cardiac scans for semantic segmentation. We present a segmentation network using synthesised cardiac volumes for extremely limited datasets. Our solution is based on a 3D cross-modality generative adversarial network to share information between modalities and generate synthesized data using unpaired datasets. Our network utilizes semantic segmentation to improve generator shape consistency, thus creating more realistic synthesised volumes to be used when re-training the segmentation network. We show that improved segmentation can be achieved on small datasets when using spatial augmentations to improve a generative adversarial network. These augmentations improve the generator capabilities, thus enhancing the performance of the Segmentor. Using only 16 CT and 16 MRI cardiovascular volumes, improved results are shown over other segmentation methods while using the suggested architecture.

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.

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.

The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-Net'), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.

Vision-Language Models (VLMs) have shown impressive performance in vision tasks, but adapting them to new domains often requires expensive fine-tuning. Prompt tuning techniques, including textual, visual, and multimodal prompting, offer efficient alternatives by leveraging learnable prompts. However, their application to Vision-Language Segmentation Models (VLSMs) and evaluation under significant domain shifts remain unexplored. This work presents an open-source benchmarking framework, TuneVLSeg, to integrate various unimodal and multimodal prompt tuning techniques into VLSMs, making prompt tuning usable for downstream segmentation datasets with any number of classes. TuneVLSeg includes 6 prompt tuning strategies on various prompt depths used in 2 VLSMs totaling of 8 different combinations. We test various prompt tuning on 8 diverse medical datasets, including 3 radiology datasets (breast tumor, echocardiograph, chest X-ray pathologies) and 5 non-radiology datasets (polyp, ulcer, skin cancer), and two natural domain segmentation datasets. Our study found that textual prompt tuning struggles under significant domain shifts, from natural-domain images to medical data. Furthermore, visual prompt tuning, with fewer hyperparameters than multimodal prompt tuning, often achieves performance competitive to multimodal approaches, making it a valuable first attempt. Our work advances the understanding and applicability of different prompt-tuning techniques for robust domain-specific segmentation. The source code is available at https://github.com/naamiinepal/tunevlseg.

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

Large, fine-grained image segmentation datasets, annotated at pixel-level, are difficult to obtain, particularly in medical imaging, where annotations also require expert knowledge. Weakly-supervised learning can train models by relying on weaker forms of annotation, such as scribbles. Here, we learn to segment using scribble annotations in an adversarial game. With unpaired segmentation masks, we train a multi-scale GAN to generate realistic segmentation masks at multiple resolutions, while we use scribbles to learn their correct position in the image. Central to the model's success is a novel attention gating mechanism, which we condition with adversarial signals to act as a shape prior, resulting in better object localization at multiple scales. Subject to adversarial conditioning, the segmentor learns attention maps that are semantic, suppress the noisy activations outside the objects, and reduce the vanishing gradient problem in the deeper layers of the segmentor. We evaluated our model on several medical (ACDC, LVSC, CHAOS) and non-medical (PPSS) datasets, and we report performance levels matching those achieved by models trained with fully annotated segmentation masks. We also demonstrate extensions in a variety of settings: semi-supervised learning; combining multiple scribble sources (a crowdsourcing scenario) and multi-task learning (combining scribble and mask supervision). We release expert-made scribble annotations for the ACDC dataset, and the code used for the experiments, at https://vios-s.github.io/multiscale-adversarial-attention-gates

Medical image segmentation methods downsample images for feature extraction and then upsample them to restore resolution for pixel-level predictions. In such a schema, upsample technique is vital in restoring information for better performance. However, existing upsample techniques leverage little information from downsampling paths. The local and detailed feature from the shallower layer such as boundary and tissue texture is particularly more important in medical segmentation compared with natural image segmentation. To this end, we propose a novel upsample approach for medical image segmentation, Window Attention Upsample (WAU), which upsamples features conditioned on local and detailed features from downsampling path in local windows by introducing attention decoders of Transformer. WAU could serve as a general upsample method and be incorporated into any segmentation model that possesses lateral connections. We first propose the Attention Upsample which consists of Attention Decoder (AD) and bilinear upsample. AD leverages pixel-level attention to model long-range dependency and global information for a better upsample. Bilinear upsample is introduced as the residual connection to complement the upsampled features. Moreover, considering the extensive memory and computation cost of pixel-level attention, we further design a window attention scheme to restrict attention computation in local windows instead of the global range. We evaluate our method (WAU) on classic U-Net structure with lateral connections and achieve state-of-the-art performance on Synapse multi-organ segmentation, Medical Segmentation Decathlon (MSD) Brain, and Automatic Cardiac Diagnosis Challenge (ACDC) datasets. We also validate the effectiveness of our method on multiple classic architectures and achieve consistent improvement.

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

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

In this paper, we present the VMSE U-Net and VM-Unet CBAM+ model, two cutting-edge deep learning architectures designed to enhance medical image segmentation. Our approach integrates Squeeze-and-Excitation (SE) and Convolutional Block Attention Module (CBAM) techniques into the traditional VM U-Net framework, significantly improving segmentation accuracy, feature localization, and computational efficiency. Both models show superior performance compared to the baseline VM-Unet across multiple datasets. Notably, VMSEUnet achieves the highest accuracy, IoU, precision, and recall while maintaining low loss values. It also exhibits exceptional computational efficiency with faster inference times and lower memory usage on both GPU and CPU. Overall, the study suggests that the enhanced architecture VMSE-Unet is a valuable tool for medical image analysis. These findings highlight its potential for real-world clinical applications, emphasizing the importance of further research to optimize accuracy, robustness, and computational efficiency.

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

The Segment Anything Model (SAM) has set a new standard in interactive image segmentation, offering robust performance across various tasks. However, its significant computational requirements limit its deployment in real-time or resource-constrained environments. To address these challenges, we propose a novel knowledge distillation approach, KD SAM, which incorporates both encoder and decoder optimization through a combination of Mean Squared Error (MSE) and Perceptual Loss. This dual-loss framework captures structural and semantic features, enabling the student model to maintain high segmentation accuracy while reducing computational complexity. Based on the model evaluation on datasets, including Kvasir-SEG, ISIC 2017, Fetal Head Ultrasound, and Breast Ultrasound, we demonstrate that KD SAM achieves comparable or superior performance to the baseline models, with significantly fewer parameters. KD SAM effectively balances segmentation accuracy and computational efficiency, making it well-suited for real-time medical image segmentation applications in resource-constrained environments.

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

Recent trends in semi-supervised learning have significantly boosted the performance of 3D semi-supervised medical image segmentation. Compared with 2D images, 3D medical volumes involve information from different directions, e.g., transverse, sagittal, and coronal planes, so as to naturally provide complementary views. These complementary views and the intrinsic similarity among adjacent 3D slices inspire us to develop a novel annotation way and its corresponding semi-supervised model for effective segmentation. Specifically, we firstly propose the orthogonal annotation by only labeling two orthogonal slices in a labeled volume, which significantly relieves the burden of annotation. Then, we perform registration to obtain the initial pseudo labels for sparsely labeled volumes. Subsequently, by introducing unlabeled volumes, we propose a dual-network paradigm named Dense-Sparse Co-training (DeSCO) that exploits dense pseudo labels in early stage and sparse labels in later stage and meanwhile forces consistent output of two networks. Experimental results on three benchmark datasets validated our effectiveness in performance and efficiency in annotation. For example, with only 10 annotated slices, our method reaches a Dice up to 86.93% on KiTS19 dataset.

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

How to ensure fairness is an important topic in federated learning (FL). Recent studies have investigated how to reward clients based on their contribution (collaboration fairness), and how to achieve uniformity of performance across clients (performance fairness). Despite achieving progress on either one, we argue that it is critical to consider them together, in order to engage and motivate more diverse clients joining FL to derive a high-quality global model. In this work, we propose a novel method to optimize both types of fairness simultaneously. Specifically, we propose to estimate client contribution in gradient and data space. In gradient space, we monitor the gradient direction differences of each client with respect to others. And in data space, we measure the prediction error on client data using an auxiliary model. Based on this contribution estimation, we propose a FL method, federated training via contribution estimation (FedCE), i.e., using estimation as global model aggregation weights. We have theoretically analyzed our method and empirically evaluated it on two real-world medical datasets. The effectiveness of our approach has been validated with significant performance improvements, better collaboration fairness, better performance fairness, and comprehensive analytical studies.

We introduce VoxTell, a vision-language model for text-prompted volumetric medical image segmentation. It maps free-form descriptions, from single words to full clinical sentences, to 3D masks. Trained on 62K+ CT, MRI, and PET volumes spanning over 1K anatomical and pathological classes, VoxTell uses multi-stage vision-language fusion across decoder layers to align textual and visual features at multiple scales. It achieves state-of-the-art zero-shot performance across modalities on unseen datasets, excelling on familiar concepts while generalizing to related unseen classes. Extensive experiments further demonstrate strong cross-modality transfer, robustness to linguistic variations and clinical language, as well as accurate instance-specific segmentation from real-world text. Code is available at: https://www.github.com/MIC-DKFZ/VoxTell

Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical image segmentation tasks. Moreover, SAM2's performance in medical image segmentation was limited by the domain shift issue, since it was originally trained on natural images and videos. To address these challenges, we proposed SAM2 with support-set guided prompting (SAM2-SGP), a framework that eliminated the need for manual prompts. The proposed model leveraged the memory mechanism of SAM2 to generate pseudo-masks using image-mask pairs from a support set via a Pseudo-mask Generation (PMG) module. We further introduced a novel Pseudo-mask Attention (PMA) module, which used these pseudo-masks to automatically generate bounding boxes and enhance localized feature extraction by guiding attention to relevant areas. Furthermore, a low-rank adaptation (LoRA) strategy was adopted to mitigate the domain shift issue. The proposed framework was evaluated on both 2D and 3D datasets across multiple medical imaging modalities, including fundus photography, X-ray, computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. The results demonstrated a significant performance improvement over state-of-the-art models, such as nnUNet and SwinUNet, as well as foundation models, such as SAM2 and MedSAM2, underscoring the effectiveness of the proposed approach. Our code is publicly available at https://github.com/astlian9/SAM_Support.

Addressing fairness in artificial intelligence (AI), particularly in medical AI, is crucial for ensuring equitable healthcare outcomes. Recent efforts to enhance fairness have introduced new methodologies and datasets in medical AI. However, the fairness issue under the setting of domain transfer is almost unexplored, while it is common that clinics rely on different imaging technologies (e.g., different retinal imaging modalities) for patient diagnosis. This paper presents FairDomain, a pioneering systemic study into algorithmic fairness under domain shifts, employing state-of-the-art domain adaptation (DA) and generalization (DG) algorithms for both medical segmentation and classification tasks to understand how biases are transferred between different domains. We also introduce a novel plug-and-play fair identity attention (FIA) module that adapts to various DA and DG algorithms to improve fairness by using self-attention to adjust feature importance based on demographic attributes. Additionally, we curate the first fairness-focused dataset with two paired imaging modalities for the same patient cohort on medical segmentation and classification tasks, to rigorously assess fairness in domain-shift scenarios. Excluding the confounding impact of demographic distribution variation between source and target domains will allow clearer quantification of the performance of domain transfer models. Our extensive evaluations reveal that the proposed FIA significantly enhances both model performance accounted for fairness across all domain shift settings (i.e., DA and DG) with respect to different demographics, which outperforms existing methods on both segmentation and classification. The code and data can be accessed at https://ophai.hms.harvard.edu/datasets/harvard-fairdomain20k.

The adoption of Vision Transformers (ViTs) based architectures represents a significant advancement in 3D Medical Image (MI) segmentation, surpassing traditional Convolutional Neural Network (CNN) models by enhancing global contextual understanding. While this paradigm shift has significantly enhanced 3D segmentation performance, state-of-the-art architectures require extremely large and complex architectures with large scale computing resources for training and deployment. Furthermore, in the context of limited datasets, often encountered in medical imaging, larger models can present hurdles in both model generalization and convergence. In response to these challenges and to demonstrate that lightweight models are a valuable area of research in 3D medical imaging, we present SegFormer3D, a hierarchical Transformer that calculates attention across multiscale volumetric features. Additionally, SegFormer3D avoids complex decoders and uses an all-MLP decoder to aggregate local and global attention features to produce highly accurate segmentation masks. The proposed memory efficient Transformer preserves the performance characteristics of a significantly larger model in a compact design. SegFormer3D democratizes deep learning for 3D medical image segmentation by offering a model with 33x less parameters and a 13x reduction in GFLOPS compared to the current state-of-the-art (SOTA). We benchmark SegFormer3D against the current SOTA models on three widely used datasets Synapse, BRaTs, and ACDC, achieving competitive results. Code: https://github.com/OSUPCVLab/SegFormer3D.git

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

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

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.

Computer-aided medical image segmentation has been applied widely in diagnosis and treatment to obtain clinically useful information of shapes and volumes of target organs and tissues. In the past several years, convolutional neural network (CNN) based methods (e.g., U-Net) have dominated this area, but still suffered from inadequate long-range information capturing. Hence, recent work presented computer vision Transformer variants for medical image segmentation tasks and obtained promising performances. Such Transformers model long-range dependency by computing pair-wise patch relations. However, they incur prohibitive computational costs, especially on 3D medical images (e.g., CT and MRI). In this paper, we propose a new method called Dilated Transformer, which conducts self-attention for pair-wise patch relations captured alternately in local and global scopes. Inspired by dilated convolution kernels, we conduct the global self-attention in a dilated manner, enlarging receptive fields without increasing the patches involved and thus reducing computational costs. Based on this design of Dilated Transformer, we construct a U-shaped encoder-decoder hierarchical architecture called D-Former for 3D medical image segmentation. Experiments on the Synapse and ACDC datasets show that our D-Former model, trained from scratch, outperforms various competitive CNN-based or Transformer-based segmentation models at a low computational cost without time-consuming per-training process.

Medical image segmentation remains particularly challenging for complex and low-contrast anatomical structures. In this paper, we introduce the U-Transformer network, which combines a U-shaped architecture for image segmentation with self- and cross-attention from Transformers. U-Transformer overcomes the inability of U-Nets to model long-range contextual interactions and spatial dependencies, which are arguably crucial for accurate segmentation in challenging contexts. To this end, attention mechanisms are incorporated at two main levels: a self-attention module leverages global interactions between encoder features, while cross-attention in the skip connections allows a fine spatial recovery in the U-Net decoder by filtering out non-semantic features. Experiments on two abdominal CT-image datasets show the large performance gain brought out by U-Transformer compared to U-Net and local Attention U-Nets. We also highlight the importance of using both self- and cross-attention, and the nice interpretability features brought out by U-Transformer.

Deep learning for medical imaging is hampered by task-specific models that lack generalizability and prognostic capabilities, while existing 'universal' approaches suffer from simplistic conditioning and poor medical semantic understanding. To address these limitations, we introduce DuPLUS, a deep learning framework for efficient multi-modal medical image analysis. DuPLUS introduces a novel vision-language framework that leverages hierarchical semantic prompts for fine-grained control over the analysis task, a capability absent in prior universal models. To enable extensibility to other medical tasks, it includes a hierarchical, text-controlled architecture driven by a unique dual-prompt mechanism. For segmentation, DuPLUS is able to generalize across three imaging modalities, ten different anatomically various medical datasets, encompassing more than 30 organs and tumor types. It outperforms the state-of-the-art task specific and universal models on 8 out of 10 datasets. We demonstrate extensibility of its text-controlled architecture by seamless integration of electronic health record (EHR) data for prognosis prediction, and on a head and neck cancer dataset, DuPLUS achieved a Concordance Index (CI) of 0.69. Parameter-efficient fine-tuning enables rapid adaptation to new tasks and modalities from varying centers, establishing DuPLUS as a versatile and clinically relevant solution for medical image analysis. The code for this work is made available at: https://anonymous.4open.science/r/DuPLUS-6C52

For equitable deployment of AI tools in hospitals and healthcare facilities, we need Deep Segmentation Networks that offer high performance and can be trained on cost-effective GPUs with limited memory and large batch sizes. In this work, we propose Wave-GMS, a lightweight and efficient multi-scale generative model for medical image segmentation. Wave-GMS has a substantially smaller number of trainable parameters, does not require loading memory-intensive pretrained vision foundation models, and supports training with large batch sizes on GPUs with limited memory. We conducted extensive experiments on four publicly available datasets (BUS, BUSI, Kvasir-Instrument, and HAM10000), demonstrating that Wave-GMS achieves state-of-the-art segmentation performance with superior cross-domain generalizability, while requiring only ~2.6M trainable parameters. Code is available at https://github.com/ATPLab-LUMS/Wave-GMS.

Obtaining pixel-level annotations in the medical domain is both expensive and time-consuming, often requiring close collaboration between clinical experts and developers. Semi-supervised medical image segmentation aims to leverage limited annotated data alongside abundant unlabeled data to achieve accurate segmentation. However, existing semi-supervised methods often struggle to structure semantic distributions in the latent space due to noise introduced by pseudo-labels. In this paper, we propose a novel diffusion-based framework for semi-supervised medical image segmentation. Our method introduces a constraint into the latent structure of semantic labels during the denoising diffusion process by enforcing prototype-based contrastive consistency. Rather than explicitly delineating semantic boundaries, the model leverages class prototypes centralized semantic representations in the latent space as anchors. This strategy improves the robustness of dense predictions, particularly in the presence of noisy pseudo-labels. We also introduce a new publicly available benchmark: Multi-Object Segmentation in X-ray Angiography Videos (MOSXAV), which provides detailed, manually annotated segmentation ground truth for multiple anatomical structures in X-ray angiography videos. Extensive experiments on the EndoScapes2023 and MOSXAV datasets demonstrate that our method outperforms state-of-the-art medical image segmentation approaches under the semi-supervised learning setting. This work presents a robust and data-efficient diffusion model that offers enhanced flexibility and strong potential for a wide range of clinical applications.

Medical image segmentation plays a crucial role in assisting healthcare professionals with accurate diagnoses and enabling automated diagnostic processes. Traditional convolutional neural networks (CNNs) often struggle with capturing long-range dependencies, while transformer-based architectures, despite their effectiveness, come with increased computational complexity. Recent efforts have focused on combining CNNs and transformers to balance performance and efficiency, but existing approaches still face challenges in achieving high segmentation accuracy while maintaining low computational costs. Furthermore, many methods underutilize the CNN encoder's capability to capture local spatial information, concentrating primarily on mitigating long-range dependency issues. To address these limitations, we propose QTSeg, a novel architecture for medical image segmentation that effectively integrates local and global information. QTSeg features a dual-mix attention decoder designed to enhance segmentation performance through: (1) a cross-attention mechanism for improved feature alignment, (2) a spatial attention module to capture long-range dependencies, and (3) a channel attention block to learn inter-channel relationships. Additionally, we introduce a multi-level feature distribution module, which adaptively balances feature propagation between the encoder and decoder, further boosting performance. Extensive experiments on five publicly available datasets covering diverse segmentation tasks, including lesion, polyp, breast cancer, cell, and retinal vessel segmentation, demonstrate that QTSeg outperforms state-of-the-art methods across multiple evaluation metrics while maintaining lower computational costs. Our implementation can be found at: https://github.com/tpnam0901/QTSeg (v1.0.0)

State Space Models (SSMs), especially Mamba, have shown great promise in medical image segmentation due to their ability to model long-range dependencies with linear computational complexity. However, accurate medical image segmentation requires the effective learning of both multi-scale detailed feature representations and global contextual dependencies. Although existing works have attempted to address this issue by integrating CNNs and SSMs to leverage their respective strengths, they have not designed specialized modules to effectively capture multi-scale feature representations, nor have they adequately addressed the directional sensitivity problem when applying Mamba to 2D image data. To overcome these limitations, we propose a Multi-Scale Vision Mamba UNet model for medical image segmentation, termed MSVM-UNet. Specifically, by introducing multi-scale convolutions in the VSS blocks, we can more effectively capture and aggregate multi-scale feature representations from the hierarchical features of the VMamba encoder and better handle 2D visual data. Additionally, the large kernel patch expanding (LKPE) layers achieve more efficient upsampling of feature maps by simultaneously integrating spatial and channel information. Extensive experiments on the Synapse and ACDC datasets demonstrate that our approach is more effective than some state-of-the-art methods in capturing and aggregating multi-scale feature representations and modeling long-range dependencies between pixels.

UNet and its variants have been widely used in medical image segmentation. However, these models, especially those based on Transformer architectures, pose challenges due to their large number of parameters and computational loads, making them unsuitable for mobile health applications. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as competitive alternatives to CNN and Transformer architectures. Building upon this, we employ Mamba as a lightweight substitute for CNN and Transformer within UNet, aiming at tackling challenges stemming from computational resource limitations in real medical settings. To this end, we introduce the Lightweight Mamba UNet (LightM-UNet) that integrates Mamba and UNet in a lightweight framework. Specifically, LightM-UNet leverages the Residual Vision Mamba Layer in a pure Mamba fashion to extract deep semantic features and model long-range spatial dependencies, with linear computational complexity. Extensive experiments conducted on two real-world 2D/3D datasets demonstrate that LightM-UNet surpasses existing state-of-the-art literature. Notably, when compared to the renowned nnU-Net, LightM-UNet achieves superior segmentation performance while drastically reducing parameter and computation costs by 116x and 21x, respectively. This highlights the potential of Mamba in facilitating model lightweighting. Our code implementation is publicly available at https://github.com/MrBlankness/LightM-UNet.

Although purely transformer-based architectures showed promising performance in many computer vision tasks, many hybrid models consisting of CNN and transformer blocks are introduced to fit more specialized tasks. Nevertheless, despite the performance gain of both pure and hybrid transformer-based architectures compared to CNNs in medical imaging segmentation, their high training cost and complexity make it challenging to use them in real scenarios. In this work, we propose simple architectures based on purely convolutional layers, and show that by just taking advantage of the attention map visualizations obtained from a self-supervised pretrained vision transformer network (e.g., DINO) one can outperform complex transformer-based networks with much less computation costs. The proposed architecture is composed of two encoder branches with the original image as input in one branch and the attention map visualizations of the same image from multiple self-attention heads from a pre-trained DINO model (as multiple channels) in the other branch. The results of our experiments on two publicly available medical imaging datasets show that the proposed pipeline outperforms U-Net and the state-of-the-art medical image segmentation models.

3D medical image segmentation methods have been successful, but their dependence on large amounts of voxel-level annotated data is a disadvantage that needs to be addressed given the high cost to obtain such annotation. Semi-supervised learning (SSL) solve this issue by training models with a large unlabelled and a small labelled dataset. The most successful SSL approaches are based on consistency learning that minimises the distance between model responses obtained from perturbed views of the unlabelled data. These perturbations usually keep the spatial input context between views fairly consistent, which may cause the model to learn segmentation patterns from the spatial input contexts instead of the segmented objects. In this paper, we introduce the Translation Consistent Co-training (TraCoCo) which is a consistency learning SSL method that perturbs the input data views by varying their spatial input context, allowing the model to learn segmentation patterns from visual objects. Furthermore, we propose the replacement of the commonly used mean squared error (MSE) semi-supervised loss by a new Cross-model confident Binary Cross entropy (CBC) loss, which improves training convergence and keeps the robustness to co-training pseudo-labelling mistakes. We also extend CutMix augmentation to 3D SSL to further improve generalisation. Our TraCoCo shows state-of-the-art results for the Left Atrium (LA) and Brain Tumor Segmentation (BRaTS19) datasets with different backbones. Our code is available at https://github.com/yyliu01/TraCoCo.

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

Accurate computer-aided polyp detection and segmentation during colonoscopy examinations can help endoscopists resect abnormal tissue and thereby decrease chances of polyps growing into cancer. Towards developing a fully automated model for pixel-wise polyp segmentation, we propose ResUNet++, which is an improved ResUNet architecture for colonoscopic image segmentation. Our experimental evaluations show that the suggested architecture produces good segmentation results on publicly available datasets. Furthermore, ResUNet++ significantly outperforms U-Net and ResUNet, two key state-of-the-art deep learning architectures, by achieving high evaluation scores with a dice coefficient of 81.33%, and a mean Intersection over Union (mIoU) of 79.27% for the Kvasir-SEG dataset and a dice coefficient of 79.55%, and a mIoU of 79.62% with CVC-612 dataset.

For the immanent challenge of insufficiently annotated samples in the medical field, semi-supervised medical image segmentation (SSMIS) offers a promising solution. Despite achieving impressive results in delineating primary target areas, most current methodologies struggle to precisely capture the subtle details of boundaries. This deficiency often leads to significant diagnostic inaccuracies. To tackle this issue, we introduce C3S3, a novel semi-supervised segmentation model that synergistically integrates complementary competition and contrastive selection. This design significantly sharpens boundary delineation and enhances overall precision. Specifically, we develop an Outcome-Driven Contrastive Learning module dedicated to refining boundary localization. Additionally, we incorporate a Dynamic Complementary Competition module that leverages two high-performing sub-networks to generate pseudo-labels, thereby further improving segmentation quality. The proposed C3S3 undergoes rigorous validation on two publicly accessible datasets, encompassing the practices of both MRI and CT scans. The results demonstrate that our method achieves superior performance compared to previous cutting-edge competitors. Especially, on the 95HD and ASD metrics, our approach achieves a notable improvement of at least 6%, highlighting the significant advancements. The code is available at https://github.com/Y-TARL/C3S3.

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.

Deep learning, particularly convolutional neural networks (CNNs) and Transformers, has significantly advanced 3D medical image segmentation. While CNNs are highly effective at capturing local features, their limited receptive fields may hinder performance in complex clinical scenarios. In contrast, Transformers excel at modeling long-range dependencies but are computationally intensive, making them expensive to train and deploy. Recently, the Mamba architecture, based on the State Space Model (SSM), has been proposed to efficiently model long-range dependencies while maintaining linear computational complexity. However, its application in medical image segmentation reveals shortcomings, particularly in capturing critical local features essential for accurate delineation of clinical regions. In this study, we propose MambaClinix, a novel U-shaped architecture for medical image segmentation that integrates a hierarchical gated convolutional network(HGCN) with Mamba in an adaptive stage-wise framework. This design significantly enhances computational efficiency and high-order spatial interactions, enabling the model to effectively capture both proximal and distal relationships in medical images. Specifically, our HGCN is designed to mimic the attention mechanism of Transformers by a purely convolutional structure, facilitating high-order spatial interactions in feature maps while avoiding the computational complexity typically associated with Transformer-based methods. Additionally, we introduce a region-specific Tversky loss, which emphasizes specific pixel regions to improve auto-segmentation performance, thereby optimizing the model's decision-making process. Experimental results on five benchmark datasets demonstrate that the proposed MambaClinix achieves high segmentation accuracy while maintaining low model complexity.

Transformers have achieved remarkable success across multiple fields, yet their impact on 3D medical image segmentation remains limited with convolutional networks still dominating major benchmarks. In this work, we a) analyze current Transformer-based segmentation models and identify critical shortcomings, particularly their over-reliance on convolutional blocks. Further, we demonstrate that in some architectures, performance is unaffected by the absence of the Transformer, thereby demonstrating their limited effectiveness. To address these challenges, we move away from hybrid architectures and b) introduce a fully Transformer-based segmentation architecture, termed Primus. Primus leverages high-resolution tokens, combined with advances in positional embeddings and block design, to maximally leverage its Transformer blocks. Through these adaptations Primus surpasses current Transformer-based methods and competes with state-of-the-art convolutional models on multiple public datasets. By doing so, we create the first pure Transformer architecture and take a significant step towards making Transformers state-of-the-art for 3D medical image segmentation.

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

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark. The code is made public at https://github.com/krishnabits001/domain_specific_cl.

Automated segmentation is a fundamental medical image analysis task, which enjoys significant advances due to the advent of deep learning. While foundation models have been useful in natural language processing and some vision tasks for some time, the foundation model developed with image segmentation in mind - Segment Anything Model (SAM) - has been developed only recently and has shown similar promise. However, there are still no systematic analyses or "best-practice" guidelines for optimal fine-tuning of SAM for medical image segmentation. This work summarizes existing fine-tuning strategies with various backbone architectures, model components, and fine-tuning algorithms across 18 combinations, and evaluates them on 17 datasets covering all common radiology modalities. Our study reveals that (1) fine-tuning SAM leads to slightly better performance than previous segmentation methods, (2) fine-tuning strategies that use parameter-efficient learning in both the encoder and decoder are superior to other strategies, (3) network architecture has a small impact on final performance, (4) further training SAM with self-supervised learning can improve final model performance. We also demonstrate the ineffectiveness of some methods popular in the literature and further expand our experiments into few-shot and prompt-based settings. Lastly, we released our code and MRI-specific fine-tuned weights, which consistently obtained superior performance over the original SAM, at https://github.com/mazurowski-lab/finetune-SAM.

In the realm of medical image segmentation, both CNN-based and Transformer-based models have been extensively explored. However, CNNs exhibit limitations in long-range modeling capabilities, whereas Transformers are hampered by their quadratic computational complexity. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as a promising approach. They not only excel in modeling long-range interactions but also maintain a linear computational complexity. In this paper, leveraging state space models, we propose a U-shape architecture model for medical image segmentation, named Vision Mamba UNet (VM-UNet). Specifically, the Visual State Space (VSS) block is introduced as the foundation block to capture extensive contextual information, and an asymmetrical encoder-decoder structure is constructed with fewer convolution layers to save calculation cost. We conduct comprehensive experiments on the ISIC17, ISIC18, and Synapse datasets, and the results indicate that VM-UNet performs competitively in medical image segmentation tasks. To our best knowledge, this is the first medical image segmentation model constructed based on the pure SSM-based model. We aim to establish a baseline and provide valuable insights for the future development of more efficient and effective SSM-based segmentation systems. Our code is available at https://github.com/JCruan519/VM-UNet.

Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net).

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.

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.

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

Convolutional Neural Networks (CNNs) and Vision Transformers (ViT) have been pivotal in biomedical image segmentation, yet their ability to manage long-range dependencies remains constrained by inherent locality and computational overhead. To overcome these challenges, in this technical report, we first propose xLSTM-UNet, a UNet structured deep learning neural network that leverages Vision-LSTM (xLSTM) as its backbone for medical image segmentation. xLSTM is a recently proposed as the successor of Long Short-Term Memory (LSTM) networks and have demonstrated superior performance compared to Transformers and State Space Models (SSMs) like Mamba in Neural Language Processing (NLP) and image classification (as demonstrated in Vision-LSTM, or ViL implementation). Here, xLSTM-UNet we designed extend the success in biomedical image segmentation domain. By integrating the local feature extraction strengths of convolutional layers with the long-range dependency capturing abilities of xLSTM, xLSTM-UNet offers a robust solution for comprehensive image analysis. We validate the efficacy of xLSTM-UNet through experiments. Our findings demonstrate that xLSTM-UNet consistently surpasses the performance of leading CNN-based, Transformer-based, and Mamba-based segmentation networks in multiple datasets in biomedical segmentation including organs in abdomen MRI, instruments in endoscopic images, and cells in microscopic images. With comprehensive experiments performed, this technical report highlights the potential of xLSTM-based architectures in advancing biomedical image analysis in both 2D and 3D. The code, models, and datasets are publicly available at http://tianrun-chen.github.io/xLSTM-UNet/{http://tianrun-chen.github.io/xLSTM-Unet/}

In the era of information explosion, efficiently leveraging large-scale unlabeled data while minimizing the reliance on high-quality pixel-level annotations remains a critical challenge in the field of medical imaging. Semi-supervised learning (SSL) enhances the utilization of unlabeled data by facilitating knowledge transfer, significantly improving the performance of fully supervised models and emerging as a highly promising research direction in medical image analysis. Inspired by the ability of Vision Foundation Models (e.g., SAM-2) to provide rich prior knowledge, we propose SSS (Semi-Supervised SAM-2), a novel approach that leverages SAM-2's robust feature extraction capabilities to uncover latent knowledge in unlabeled medical images, thus effectively enhancing feature support for fully supervised medical image segmentation. Specifically, building upon the single-stream "weak-to-strong" consistency regularization framework, this paper introduces a Discriminative Feature Enhancement (DFE) mechanism to further explore the feature discrepancies introduced by various data augmentation strategies across multiple views. By leveraging feature similarity and dissimilarity across multi-scale augmentation techniques, the method reconstructs and models the features, thereby effectively optimizing the salient regions. Furthermore, a prompt generator is developed that integrates Physical Constraints with a Sliding Window (PCSW) mechanism to generate input prompts for unlabeled data, fulfilling SAM-2's requirement for additional prompts. Extensive experiments demonstrate the superiority of the proposed method for semi-supervised medical image segmentation on two multi-label datasets, i.e., ACDC and BHSD. Notably, SSS achieves an average Dice score of 53.15 on BHSD, surpassing the previous state-of-the-art method by +3.65 Dice. Code will be available at https://github.com/AIGeeksGroup/SSS.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

Recently, many attempts have been made to construct a transformer base U-shaped architecture, and new methods have been proposed that outperformed CNN-based rivals. However, serious problems such as blockiness and cropped edges in predicted masks remain because of transformers' patch partitioning operations. In this work, we propose a new U-shaped architecture for medical image segmentation with the help of the newly introduced focal modulation mechanism. The proposed architecture has asymmetric depths for the encoder and decoder. Due to the ability of the focal module to aggregate local and global features, our model could simultaneously benefit the wide receptive field of transformers and local viewing of CNNs. This helps the proposed method balance the local and global feature usage to outperform one of the most powerful transformer-based U-shaped models called Swin-UNet. We achieved a 1.68% higher DICE score and a 0.89 better HD metric on the Synapse dataset. Also, with extremely limited data, we had a 4.25% higher DICE score on the NeoPolyp dataset. Our implementations are available at: https://github.com/givkashi/Focal-UNet

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.

In recent years, artificial intelligence has significantly advanced medical image segmentation. Nonetheless, challenges remain, including efficient 3D medical image processing across diverse modalities and handling data variability. In this work, we introduce Hierarchical Soft Mixture-of-Experts (HoME), a two-level token-routing layer for efficient long-context modeling, specifically designed for 3D medical image segmentation. Built on the Mamba Selective State Space Model (SSM) backbone, HoME enhances sequential modeling through adaptive expert routing. In the first level, a Soft Mixture-of-Experts (SMoE) layer partitions input sequences into local groups, routing tokens to specialized per-group experts for localized feature extraction. The second level aggregates these outputs through a global SMoE layer, enabling cross-group information fusion and global context refinement. This hierarchical design, combining local expert routing with global expert refinement, enhances generalizability and segmentation performance, surpassing state-of-the-art results across datasets from the three most widely used 3D medical imaging modalities and varying data qualities. The code is publicly available at https://github.com/gmum/MambaHoME.

Medical image segmentation remains a formidable challenge due to the label scarcity. Pre-training Vision Transformer (ViT) through masked image modeling (MIM) on large-scale unlabeled medical datasets presents a promising solution, providing both computational efficiency and model generalization for various downstream tasks. However, current ViT-based MIM pre-training frameworks predominantly emphasize local aggregation representations in output layers and fail to exploit the rich representations across different ViT layers that better capture fine-grained semantic information needed for more precise medical downstream tasks. To fill the above gap, we hereby present Hierarchical Encoder-driven MAE (Hi-End-MAE), a simple yet effective ViT-based pre-training solution, which centers on two key innovations: (1) Encoder-driven reconstruction, which encourages the encoder to learn more informative features to guide the reconstruction of masked patches; and (2) Hierarchical dense decoding, which implements a hierarchical decoding structure to capture rich representations across different layers. We pre-train Hi-End-MAE on a large-scale dataset of 10K CT scans and evaluated its performance across seven public medical image segmentation benchmarks. Extensive experiments demonstrate that Hi-End-MAE achieves superior transfer learning capabilities across various downstream tasks, revealing the potential of ViT in medical imaging applications. The code is available at: https://github.com/FengheTan9/Hi-End-MAE

The release of nnU-Net marked a paradigm shift in 3D medical image segmentation, demonstrating that a properly configured U-Net architecture could still achieve state-of-the-art results. Despite this, the pursuit of novel architectures, and the respective claims of superior performance over the U-Net baseline, continued. In this study, we demonstrate that many of these recent claims fail to hold up when scrutinized for common validation shortcomings, such as the use of inadequate baselines, insufficient datasets, and neglected computational resources. By meticulously avoiding these pitfalls, we conduct a thorough and comprehensive benchmarking of current segmentation methods including CNN-based, Transformer-based, and Mamba-based approaches. In contrast to current beliefs, we find that the recipe for state-of-the-art performance is 1) employing CNN-based U-Net models, including ResNet and ConvNeXt variants, 2) using the nnU-Net framework, and 3) scaling models to modern hardware resources. These results indicate an ongoing innovation bias towards novel architectures in the field and underscore the need for more stringent validation standards in the quest for scientific progress.

Medical image segmentation of anatomical structures and pathology is crucial in modern clinical diagnosis, disease study, and treatment planning. To date, great progress has been made in deep learning-based segmentation techniques, but most methods still lack data efficiency, generalizability, and interactability. Consequently, the development of new, precise segmentation methods that demand fewer labeled datasets is of utmost importance in medical image analysis. Recently, the emergence of foundation models, such as CLIP and Segment-Anything-Model (SAM), with comprehensive cross-domain representation opened the door for interactive and universal image segmentation. However, exploration of these models for data-efficient medical image segmentation is still limited, but is highly necessary. In this paper, we propose a novel framework, called MedCLIP-SAM that combines CLIP and SAM models to generate segmentation of clinical scans using text prompts in both zero-shot and weakly supervised settings. To achieve this, we employed a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss to fine-tune the BiomedCLIP model and the recent gScoreCAM to generate prompts to obtain segmentation masks from SAM in a zero-shot setting. Additionally, we explored the use of zero-shot segmentation labels in a weakly supervised paradigm to improve the segmentation quality further. By extensively testing three diverse segmentation tasks and medical image modalities (breast tumor ultrasound, brain tumor MRI, and lung X-ray), our proposed framework has demonstrated excellent accuracy. Code is available at https://github.com/HealthX-Lab/MedCLIP-SAM.

Deep learning models have emerged as the cornerstone of medical image segmentation, but their efficacy hinges on the availability of extensive manually labeled datasets and their adaptability to unforeseen categories remains a challenge. Few-shot segmentation (FSS) offers a promising solution by endowing models with the capacity to learn novel classes from limited labeled examples. A leading method for FSS is ALPNet, which compares features between the query image and the few available support segmented images. A key question about using ALPNet is how to design its features. In this work, we delve into the potential of using features from DINOv2, which is a foundational self-supervised learning model in computer vision. Leveraging the strengths of ALPNet and harnessing the feature extraction capabilities of DINOv2, we present a novel approach to few-shot segmentation that not only enhances performance but also paves the way for more robust and adaptable medical image analysis.

Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each new set of imaging data and task can be labor intensive and inconsistent among annotators. We present CUTS, an unsupervised deep learning framework for medical image segmentation. CUTS operates in two stages. For each image, it produces an embedding map via intra-image contrastive learning and local patch reconstruction. Then, these embeddings are partitioned at dynamic granularity levels that correspond to the data topology. CUTS yields a series of coarse-to-fine-grained segmentations that highlight features at various granularities. We applied CUTS to retinal fundus images and two types of brain MRI images to delineate structures and patterns at different scales. When evaluated against predefined anatomical masks, CUTS improved the dice coefficient and Hausdorff distance by at least 10% compared to existing unsupervised methods. Finally, CUTS showed performance on par with Segment Anything Models (SAM, MedSAM, SAM-Med2D) pre-trained on gigantic labeled datasets.

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

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

Multi-annotator medical image segmentation is an important research problem, but requires annotated datasets that are expensive to collect. Dermoscopic skin lesion imaging allows human experts and AI systems to observe morphological structures otherwise not discernable from regular clinical photographs. However, currently there are no large-scale publicly available multi-annotator skin lesion segmentation (SLS) datasets with annotator-labels for dermoscopic skin lesion imaging. We introduce ISIC MultiAnnot++, a large public multi-annotator skin lesion segmentation dataset for images from the ISIC Archive. The final dataset contains 17,684 segmentation masks spanning 14,967 dermoscopic images, where 2,394 dermoscopic images have 2-5 segmentations per image, making it the largest publicly available SLS dataset. Further, metadata about the segmentation, including the annotators' skill level and segmentation tool, is included, enabling research on topics such as annotator-specific preference modeling for segmentation and annotator metadata analysis. We provide an analysis on the characteristics of this dataset, curated data partitions, and consensus segmentation masks.

In recent years, the Segmentation Anything Model (SAM) has attracted considerable attention as a foundational model well-known for its robust generalization capabilities across various downstream tasks. However, SAM does not exhibit satisfactory performance in the realm of medical image analysis. In this study, we introduce the first study on adapting SAM on video segmentation, called MediViSTA-SAM, a novel approach designed for medical video segmentation. Given video data, MediViSTA, spatio-temporal adapter captures long and short range temporal attention with cross-frame attention mechanism effectively constraining it to consider the immediately preceding video frame as a reference, while also considering spatial information effectively. Additionally, it incorporates multi-scale fusion by employing a U-shaped encoder and a modified mask decoder to handle objects of varying sizes. To evaluate our approach, extensive experiments were conducted using state-of-the-art (SOTA) methods, assessing its generalization abilities on multi-vendor in-house echocardiography datasets. The results highlight the accuracy and effectiveness of our network in medical video segmentation.

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

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

While making a tremendous impact in various fields, deep neural networks usually require large amounts of labeled data for training which are expensive to collect in many applications, especially in the medical domain. Unlabeled data, on the other hand, is much more abundant. Semi-supervised learning techniques, such as co-training, could provide a powerful tool to leverage unlabeled data. In this paper, we propose a novel framework, uncertainty-aware multi-view co-training (UMCT), to address semi-supervised learning on 3D data, such as volumetric data from medical imaging. In our work, co-training is achieved by exploiting multi-viewpoint consistency of 3D data. We generate different views by rotating or permuting the 3D data and utilize asymmetrical 3D kernels to encourage diversified features in different sub-networks. In addition, we propose an uncertainty-weighted label fusion mechanism to estimate the reliability of each view's prediction with Bayesian deep learning. As one view requires the supervision from other views in co-training, our self-adaptive approach computes a confidence score for the prediction of each unlabeled sample in order to assign a reliable pseudo label. Thus, our approach can take advantage of unlabeled data during training. We show the effectiveness of our proposed semi-supervised method on several public datasets from medical image segmentation tasks (NIH pancreas & LiTS liver tumor dataset). Meanwhile, a fully-supervised method based on our approach achieved state-of-the-art performances on both the LiTS liver tumor segmentation and the Medical Segmentation Decathlon (MSD) challenge, demonstrating the robustness and value of our framework, even when fully supervised training is feasible.

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.

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

The goal of this paper is to interactively refine the automatic segmentation on challenging structures that fall behind human performance, either due to the scarcity of available annotations or the difficulty nature of the problem itself, for example, on segmenting cancer or small organs. Specifically, we propose a novel Transformer-based architecture for Interactive Segmentation (TIS), that treats the refinement task as a procedure for grouping pixels with similar features to those clicks given by the end users. Our proposed architecture is composed of Transformer Decoder variants, which naturally fulfills feature comparison with the attention mechanisms. In contrast to existing approaches, our proposed TIS is not limited to binary segmentations, and allows the user to edit masks for arbitrary number of categories. To validate the proposed approach, we conduct extensive experiments on three challenging datasets and demonstrate superior performance over the existing state-of-the-art methods. The project page is: https://wtliu7.github.io/tis/.

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.

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

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

Medical image segmentation is crucial for many healthcare tasks, including disease diagnosis and treatment planning. One key area is the segmentation of skin lesions, which is vital for diagnosing skin cancer and monitoring patients. In this context, this paper introduces SegDT, a new segmentation model based on diffusion transformer (DiT). SegDT is designed to work on low-cost hardware and incorporates Rectified Flow, which improves the generation quality at reduced inference steps and maintains the flexibility of standard diffusion models. Our method is evaluated on three benchmarking datasets and compared against several existing works, achieving state-of-the-art results while maintaining fast inference speeds. This makes the proposed model appealing for real-world medical applications. This work advances the performance and capabilities of deep learning models in medical image analysis, enabling faster, more accurate diagnostic tools for healthcare professionals. The code is made publicly available at https://github.com/Bekhouche/SegDT{GitHub}.

Recent advances in medical image segmentation have been driven by deep learning; however, most existing methods remain limited by modality-specific designs and exhibit poor adaptability to dynamic medical imaging scenarios. The Segment Anything Model 2 (SAM2) and its related variants, which introduce a streaming memory mechanism for real-time video segmentation, present new opportunities for prompt-based, generalizable solutions. Nevertheless, adapting these models to medical video scenarios typically requires large-scale datasets for retraining or transfer learning, leading to high computational costs and the risk of catastrophic forgetting. To address these challenges, we propose DD-SAM2, an efficient adaptation framework for SAM2 that incorporates a Depthwise-Dilated Adapter (DD-Adapter) to enhance multi-scale feature extraction with minimal parameter overhead. This design enables effective fine-tuning of SAM2 on medical videos with limited training data. Unlike existing adapter-based methods focused solely on static images, DD-SAM2 fully exploits SAM2's streaming memory for medical video object tracking and segmentation. Comprehensive evaluations on TrackRad2025 (tumor segmentation) and EchoNet-Dynamic (left ventricle tracking) datasets demonstrate superior performance, achieving Dice scores of 0.93 and 0.97, respectively. To the best of our knowledge, this work provides an initial attempt at systematically exploring adapter-based SAM2 fine-tuning for medical video segmentation and tracking. Code, datasets, and models will be publicly available at https://github.com/apple1986/DD-SAM2.

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

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.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

Segment Anything Model (SAM) has demonstrated impressive performance on a wide range of natural image segmentation tasks. However, its performance significantly deteriorates when directly applied to medical domain, due to the remarkable differences between natural images and medical images. Some researchers have attempted to train SAM on large scale medical datasets. However, poor zero-shot performance is observed from the experimental results. In this context, inspired by the superior performance of U-Net-like models in medical image segmentation, we propose SAMUNet, a new foundation model which incorporates U-Net to the original SAM, to fully leverage the powerful contextual modeling ability of convolutions. To be specific, we parallel a convolutional branch in the image encoder, which is trained independently with the vision Transformer branch frozen. Additionally, we employ multi-scale fusion in the mask decoder, to facilitate accurate segmentation of objects with different scales. We train SAM-UNet on SA-Med2D-16M, the largest 2-dimensional medical image segmentation dataset to date, yielding a universal pretrained model for medical images. Extensive experiments are conducted to evaluate the performance of the model, and state-of-the-art result is achieved, with a dice similarity coefficient score of 0.883 on SA-Med2D-16M dataset. Specifically, in zero-shot segmentation experiments, our model not only significantly outperforms previous large medical SAM models across all modalities, but also substantially mitigates the performance degradation seen on unseen modalities. It should be highlighted that SAM-UNet is an efficient and extensible foundation model, which can be further fine-tuned for other downstream tasks in medical community. The code is available at https://github.com/Hhankyangg/sam-unet.

Mamba, a special case of the State Space Model, is gaining popularity as an alternative to template-based deep learning approaches in medical image analysis. While transformers are powerful architectures, they have drawbacks, including quadratic computational complexity and an inability to address long-range dependencies efficiently. This limitation affects the analysis of large and complex datasets in medical imaging, where there are many spatial and temporal relationships. In contrast, Mamba offers benefits that make it well-suited for medical image analysis. It has linear time complexity, which is a significant improvement over transformers. Mamba processes longer sequences without attention mechanisms, enabling faster inference and requiring less memory. Mamba also demonstrates strong performance in merging multimodal data, improving diagnosis accuracy and patient outcomes. The organization of this paper allows readers to appreciate the capabilities of Mamba in medical imaging step by step. We begin by defining core concepts of SSMs and models, including S4, S5, and S6, followed by an exploration of Mamba architectures such as pure Mamba, U-Net variants, and hybrid models with convolutional neural networks, transformers, and Graph Neural Networks. We also cover Mamba optimizations, techniques and adaptations, scanning, datasets, applications, experimental results, and conclude with its challenges and future directions in medical imaging. This review aims to demonstrate the transformative potential of Mamba in overcoming existing barriers within medical imaging while paving the way for innovative advancements in the field. A comprehensive list of Mamba architectures applied in the medical field, reviewed in this work, is available at Github.

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

Whole-heart segmentation from CT and MRI scans is crucial for cardiovascular disease analysis, yet existing methods struggle with modality-specific biases and the need for extensive labeled datasets. To address these challenges, we propose a foundation model for whole-heart segmentation using a self-supervised learning (SSL) framework based on a student-teacher architecture. Our model is pretrained on a large, unlabeled dataset of CT and MRI scans, leveraging the xLSTM backbone to capture long-range spatial dependencies and complex anatomical structures in 3D medical images. By incorporating multi-modal pretraining, our approach ensures strong generalization across both CT and MRI modalities, mitigating modality-specific variations and improving segmentation accuracy in diverse clinical settings. The use of large-scale unlabeled data significantly reduces the dependency on manual annotations, enabling robust performance even with limited labeled data. We further introduce an xLSTM-UNet-based architecture for downstream whole-heart segmentation tasks, demonstrating its effectiveness on few-label CT and MRI datasets. Our results validate the robustness and adaptability of the proposed model, highlighting its potential for advancing automated whole-heart segmentation in medical imaging.

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.

Recent vision-language models (e.g., CLIP) have demonstrated remarkable class-generalizable ability to unseen classes in few-shot anomaly segmentation (FSAS), leveraging supervised prompt learning or fine-tuning on seen classes. However, their cross-category generalization largely depends on prior knowledge of real seen anomaly samples. In this paper, we propose a novel framework, namely DictAS, which enables a unified model to detect visual anomalies in unseen object categories without any retraining on the target data, only employing a few normal reference images as visual prompts. The insight behind DictAS is to transfer dictionary lookup capabilities to the FSAS task for unseen classes via self-supervised learning, instead of merely memorizing the normal and abnormal feature patterns from the training set. Specifically, DictAS mainly consists of three components: (1) **Dictionary Construction** - to simulate the index and content of a real dictionary using features from normal reference images. (2) **Dictionary Lookup** - to retrieve queried region features from the dictionary via a sparse lookup strategy. When a query feature cannot be retrieved, it is classified as an anomaly. (3) **Query Discrimination Regularization**- to enhance anomaly discrimination by making abnormal features harder to retrieve from the dictionary. To achieve this, Contrastive Query Constraint and Text Alignment Constraint are further proposed. Extensive experiments on seven public industrial and medical datasets demonstrate that DictAS consistently outperforms state-of-the-art FSAS methods.

Foundation Vision-Language Models (VLMs) trained using large-scale open-domain images and text pairs have recently been adapted to develop Vision-Language Segmentation Models (VLSMs) that allow providing text prompts during inference to guide image segmentation. If robust and powerful VLSMs can be built for medical images, it could aid medical professionals in many clinical tasks where they must spend substantial time delineating the target structure of interest. VLSMs for medical images resort to fine-tuning base VLM or VLSM pretrained on open-domain natural image datasets due to fewer annotated medical image datasets; this fine-tuning is resource-consuming and expensive as it usually requires updating all or a significant fraction of the pretrained parameters. Recently, lightweight blocks called adapters have been proposed in VLMs that keep the pretrained model frozen and only train adapters during fine-tuning, substantially reducing the computing resources required. We introduce a novel adapter, VLSM-Adapter, that can fine-tune pretrained vision-language segmentation models using transformer encoders. Our experiments in widely used CLIP-based segmentation models show that with only 3 million trainable parameters, the VLSM-Adapter outperforms state-of-the-art and is comparable to the upper bound end-to-end fine-tuning. The source code is available at: https://github.com/naamiinepal/vlsm-adapter.

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

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.

In 2015 we began a sub-challenge at the EndoVis workshop at MICCAI in Munich using endoscope images of ex-vivo tissue with automatically generated annotations from robot forward kinematics and instrument CAD models. However, the limited background variation and simple motion rendered the dataset uninformative in learning about which techniques would be suitable for segmentation in real surgery. In 2017, at the same workshop in Quebec we introduced the robotic instrument segmentation dataset with 10 teams participating in the challenge to perform binary, articulating parts and type segmentation of da Vinci instruments. This challenge included realistic instrument motion and more complex porcine tissue as background and was widely addressed with modifications on U-Nets and other popular CNN architectures. In 2018 we added to the complexity by introducing a set of anatomical objects and medical devices to the segmented classes. To avoid over-complicating the challenge, we continued with porcine data which is dramatically simpler than human tissue due to the lack of fatty tissue occluding many organs.

Task-generic promptable image segmentation aims to achieve segmentation of diverse samples under a single task description by utilizing only one task-generic prompt. Current methods leverage the generalization capabilities of Vision-Language Models (VLMs) to infer instance-specific prompts from these task-generic prompts in order to guide the segmentation process. However, when VLMs struggle to generalise to some image instances, predicting instance-specific prompts becomes poor. To solve this problem, we introduce Instance-specific Negative Mining for Task-Generic Promptable Segmentation (INT). The key idea of INT is to adaptively reduce the influence of irrelevant (negative) prior knowledge whilst to increase the use the most plausible prior knowledge, selected by negative mining with higher contrast, in order to optimise instance-specific prompts generation. Specifically, INT consists of two components: (1) instance-specific prompt generation, which progressively fliters out incorrect information in prompt generation; (2) semantic mask generation, which ensures each image instance segmentation matches correctly the semantics of the instance-specific prompts. INT is validated on six datasets, including camouflaged objects and medical images, demonstrating its effectiveness, robustness and scalability.

Language promptable X-ray image segmentation would enable greater flexibility for human-in-the-loop workflows in diagnostic and interventional precision medicine. Prior efforts have contributed task-specific models capable of solving problems within a narrow scope, but expanding to broader use requires additional data, annotations, and training time. Recently, language-aligned foundation models (LFMs) -- machine learning models trained on large amounts of highly variable image and text data thus enabling broad applicability -- have emerged as promising tools for automated image analysis. Existing foundation models for medical image analysis focus on scenarios and modalities where large, richly annotated datasets are available. However, the X-ray imaging modality features highly variable image appearance and applications, from diagnostic chest X-rays to interventional fluoroscopy, with varying availability of data. To pave the way toward an LFM for comprehensive and language-aligned analysis of arbitrary medical X-ray images, we introduce FluoroSAM, a language-promptable variant of the Segment Anything Model, trained from scratch on 3M synthetic X-ray images from a wide variety of human anatomies, imaging geometries, and viewing angles. These include pseudo-ground truth masks for 128 organ types and 464 tools with associated text descriptions. FluoroSAM is capable of segmenting myriad anatomical structures and tools based on natural language prompts, thanks to the novel incorporation of vector quantization (VQ) of text embeddings in the training process. We demonstrate FluoroSAM's performance quantitatively on real X-ray images and showcase on several applications how FluoroSAM is a key enabler for rich human-machine interaction in the X-ray image acquisition and analysis context. Code is available at https://github.com/arcadelab/fluorosam.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

Accurate segmentation and classification of brain tumors from Magnetic Resonance Imaging (MRI) remain key challenges in medical image analysis, primarily due to the lack of high-quality, balanced, and diverse datasets with expert annotations. In this work, we address this gap by introducing BRISC, a dataset designed for brain tumor segmentation and classification tasks, featuring high-resolution segmentation masks. The dataset comprises 6,000 contrast-enhanced T1-weighted MRI scans, which were collated from multiple public datasets that lacked segmentation labels. Our primary contribution is the subsequent expert annotation of these images, performed by certified radiologists and physicians. It includes three major tumor types, namely glioma, meningioma, and pituitary, as well as non-tumorous cases. Each sample includes high-resolution labels and is categorized across axial, sagittal, and coronal imaging planes to facilitate robust model development and cross-view generalization. To demonstrate the utility of the dataset, we provide benchmark results for both tasks using standard deep learning models. The BRISC dataset is made publicly available. datasetlink: Kaggle (https://www.kaggle.com/datasets/briscdataset/brisc2025/), Figshare (https://doi.org/10.6084/m9.figshare.30533120), Zenodo (https://doi.org/10.5281/zenodo.17524350)

Building trusted datasets is critical for transparent and responsible Medical AI (MAI) research, but creating even small, high-quality datasets can take years of effort from multidisciplinary teams. This process often delays AI benefits, as human-centric data creation and AI-centric model development are treated as separate, sequential steps. To overcome this, we propose ScaleMAI, an agent of AI-integrated data curation and annotation, allowing data quality and AI performance to improve in a self-reinforcing cycle and reducing development time from years to months. We adopt pancreatic tumor detection as an example. First, ScaleMAI progressively creates a dataset of 25,362 CT scans, including per-voxel annotations for benign/malignant tumors and 24 anatomical structures. Second, through progressive human-in-the-loop iterations, ScaleMAI provides Flagship AI Model that can approach the proficiency of expert annotators (30-year experience) in detecting pancreatic tumors. Flagship Model significantly outperforms models developed from smaller, fixed-quality datasets, with substantial gains in tumor detection (+14%), segmentation (+5%), and classification (72%) on three prestigious benchmarks. In summary, ScaleMAI transforms the speed, scale, and reliability of medical dataset creation, paving the way for a variety of impactful, data-driven applications.

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework.

The application of machine learning to medical ultrasound videos of the heart, i.e., echocardiography, has recently gained traction with the availability of large public datasets. Traditional supervised tasks, such as ejection fraction regression, are now making way for approaches focusing more on the latent structure of data distributions, as well as generative methods. We propose a model trained exclusively by knowledge distillation, either on real or synthetical data, involving retrieving masks suggested by a teacher model. We achieve state-of-the-art (SOTA) values on the task of identifying end-diastolic and end-systolic frames. By training the model only on synthetic data, it reaches segmentation capabilities close to the performance when trained on real data with a significantly reduced number of weights. A comparison with the 5 main existing methods shows that our method outperforms the others in most cases. We also present a new evaluation method that does not require human annotation and instead relies on a large auxiliary model. We show that this method produces scores consistent with those obtained from human annotations. Relying on the integrated knowledge from a vast amount of records, this method overcomes certain inherent limitations of human annotator labeling. Code: https://github.com/GregoirePetit/EchoDFKD

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

In computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown superior segmentation performances compared to classical machine learning and image processing techniques. However, these models need fully annotated datasets for training which is challenging to acquire, especially in the medical domain. In this work, we release one of the biggest fully manually annotated datasets of nuclei in Hematoxylin and Eosin (H&E)-stained histological images, called NuInsSeg. This dataset contains 665 image patches with more than 30,000 manually segmented nuclei from 31 human and mouse organs. Moreover, for the first time, we provide additional ambiguous area masks for the entire dataset. These vague areas represent the parts of the images where precise and deterministic manual annotations are impossible, even for human experts. The dataset and detailed step-by-step instructions to generate related segmentation masks are publicly available at https://www.kaggle.com/datasets/ipateam/nuinsseg and https://github.com/masih4/NuInsSeg, respectively.

According to the 2021 World Health Organization (WHO) Classification scheme for gliomas, glioma segmentation is a very important basis for diagnosis and genotype prediction. In general, 3D multimodal brain MRI is an effective diagnostic tool. In the past decade, there has been an increase in the use of machine learning, particularly deep learning, for medical images processing. Thanks to the development of foundation models, models pre-trained with large-scale datasets have achieved better results on a variety of tasks. However, for medical images with small dataset sizes, deep learning methods struggle to achieve better results on real-world image datasets. In this paper, we propose a cross-modality attention adapter based on multimodal fusion to fine-tune the foundation model to accomplish the task of glioma segmentation in multimodal MRI brain images with better results. The effectiveness of the proposed method is validated via our private glioma data set from the First Affiliated Hospital of Zhengzhou University (FHZU) in Zhengzhou, China. Our proposed method is superior to current state-of-the-art methods with a Dice of 88.38% and Hausdorff distance of 10.64, thereby exhibiting a 4% increase in Dice to segment the glioma region for glioma treatment.

Segment Anything Model (SAM) has achieved impressive results for natural image segmentation with input prompts such as points and bounding boxes. Its success largely owes to massive labeled training data. However, directly applying SAM to medical image segmentation cannot perform well because SAM lacks medical knowledge -- it does not use medical images for training. To incorporate medical knowledge into SAM, we introduce SA-Med2D-20M, a large-scale segmentation dataset of 2D medical images built upon numerous public and private datasets. It consists of 4.6 million 2D medical images and 19.7 million corresponding masks, covering almost the whole body and showing significant diversity. This paper describes all the datasets collected in SA-Med2D-20M and details how to process these datasets. Furthermore, comprehensive statistics of SA-Med2D-20M are presented to facilitate the better use of our dataset, which can help the researchers build medical vision foundation models or apply their models to downstream medical applications. We hope that the large scale and diversity of SA-Med2D-20M can be leveraged to develop medical artificial intelligence for enhancing diagnosis, medical image analysis, knowledge sharing, and education. The data with the redistribution license is publicly available at https://github.com/OpenGVLab/SAM-Med2D.

Medical Vision-Language Pretraining (MedVLP) shows promise in learning generalizable and transferable visual representations from paired and unpaired medical images and reports. MedVLP can provide useful features to downstream tasks and facilitate adapting task-specific models to new setups using fewer examples. However, existing MedVLP methods often differ in terms of datasets, preprocessing, and finetuning implementations. This pose great challenges in evaluating how well a MedVLP method generalizes to various clinically-relevant tasks due to the lack of unified, standardized, and comprehensive benchmark. To fill this gap, we propose BenchX, a unified benchmark framework that enables head-to-head comparison and systematical analysis between MedVLP methods using public chest X-ray datasets. Specifically, BenchX is composed of three components: 1) Comprehensive datasets covering nine datasets and four medical tasks; 2) Benchmark suites to standardize data preprocessing, train-test splits, and parameter selection; 3) Unified finetuning protocols that accommodate heterogeneous MedVLP methods for consistent task adaptation in classification, segmentation, and report generation, respectively. Utilizing BenchX, we establish baselines for nine state-of-the-art MedVLP methods and found that the performance of some early MedVLP methods can be enhanced to surpass more recent ones, prompting a revisiting of the developments and conclusions from prior works in MedVLP. Our code are available at https://github.com/yangzhou12/BenchX.

Active contour models have achieved prominent success in the area of image segmentation, allowing complex objects to be segmented from the background for further analysis. Existing models can be divided into region-based active contour models and edge-based active contour models. However, both models use direct image data to achieve segmentation and face many challenging problems in terms of the initial contour position, noise sensitivity, local minima and inefficiency owing to the in-homogeneity of image intensities. The saliency map of an image changes the image representation, making it more visual and meaningful. In this study, we propose a novel model that uses the advantages of a saliency map with local image information (LIF) and overcomes the drawbacks of previous models. The proposed model is driven by a saliency map of an image and the local image information to enhance the progress of the active contour models. In this model, the saliency map of an image is first computed to find the saliency driven local fitting energy. Then, the saliency-driven local fitting energy is combined with the LIF model, resulting in a final novel energy functional. This final energy functional is formulated through a level set formulation, and regulation terms are added to evolve the contour more precisely across the object boundaries. The quality of the proposed method was verified on different synthetic images, real images and publicly available datasets, including medical images. The image segmentation results, and quantitative comparisons confirmed the contour initialization independence, noise insensitivity, and superior segmentation accuracy of the proposed model in comparison to the other segmentation models.

Bridging clinical diagnostic reasoning with AI remains a central challenge in medical imaging. We introduce MedCLM, an automated pipeline that converts detection datasets into large-scale medical visual question answering (VQA) data with Chain-of-Thought (CoT) reasoning by linking lesion boxes to organ segmentation and structured rationales. These contextual signals enable medical vision-language models to generate question-answer pairs with step-by-step reasoning. To utilize this data effectively, we propose an Integrated CoT-Curriculum Strategy composed of an Easy stage with explicit lesion boxes for visual grounding, a Medium stage that encourages implicit localization, and a Hard stage for weakly supervised reasoning. Experimental results demonstrate that MedCLM attains state-of-the-art performance on several medical VQA benchmarks, providing a scalable framework for developing clinically aligned medical vision-language models.