Daily Papers

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

The Segment Anything Model (SAM) has demonstrated outstanding adaptation to medical image segmentation but still faces three major challenges. Firstly, the huge computational costs of SAM limit its real-world applicability. Secondly, SAM depends on manual annotations (e.g., points, boxes) as prompts, which are laborious and impractical in clinical scenarios. Thirdly, SAM handles all segmentation targets equally, which is suboptimal for diverse medical modalities with inherent heterogeneity. To address these issues, we propose an Efficient Self-Prompting SAM for universal medical image segmentation, named ESP-MedSAM. We devise a Multi-Modal Decoupled Knowledge Distillation (MMDKD) strategy to distil common image knowledge and domain-specific medical knowledge from the foundation model to train a lightweight image encoder and a modality controller. Further, they combine with the additionally introduced Self-Patch Prompt Generator (SPPG) and Query-Decoupled Modality Decoder (QDMD) to construct ESP-MedSAM. Specifically, SPPG aims to generate a set of patch prompts automatically and QDMD leverages a one-to-one strategy to provide an independent decoding channel for every modality. Extensive experiments indicate that ESP-MedSAM outperforms state-of-the-arts in diverse medical imaging segmentation takes, displaying superior zero-shot learning and modality transfer ability. Especially, our framework uses only 31.4% parameters compared to SAM-Base.

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.

Medical image segmentation is an important analysis task in clinical practice and research. Deep learning has massively advanced the field, but current approaches are mostly based on models trained for a specific task. Training such models or adapting them to a new condition is costly due to the need for (manually) labeled data. The emergence of vision foundation models, especially Segment Anything, offers a path to universal segmentation for medical images, overcoming these issues. Here, we study how to improve Segment Anything for medical images by comparing different finetuning strategies on a large and diverse dataset. We evaluate the finetuned models on a wide range of interactive and (automatic) semantic segmentation tasks. We find that the performance can be clearly improved for interactive segmentation. However, semantic segmentation does not benefit from pretraining on medical images. Our best model, MedicoSAM, is publicly available at https://github.com/computational-cell-analytics/medico-sam. We show that it is compatible with existing tools for data annotation and believe that it will be of great practical value.

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.

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.

Segmenting 3D blood vessels is a critical yet challenging task in medical image analysis. This is due to significant imaging modality-specific variations in artifacts, vascular patterns and scales, signal-to-noise ratios, and background tissues. These variations, along with domain gaps arising from varying imaging protocols, limit the generalization of existing supervised learning-based methods, requiring tedious voxel-level annotations for each dataset separately. While foundation models promise to alleviate this limitation, they typically fail to generalize to the task of blood vessel segmentation, posing a unique, complex problem. In this work, we present vesselFM, a foundation model designed specifically for the broad task of 3D blood vessel segmentation. Unlike previous models, vesselFM can effortlessly generalize to unseen domains. To achieve zero-shot generalization, we train vesselFM on three heterogeneous data sources: a large, curated annotated dataset, data generated by a domain randomization scheme, and data sampled from a flow matching-based generative model. Extensive evaluations show that vesselFM outperforms state-of-the-art medical image segmentation foundation models across four (pre-)clinically relevant imaging modalities in zero-, one-, and few-shot scenarios, therefore providing a universal solution for 3D blood vessel segmentation.

The Segment Anything Model (SAM) has achieved remarkable successes in the realm of natural image segmentation, but its deployment in the medical imaging sphere has encountered challenges. Specifically, the model struggles with medical images that feature low contrast, faint boundaries, intricate morphologies, and small-sized objects. To address these challenges and enhance SAM's performance in the medical domain, we introduce a comprehensive modification. Firstly, we incorporate a frozen Convolutional Neural Network (CNN) branch as an image encoder, which synergizes with SAM's original Vision Transformer (ViT) encoder through a novel variational attention fusion module. This integration bolsters the model's capability to capture local spatial information, which is often paramount in medical imagery. Moreover, to further optimize SAM for medical imaging, we introduce feature and position adapters within the ViT branch, refining the encoder's representations. We see that compared to current prompting strategies to fine-tune SAM for ultrasound medical segmentation, the use of text descriptions that serve as text prompts for SAM helps significantly improve the performance. Leveraging ChatGPT's natural language understanding capabilities, we generate prompts that offer contextual information and guidance to SAM, enabling it to better understand the nuances of ultrasound medical images and improve its segmentation accuracy. Our method, in its entirety, represents a significant stride towards making universal image segmentation models more adaptable and efficient in the medical domain.

When reading medical images such as a computed tomography (CT) scan, radiologists generally search across the image to find lesions, characterize and measure them, and then describe them in the radiological report. To automate this process, we propose a multitask universal lesion analysis network (MULAN) for joint detection, tagging, and segmentation of lesions in a variety of body parts, which greatly extends existing work of single-task lesion analysis on specific body parts. MULAN is based on an improved Mask R-CNN framework with three head branches and a 3D feature fusion strategy. It achieves the state-of-the-art accuracy in the detection and tagging tasks on the DeepLesion dataset, which contains 32K lesions in the whole body. We also analyze the relationship between the three tasks and show that tag predictions can improve detection accuracy via a score refinement layer.

Segment anything model (SAM) has revolutionized natural image segmentation, but its performance on medical images is limited. This work presents MedSAM, the first attempt at extending the success of SAM to medical images, with the goal of creating a universal tool for the segmentation of various medical targets. Specifically, we first curate a large-scale medical image dataset, encompassing over 200,000 masks across 11 different modalities. Then, we develop a simple fine-tuning method to adapt SAM to general medical image segmentation. Comprehensive experiments on 21 3D segmentation tasks and 9 2D segmentation tasks demonstrate that MedSAM outperforms the default SAM model with an average Dice Similarity Coefficient (DSC) of 22.5% and 17.6% on 3D and 2D segmentation tasks, respectively. The code and trained model are publicly available at https://github.com/bowang-lab/MedSAM.

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.

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

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

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

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

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.

Recent advances in segmentation foundation models have enabled accurate and efficient segmentation across a wide range of natural images and videos, but their utility to medical data remains unclear. In this work, we first present a comprehensive benchmarking of the Segment Anything Model 2 (SAM2) across 11 medical image modalities and videos and point out its strengths and weaknesses by comparing it to SAM1 and MedSAM. Then, we develop a transfer learning pipeline and demonstrate SAM2 can be quickly adapted to medical domain by fine-tuning. Furthermore, we implement SAM2 as a 3D slicer plugin and Gradio API for efficient 3D image and video segmentation. The code has been made publicly available at https://github.com/bowang-lab/MedSAM.

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.

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.

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.

Medical image segmentation has immense clinical applicability but remains a challenge despite advancements in deep learning. The Segment Anything Model (SAM) exhibits potential in this field, yet the requirement for expertise intervention and the domain gap between natural and medical images poses significant obstacles. This paper introduces a novel training-free evidential prompt generation method named EviPrompt to overcome these issues. The proposed method, built on the inherent similarities within medical images, requires only a single reference image-annotation pair, making it a training-free solution that significantly reduces the need for extensive labeling and computational resources. First, to automatically generate prompts for SAM in medical images, we introduce an evidential method based on uncertainty estimation without the interaction of clinical experts. Then, we incorporate the human prior into the prompts, which is vital for alleviating the domain gap between natural and medical images and enhancing the applicability and usefulness of SAM in medical scenarios. EviPrompt represents an efficient and robust approach to medical image segmentation, with evaluations across a broad range of tasks and modalities confirming its efficacy.

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.

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.

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.

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.

Universal Image Segmentation is not a new concept. Past attempts to unify image segmentation in the last decades include scene parsing, panoptic segmentation, and, more recently, new panoptic architectures. However, such panoptic architectures do not truly unify image segmentation because they need to be trained individually on the semantic, instance, or panoptic segmentation to achieve the best performance. Ideally, a truly universal framework should be trained only once and achieve SOTA performance across all three image segmentation tasks. To that end, we propose OneFormer, a universal image segmentation framework that unifies segmentation with a multi-task train-once design. We first propose a task-conditioned joint training strategy that enables training on ground truths of each domain (semantic, instance, and panoptic segmentation) within a single multi-task training process. Secondly, we introduce a task token to condition our model on the task at hand, making our model task-dynamic to support multi-task training and inference. Thirdly, we propose using a query-text contrastive loss during training to establish better inter-task and inter-class distinctions. Notably, our single OneFormer model outperforms specialized Mask2Former models across all three segmentation tasks on ADE20k, CityScapes, and COCO, despite the latter being trained on each of the three tasks individually with three times the resources. With new ConvNeXt and DiNAT backbones, we observe even more performance improvement. We believe OneFormer is a significant step towards making image segmentation more universal and accessible. To support further research, we open-source our code and models at https://github.com/SHI-Labs/OneFormer

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.

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

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

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

In this paper, we introduce Medical SAM 2 (MedSAM-2), an advanced segmentation model that utilizes the SAM 2 framework to address both 2D and 3D medical image segmentation tasks. By adopting the philosophy of taking medical images as videos, MedSAM-2 not only applies to 3D medical images but also unlocks new One-prompt Segmentation capability. That allows users to provide a prompt for just one or a specific image targeting an object, after which the model can autonomously segment the same type of object in all subsequent images, regardless of temporal relationships between the images. We evaluated MedSAM-2 across a variety of medical imaging modalities, including abdominal organs, optic discs, brain tumors, thyroid nodules, and skin lesions, comparing it against state-of-the-art models in both traditional and interactive segmentation settings. Our findings show that MedSAM-2 not only surpasses existing models in performance but also exhibits superior generalization across a range of medical image segmentation tasks. Our code will be released at: https://github.com/MedicineToken/Medical-SAM2

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

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.

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.

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

Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of high clinical relevance because diagnostic decisions often depend on rating of objects rather than e.g. pixels. For this task, the cumbersome and iterative process of method configuration constitutes a major research bottleneck. Recently, nnU-Net has tackled this challenge for the task of image segmentation with great success. Following nnU-Net's agenda, in this work we systematize and automate the configuration process for medical object detection. The resulting self-configuring method, nnDetection, adapts itself without any manual intervention to arbitrary medical detection problems while achieving results en par with or superior to the state-of-the-art. We demonstrate the effectiveness of nnDetection on two public benchmarks, ADAM and LUNA16, and propose 11 further medical object detection tasks on public data sets for comprehensive method evaluation. Code is at https://github.com/MIC-DKFZ/nnDetection .

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

Fully automatic cardiac segmentation can be a fast and reproducible method to extract clinical measurements from an echocardiography examination. The U-Net architecture is the current state-of-the-art deep learning architecture for medical segmentation and can segment cardiac structures in real-time with average errors comparable to inter-observer variability. However, this architecture still generates large outliers that are often anatomically incorrect. This work uses the concept of graph convolutional neural networks that predict the contour points of the structures of interest instead of labeling each pixel. We propose a graph architecture that uses two convolutional rings based on cardiac anatomy and show that this eliminates anatomical incorrect multi-structure segmentations on the publicly available CAMUS dataset. Additionally, this work contributes with an ablation study on the graph convolutional architecture and an evaluation of clinical measurements on the clinical HUNT4 dataset. Finally, we propose to use the inter-model agreement of the U-Net and the graph network as a predictor of both the input and segmentation quality. We show this predictor can detect out-of-distribution and unsuitable input images in real-time. Source code is available online: https://github.com/gillesvntnu/GCN_multistructure

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

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models.

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

One of the major difficulties in medical image segmentation is the high variability of these images, which is caused by their origin (multi-centre), the acquisition protocols (multi-parametric), as well as the variability of human anatomy, the severity of the illness, the effect of age and gender, among others. The problem addressed in this work is the automatic semantic segmentation of lumbar spine Magnetic Resonance images using convolutional neural networks. The purpose is to assign a class label to each pixel of an image. Classes were defined by radiologists and correspond to different structural elements like vertebrae, intervertebral discs, nerves, blood vessels, and other tissues. The proposed network topologies are variants of the U-Net architecture. Several complementary blocks were used to define the variants: Three types of convolutional blocks, spatial attention models, deep supervision and multilevel feature extractor. This document describes the topologies and analyses the results of the neural network designs that obtained the most accurate segmentations. Several of the proposed designs outperform the standard U-Net used as baseline, especially when used in ensembles where the output of multiple neural networks is combined according to different strategies.

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.

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

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

Segment Anything Model (SAM) has gained significant attention because of its ability to segment a variety of objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we provide an extensive evaluation of SAM 2's ability to segment both 2D and 3D medical images. We collect 18 medical imaging datasets, including common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. We consider two evaluation pipelines of SAM 2: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former is only applicable to 3D modalities, while the latter applies to both 2D and 3D modalities. We learn that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc.

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.

U-Net and its variants have been widely used in medical image segmentation. However, most current U-Net variants confine their improvement strategies to building more complex encoder, while leaving the decoder unchanged or adopting a simple symmetric structure. These approaches overlook the true functionality of the decoder: receiving low-resolution feature maps from the encoder and restoring feature map resolution and lost information through upsampling. As a result, the decoder, especially its upsampling component, plays a crucial role in enhancing segmentation outcomes. However, in 3D medical image segmentation, the commonly used transposed convolution can result in visual artifacts. This issue stems from the absence of direct relationship between adjacent pixels in the output feature map. Furthermore, plain encoder has already possessed sufficient feature extraction capability because downsampling operation leads to the gradual expansion of the receptive field, but the loss of information during downsampling process is unignorable. To address the gap in relevant research, we extend our focus beyond the encoder and introduce neU-Net (i.e., not complex encoder U-Net), which incorporates a novel Sub-pixel Convolution for upsampling to construct a powerful decoder. Additionally, we introduce multi-scale wavelet inputs module on the encoder side to provide additional information. Our model design achieves excellent results, surpassing other state-of-the-art methods on both the Synapse and ACDC datasets.

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.

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

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of generalizability, and the necessity to incorporate multi-modal data effectively. A foundation model, which is a large-scale pre-trained AI model, offers a versatile base that can be adapted to a variety of specific tasks and contexts. Here, we present a novel foundation model, VISION-MAE, specifically designed for medical imaging. Specifically, VISION-MAE is trained on a dataset of 2.5 million unlabeled images from various modalities (CT, MR, PET, X-rays, and ultrasound), using self-supervised learning techniques. It is then adapted to classification and segmentation tasks using explicit labels. VISION-MAE has high label efficiency, outperforming several benchmark models in both in-domain and out-of-domain applications, and achieves high performance even with reduced availability of labeled data. This model represents a significant advancement in medical imaging AI, offering a generalizable and robust solution for improving segmentation and classification tasks while reducing the data annotation workload.

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

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

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 this study, we evaluate the performance of the Segment Anything Model (SAM) in clinical radiotherapy. Our results indicate that SAM's 'segment anything' mode can achieve clinically acceptable segmentation results in most organs-at-risk (OARs) with Dice scores higher than 0.7. SAM's 'box prompt' mode further improves the Dice scores by 0.1 to 0.5. Considering the size of the organ and the clarity of its boundary, SAM displays better performance for large organs with clear boundaries but performs worse for smaller organs with unclear boundaries. Given that SAM, a model pre-trained purely on natural images, can handle the delineation of OARs from medical images with clinically acceptable accuracy, these results highlight SAM's robust generalization capabilities with consistent accuracy in automatic segmentation for radiotherapy. In other words, SAM can achieve delineation of different OARs at different sites using a generic automatic segmentation model. SAM's generalization capabilities across different disease sites suggest that it is technically feasible to develop a generic model for automatic segmentation in radiotherapy.

Deep learning presents novel opportunities for the auto-segmentation of gross tumor volume (GTV) in head and neck cancer (HNC), yet fully automatic methods usually necessitate significant manual refinement. This study investigates the Segment Anything Model (SAM), recognized for requiring minimal human prompting and its zero-shot generalization ability across natural images. We specifically examine MedSAM, a version of SAM fine-tuned with large-scale public medical images. Despite its progress, the integration of multi-modality images (CT, PET, MRI) for effective GTV delineation remains a challenge. Focusing on SAM's application in HNC GTV segmentation, we assess its performance in both zero-shot and fine-tuned scenarios using single (CT-only) and fused multi-modality images. Our study demonstrates that fine-tuning SAM significantly enhances its segmentation accuracy, building upon the already effective zero-shot results achieved with bounding box prompts. These findings open a promising avenue for semi-automatic HNC GTV segmentation.

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

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.

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

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

Collective insights from a group of experts have always proven to outperform an individual's best diagnostic for clinical tasks. For the task of medical image segmentation, existing research on AI-based alternatives focuses more on developing models that can imitate the best individual rather than harnessing the power of expert groups. In this paper, we introduce a single diffusion model-based approach that produces multiple plausible outputs by learning a distribution over group insights. Our proposed model generates a distribution of segmentation masks by leveraging the inherent stochastic sampling process of diffusion using only minimal additional learning. We demonstrate on three different medical image modalities- CT, ultrasound, and MRI that our model is capable of producing several possible variants while capturing the frequencies of their occurrences. Comprehensive results show that our proposed approach outperforms existing state-of-the-art ambiguous segmentation networks in terms of accuracy while preserving naturally occurring variation. We also propose a new metric to evaluate the diversity as well as the accuracy of segmentation predictions that aligns with the interest of clinical practice of collective insights.

Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited kernel size of convolution layers in FCNNs, their performance of modeling long-range information is sub-optimal, and this can lead to deficiencies in the segmentation of tumors with variable sizes. On the other hand, transformer models have demonstrated excellent capabilities in capturing such long-range information in multiple domains, including natural language processing and computer vision. Inspired by the success of vision transformers and their variants, we propose a novel segmentation model termed Swin UNEt TRansformers (Swin UNETR). Specifically, the task of 3D brain tumor semantic segmentation is reformulated as a sequence to sequence prediction problem wherein multi-modal input data is projected into a 1D sequence of embedding and used as an input to a hierarchical Swin transformer as the encoder. The swin transformer encoder extracts features at five different resolutions by utilizing shifted windows for computing self-attention and is connected to an FCNN-based decoder at each resolution via skip connections. We have participated in BraTS 2021 segmentation challenge, and our proposed model ranks among the top-performing approaches in the validation phase. Code: https://monai.io/research/swin-unetr

The retroperitoneum hosts a variety of tumors, including rare benign and malignant types, which pose diagnostic and treatment challenges due to their infrequency and proximity to vital structures. Estimating tumor volume is difficult due to their irregular shapes, and manual segmentation is time-consuming. Automatic segmentation using U-Net and its variants, incorporating Vision Transformer (ViT) elements, has shown promising results but struggles with high computational demands. To address this, architectures like the Mamba State Space Model (SSM) and Extended Long-Short Term Memory (xLSTM) offer efficient solutions by handling long-range dependencies with lower resource consumption. This study evaluates U-Net enhancements, including CNN, ViT, Mamba, and xLSTM, on a new in-house CT dataset and a public organ segmentation dataset. The proposed ViLU-Net model integrates Vi-blocks for improved segmentation. Results highlight xLSTM's efficiency in the U-Net framework. The code is publicly accessible on GitHub.

Several unsupervised image segmentation approaches have been proposed which eliminate the need for dense manually-annotated segmentation masks; current models separately handle either semantic segmentation (e.g., STEGO) or class-agnostic instance segmentation (e.g., CutLER), but not both (i.e., panoptic segmentation). We propose an Unsupervised Universal Segmentation model (U2Seg) adept at performing various image segmentation tasks -- instance, semantic and panoptic -- using a novel unified framework. U2Seg generates pseudo semantic labels for these segmentation tasks via leveraging self-supervised models followed by clustering; each cluster represents different semantic and/or instance membership of pixels. We then self-train the model on these pseudo semantic labels, yielding substantial performance gains over specialized methods tailored to each task: a +2.6 AP^{box} boost vs. CutLER in unsupervised instance segmentation on COCO and a +7.0 PixelAcc increase (vs. STEGO) in unsupervised semantic segmentation on COCOStuff. Moreover, our method sets up a new baseline for unsupervised panoptic segmentation, which has not been previously explored. U2Seg is also a strong pretrained model for few-shot segmentation, surpassing CutLER by +5.0 AP^{mask} when trained on a low-data regime, e.g., only 1% COCO labels. We hope our simple yet effective method can inspire more research on unsupervised universal image segmentation.

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

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

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

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

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

Deep learning-based segmentation of the liver and hepatic lesions therein steadily gains relevance in clinical practice due to the increasing incidence of liver cancer each year. Whereas various network variants with overall promising results in the field of medical image segmentation have been successfully developed over the last years, almost all of them struggle with the challenge of accurately segmenting hepatic lesions in magnetic resonance imaging (MRI). This led to the idea of combining elements of convolutional and transformer-based architectures to overcome the existing limitations. This work presents a hybrid network called SWTR-Unet, consisting of a pretrained ResNet, transformer blocks as well as a common Unet-style decoder path. This network was primarily applied to single-modality non-contrast-enhanced liver MRI and additionally to the publicly available computed tomography (CT) data of the liver tumor segmentation (LiTS) challenge to verify the applicability on other modalities. For a broader evaluation, multiple state-of-the-art networks were implemented and applied, ensuring a direct comparability. Furthermore, correlation analysis and an ablation study were carried out, to investigate various influencing factors on the segmentation accuracy of the presented method. With Dice scores of averaged 98+-2% for liver and 81+-28% lesion segmentation on the MRI dataset and 97+-2% and 79+-25%, respectively on the CT dataset, the proposed SWTR-Unet proved to be a precise approach for liver and hepatic lesion segmentation with state-of-the-art results for MRI and competing accuracy in CT imaging. The achieved segmentation accuracy was found to be on par with manually performed expert segmentations as indicated by inter-observer variabilities for liver lesion segmentation. In conclusion, the presented method could save valuable time and resources in clinical practice.

Coronary microvascular disease constitutes a substantial risk to human health. Employing computer-aided analysis and diagnostic systems, medical professionals can intervene early in disease progression, with 3D vessel segmentation serving as a crucial component. Nevertheless, conventional U-Net architectures tend to yield incoherent and imprecise segmentation outcomes, particularly for small vessel structures. While models with attention mechanisms, such as Transformers and large convolutional kernels, demonstrate superior performance, their extensive computational demands during training and inference lead to increased time complexity. In this study, we leverage Fourier domain learning as a substitute for multi-scale convolutional kernels in 3D hierarchical segmentation models, which can reduce computational expenses while preserving global receptive fields within the network. Furthermore, a zero-parameter frequency domain fusion method is designed to improve the skip connections in U-Net architecture. Experimental results on a public dataset and an in-house dataset indicate that our novel Fourier transformation-based network achieves remarkable dice performance (84.37\% on ASACA500 and 80.32\% on ImageCAS) in tubular vessel segmentation tasks and substantially reduces computational requirements without compromising global receptive fields.

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.

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

Echocardiogram video segmentation plays an important role in cardiac disease diagnosis. This paper studies the unsupervised domain adaption (UDA) for echocardiogram video segmentation, where the goal is to generalize the model trained on the source domain to other unlabelled target domains. Existing UDA segmentation methods are not suitable for this task because they do not model local information and the cyclical consistency of heartbeat. In this paper, we introduce a newly collected CardiacUDA dataset and a novel GraphEcho method for cardiac structure segmentation. Our GraphEcho comprises two innovative modules, the Spatial-wise Cross-domain Graph Matching (SCGM) and the Temporal Cycle Consistency (TCC) module, which utilize prior knowledge of echocardiogram videos, i.e., consistent cardiac structure across patients and centers and the heartbeat cyclical consistency, respectively. These two modules can better align global and local features from source and target domains, improving UDA segmentation results. Experimental results showed that our GraphEcho outperforms existing state-of-the-art UDA segmentation methods. Our collected dataset and code will be publicly released upon acceptance. This work will lay a new and solid cornerstone for cardiac structure segmentation from echocardiogram videos. Code and dataset are available at: https://github.com/xmed-lab/GraphEcho

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.

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.

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

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

Melanoma is caused by the abnormal growth of melanocytes in human skin. Like other cancers, this life-threatening skin cancer can be treated with early diagnosis. To support a diagnosis by automatic skin lesion segmentation, several Fully Convolutional Network (FCN) approaches, specifically the U-Net architecture, have been proposed. The U-Net model with a symmetrical architecture has exhibited superior performance in the segmentation task. However, the locality restriction of the convolutional operation incorporated in the U-Net architecture limits its performance in capturing long-range dependency, which is crucial for the segmentation task in medical images. To address this limitation, recently a Transformer based U-Net architecture that replaces the CNN blocks with the Swin Transformer module has been proposed to capture both local and global representation. In this paper, we propose Att-SwinU-Net, an attention-based Swin U-Net extension, for medical image segmentation. In our design, we seek to enhance the feature re-usability of the network by carefully designing the skip connection path. We argue that the classical concatenation operation utilized in the skip connection path can be further improved by incorporating an attention mechanism. By performing a comprehensive ablation study on several skin lesion segmentation datasets, we demonstrate the effectiveness of our proposed attention mechanism.

Melanoma is a dangerous form of skin cancer caused by the abnormal growth of skin cells. Fully Convolutional Network (FCN) approaches, including the U-Net architecture, can automatically segment skin lesions to aid diagnosis. The symmetrical U-Net model has shown outstanding results, but its use of a convolutional operation limits its ability to capture long-range dependencies, which are essential for accurate medical image segmentation. In addition, the U-shaped structure suffers from the semantic gaps between the encoder and decoder. In this study, we developed and evaluated a U-shaped hierarchical Transformer-based structure for skin lesion segmentation while we proposed an Inter-scale Context Fusion (ISCF) to utilize the attention correlations in each stage of the encoder to adaptively combine the contexts coming from each stage to hinder the semantic gaps. The preliminary results of the skin lesion segmentation benchmark endorse the applicability and efficacy of the ISCF module.

The emergence of large models, also known as foundation models, has brought significant advancements to AI research. One such model is Segment Anything (SAM), which is designed for image segmentation tasks. However, as with other foundation models, our experimental findings suggest that SAM may fail or perform poorly in certain segmentation tasks, such as shadow detection and camouflaged object detection (concealed object detection). This study first paves the way for applying the large pre-trained image segmentation model SAM to these downstream tasks, even in situations where SAM performs poorly. Rather than fine-tuning the SAM network, we propose SAM-Adapter, which incorporates domain-specific information or visual prompts into the segmentation network by using simple yet effective adapters. By integrating task-specific knowledge with general knowledge learnt by the large model, SAM-Adapter can significantly elevate the performance of SAM in challenging tasks as shown in extensive experiments. We can even outperform task-specific network models and achieve state-of-the-art performance in the task we tested: camouflaged object detection, shadow detection. We also tested polyp segmentation (medical image segmentation) and achieves better results. We believe our work opens up opportunities for utilizing SAM in downstream tasks, with potential applications in various fields, including medical image processing, agriculture, remote sensing, and more.

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

We introduce the Segment Anything (SA) project: a new task, model, and dataset for image segmentation. Using our efficient model in a data collection loop, we built the largest segmentation dataset to date (by far), with over 1 billion masks on 11M licensed and privacy respecting images. The model is designed and trained to be promptable, so it can transfer zero-shot to new image distributions and tasks. We evaluate its capabilities on numerous tasks and find that its zero-shot performance is impressive -- often competitive with or even superior to prior fully supervised results. We are releasing the Segment Anything Model (SAM) and corresponding dataset (SA-1B) of 1B masks and 11M images at https://segment-anything.com to foster research into foundation models for computer vision.

Semantic segmentation is one of the most popular research areas in medical image computing. Perhaps surprisingly, despite its conceptualization dating back to 2018, nnU-Net continues to provide competitive out-of-the-box solutions for a broad variety of segmentation problems and is regularly used as a development framework for challenge-winning algorithms. Here we use nnU-Net to participate in the AMOS2022 challenge, which comes with a unique set of tasks: not only is the dataset one of the largest ever created and boasts 15 target structures, but the competition also requires submitted solutions to handle both MRI and CT scans. Through careful modification of nnU-net's hyperparameters, the addition of residual connections in the encoder and the design of a custom postprocessing strategy, we were able to substantially improve upon the nnU-Net baseline. Our final ensemble achieves Dice scores of 90.13 for Task 1 (CT) and 89.06 for Task 2 (CT+MRI) in a 5-fold cross-validation on the provided training cases.

Despite increasing efforts on universal representations for visual recognition, few have addressed object detection. In this paper, we develop an effective and efficient universal object detection system that is capable of working on various image domains, from human faces and traffic signs to medical CT images. Unlike multi-domain models, this universal model does not require prior knowledge of the domain of interest. This is achieved by the introduction of a new family of adaptation layers, based on the principles of squeeze and excitation, and a new domain-attention mechanism. In the proposed universal detector, all parameters and computations are shared across domains, and a single network processes all domains all the time. Experiments, on a newly established universal object detection benchmark of 11 diverse datasets, show that the proposed detector outperforms a bank of individual detectors, a multi-domain detector, and a baseline universal detector, with a 1.3x parameter increase over a single-domain baseline detector. The code and benchmark will be released at http://www.svcl.ucsd.edu/projects/universal-detection/.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

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.

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

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

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.

Recent advances in Vision Transformers (ViTs) have significantly enhanced medical image segmentation by facilitating the learning of global relationships. However, these methods face a notable challenge in capturing diverse local and global long-range sequential feature representations, particularly evident in whole-body CT (WBCT) scans. To overcome this limitation, we introduce Swin Soft Mixture Transformer (Swin SMT), a novel architecture based on Swin UNETR. This model incorporates a Soft Mixture-of-Experts (Soft MoE) to effectively handle complex and diverse long-range dependencies. The use of Soft MoE allows for scaling up model parameters maintaining a balance between computational complexity and segmentation performance in both training and inference modes. We evaluate Swin SMT on the publicly available TotalSegmentator-V2 dataset, which includes 117 major anatomical structures in WBCT images. Comprehensive experimental results demonstrate that Swin SMT outperforms several state-of-the-art methods in 3D anatomical structure segmentation, achieving an average Dice Similarity Coefficient of 85.09%. The code and pre-trained weights of Swin SMT are publicly available at https://github.com/MI2DataLab/SwinSMT.

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

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

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.

The success of Deep Neural Network (DNN) models significantly depends on the quality of provided annotations. In medical image segmentation, for example, having multiple expert annotations for each data point is common to minimize subjective annotation bias. Then, the goal of estimation is to filter out the label noise and recover the ground-truth masks, which are not explicitly given. This paper proposes a probabilistic model for noisy observations that allows us to build a confident classification and segmentation models. To accomplish it, we explicitly model label noise and introduce a new information-based regularization that pushes the network to recover the ground-truth labels. In addition, for segmentation task we adjust the loss function by prioritizing learning in high-confidence regions where all the annotators agree on labeling. We evaluate the proposed method on a series of classification tasks such as noisy versions of MNIST, CIFAR-10, Fashion-MNIST datasets as well as CIFAR-10N, which is real-world dataset with noisy human annotations. Additionally, for segmentation task, we consider several medical imaging datasets, such as, LIDC and RIGA that reflect real-world inter-variability among multiple annotators. Our experiments show that our algorithm outperforms state-of-the-art solutions for the considered classification and segmentation problems.

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

Segment anything model (SAM) has shown its spectacular performance in segmenting universal objects, especially when elaborate prompts are provided. However, the drawback of SAM is twofold. On the first hand, it fails to segment specific targets, e.g., shadow images or lesions in medical images. On the other hand, manually specifying prompts is extremely time-consuming. To overcome the problems, we propose AdapterShadow, which adapts SAM model for shadow detection. To adapt SAM for shadow images, trainable adapters are inserted into the frozen image encoder of SAM, since the training of the full SAM model is both time and memory consuming. Moreover, we introduce a novel grid sampling method to generate dense point prompts, which helps to automatically segment shadows without any manual interventions. Extensive experiments are conducted on four widely used benchmark datasets to demonstrate the superior performance of our proposed method. Codes will are publicly available at https://github.com/LeipingJie/AdapterShadow.

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

Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised learning framework with tailored proxy tasks for medical image analysis. Specifically, we propose: (i) a new 3D transformer-based model, dubbed Swin UNEt TRansformers (Swin UNETR), with a hierarchical encoder for self-supervised pre-training; (ii) tailored proxy tasks for learning the underlying pattern of human anatomy. We demonstrate successful pre-training of the proposed model on 5,050 publicly available computed tomography (CT) images from various body organs. The effectiveness of our approach is validated by fine-tuning the pre-trained models on the Beyond the Cranial Vault (BTCV) Segmentation Challenge with 13 abdominal organs and segmentation tasks from the Medical Segmentation Decathlon (MSD) dataset. Our model is currently the state-of-the-art (i.e. ranked 1st) on the public test leaderboards of both MSD and BTCV datasets. Code: https://monai.io/research/swin-unetr

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

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

The Segmentation Anything Model (SAM) requires labor-intensive data labeling. We present Unsupervised SAM (UnSAM) for promptable and automatic whole-image segmentation that does not require human annotations. UnSAM utilizes a divide-and-conquer strategy to "discover" the hierarchical structure of visual scenes. We first leverage top-down clustering methods to partition an unlabeled image into instance/semantic level segments. For all pixels within a segment, a bottom-up clustering method is employed to iteratively merge them into larger groups, thereby forming a hierarchical structure. These unsupervised multi-granular masks are then utilized to supervise model training. Evaluated across seven popular datasets, UnSAM achieves competitive results with the supervised counterpart SAM, and surpasses the previous state-of-the-art in unsupervised segmentation by 11% in terms of AR. Moreover, we show that supervised SAM can also benefit from our self-supervised labels. By integrating our unsupervised pseudo masks into SA-1B's ground-truth masks and training UnSAM with only 1% of SA-1B, a lightly semi-supervised UnSAM can often segment entities overlooked by supervised SAM, exceeding SAM's AR by over 6.7% and AP by 3.9% on SA-1B.

Large Language Models (LLMs), known for their versatility in textual data, are increasingly being explored for their potential to enhance medical image segmentation, a crucial task for accurate diagnostic imaging. This study explores enhancing Vision Transformers (ViTs) for medical image segmentation by integrating pre-trained LLM transformer blocks. Our approach, which incorporates a frozen LLM transformer block into the encoder of a ViT-based model, leads to substantial improvements in segmentation performance across various medical imaging modalities. We propose a Hybrid Attention Mechanism that combines global and local feature learning with a Multi-Scale Fusion Block for aggregating features across different scales. The enhanced model shows significant performance gains, including an average Dice score increase from 0.74 to 0.79 and improvements in accuracy, precision, and the Jaccard Index. These results demonstrate the effectiveness of LLM-based transformers in refining medical image segmentation, highlighting their potential to significantly boost model accuracy and robustness. The source code and our implementation are available at: https://bit.ly/3zf2CVs

Foundation models for interactive segmentation in 2D natural images and videos have sparked significant interest in building 3D foundation models for medical imaging. However, the domain gaps and clinical use cases for 3D medical imaging require a dedicated model that diverges from existing 2D solutions. Specifically, such foundation models should support a full workflow that can actually reduce human effort. Treating 3D medical images as sequences of 2D slices and reusing interactive 2D foundation models seems straightforward, but 2D annotation is too time-consuming for 3D tasks. Moreover, for large cohort analysis, it's the highly accurate automatic segmentation models that reduce the most human effort. However, these models lack support for interactive corrections and lack zero-shot ability for novel structures, which is a key feature of "foundation". While reusing pre-trained 2D backbones in 3D enhances zero-shot potential, their performance on complex 3D structures still lags behind leading 3D models. To address these issues, we present VISTA3D, Versatile Imaging SegmenTation and Annotation model, that targets to solve all these challenges and requirements with one unified foundation model. VISTA3D is built on top of the well-established 3D segmentation pipeline, and it is the first model to achieve state-of-the-art performance in both 3D automatic (supporting 127 classes) and 3D interactive segmentation, even when compared with top 3D expert models on large and diverse benchmarks. Additionally, VISTA3D's 3D interactive design allows efficient human correction, and a novel 3D supervoxel method that distills 2D pretrained backbones grants VISTA3D top 3D zero-shot performance. We believe the model, recipe, and insights represent a promising step towards a clinically useful 3D foundation model. Code and weights are publicly available at https://github.com/Project-MONAI/VISTA.

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.

The reference-based object segmentation tasks, namely referring image segmentation (RIS), few-shot image segmentation (FSS), referring video object segmentation (RVOS), and video object segmentation (VOS), aim to segment a specific object by utilizing either language or annotated masks as references. Despite significant progress in each respective field, current methods are task-specifically designed and developed in different directions, which hinders the activation of multi-task capabilities for these tasks. In this work, we end the current fragmented situation and propose UniRef++ to unify the four reference-based object segmentation tasks with a single architecture. At the heart of our approach is the proposed UniFusion module which performs multiway-fusion for handling different tasks with respect to their specified references. And a unified Transformer architecture is then adopted for achieving instance-level segmentation. With the unified designs, UniRef++ can be jointly trained on a broad range of benchmarks and can flexibly complete multiple tasks at run-time by specifying the corresponding references. We evaluate our unified models on various benchmarks. Extensive experimental results indicate that our proposed UniRef++ achieves state-of-the-art performance on RIS and RVOS, and performs competitively on FSS and VOS with a parameter-shared network. Moreover, we showcase that the proposed UniFusion module could be easily incorporated into the current advanced foundation model SAM and obtain satisfactory results with parameter-efficient finetuning. Codes and models are available at https://github.com/FoundationVision/UniRef.

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.

The recent Segment Anything Model (SAM) 2 has demonstrated remarkable foundational competence in semantic segmentation, with its memory mechanism and mask decoder further addressing challenges in video tracking and object occlusion, thereby achieving superior results in interactive segmentation for both images and videos. Building upon our previous empirical studies, we further explore the zero-shot segmentation performance of SAM 2 in robot-assisted surgery based on prompts, alongside its robustness against real-world corruption. For static images, we employ two forms of prompts: 1-point and bounding box, while for video sequences, the 1-point prompt is applied to the initial frame. Through extensive experimentation on the MICCAI EndoVis 2017 and EndoVis 2018 benchmarks, SAM 2, when utilizing bounding box prompts, outperforms state-of-the-art (SOTA) methods in comparative evaluations. The results with point prompts also exhibit a substantial enhancement over SAM's capabilities, nearing or even surpassing existing unprompted SOTA methodologies. Besides, SAM 2 demonstrates improved inference speed and less performance degradation against various image corruption. Although slightly unsatisfactory results remain in specific edges or regions, SAM 2's robust adaptability to 1-point prompts underscores its potential for downstream surgical tasks with limited prompt requirements.

Surgical video segmentation is a critical task in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, the Segment Anything Model 2 (SAM2) framework has shown superior advancements in image and video segmentation. However, SAM2 struggles with efficiency due to the high computational demands of processing high-resolution images and complex and long-range temporal dynamics in surgical videos. To address these challenges, we introduce Surgical SAM 2 (SurgSAM-2), an advanced model to utilize SAM2 with an Efficient Frame Pruning (EFP) mechanism, to facilitate real-time surgical video segmentation. The EFP mechanism dynamically manages the memory bank by selectively retaining only the most informative frames, reducing memory usage and computational cost while maintaining high segmentation accuracy. Our extensive experiments demonstrate that SurgSAM-2 significantly improves both efficiency and segmentation accuracy compared to the vanilla SAM2. Remarkably, SurgSAM-2 achieves a 3times FPS compared with SAM2, while also delivering state-of-the-art performance after fine-tuning with lower-resolution data. These advancements establish SurgSAM-2 as a leading model for surgical video analysis, making real-time surgical video segmentation in resource-constrained environments a feasible reality.

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.

We propose an adaptive training scheme for unsupervised medical image registration. Existing methods rely on image reconstruction as the primary supervision signal. However, nuisance variables (e.g. noise and covisibility), violation of the Lambertian assumption in physical waves (e.g. ultrasound), and inconsistent image acquisition can all cause a loss of correspondence between medical images. As the unsupervised learning scheme relies on intensity constancy between images to establish correspondence for reconstruction, this introduces spurious error residuals that are not modeled by the typical training objective. To mitigate this, we propose an adaptive framework that re-weights the error residuals with a correspondence scoring map during training, preventing the parametric displacement estimator from drifting away due to noisy gradients, which leads to performance degradation. To illustrate the versatility and effectiveness of our method, we tested our framework on three representative registration architectures across three medical image datasets along with other baselines. Our adaptive framework consistently outperforms other methods both quantitatively and qualitatively. Paired t-tests show that our improvements are statistically significant. Code available at: https://voldemort108x.github.io/AdaCS/.

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

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.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

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

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

Accurate localization and segmentation of intervertebral disc (IVD) is crucial for the assessment of spine disease diagnosis. Despite the technological advances in medical imaging, IVD localization and segmentation are still manually performed, which is time-consuming and prone to errors. If, in addition, multi-modal imaging is considered, the burden imposed on disease assessments increases substantially. In this paper, we propose an architecture for IVD localization and segmentation in multi-modal MRI, which extends the well-known UNet. Compared to single images, multi-modal data brings complementary information, contributing to better data representation and discriminative power. Our contributions are three-fold. First, how to effectively integrate and fully leverage multi-modal data remains almost unexplored. In this work, each MRI modality is processed in a different path to better exploit their unique information. Second, inspired by HyperDenseNet, the network is densely-connected both within each path and across different paths, granting the model the freedom to learn where and how the different modalities should be processed and combined. Third, we improved standard U-Net modules by extending inception modules with two dilated convolutions blocks of different scale, which helps handling multi-scale context. We report experiments over the data set of the public MICCAI 2018 Challenge on Automatic Intervertebral Disc Localization and Segmentation, with 13 multi-modal MRI images used for training and 3 for validation. We trained IVD-Net on an NVidia TITAN XP GPU with 16 GBs RAM, using ADAM as optimizer and a learning rate of 10e-5 during 200 epochs. Training took about 5 hours, and segmentation of a whole volume about 2-3 seconds, on average. Several baselines, with different multi-modal fusion strategies, were used to demonstrate the effectiveness of the proposed architecture.

Interactive image segmentation enables annotators to efficiently perform pixel-level annotation for segmentation tasks. However, the existing interactive segmentation pipeline suffers from inefficient computations of interactive models because of the following two issues. First, annotators' later click is based on models' feedback of annotators' former click. This serial interaction is unable to utilize model's parallelism capabilities. Second, in each interaction step, the model handles the invariant image along with the sparse variable clicks, resulting in a process that's highly repetitive and redundant. For efficient computations, we propose a method named InterFormer that follows a new pipeline to address these issues. InterFormer extracts and preprocesses the computationally time-consuming part i.e. image processing from the existing process. Specifically, InterFormer employs a large vision transformer (ViT) on high-performance devices to preprocess images in parallel, and then uses a lightweight module called interactive multi-head self attention (I-MSA) for interactive segmentation. Furthermore, the I-MSA module's deployment on low-power devices extends the practical application of interactive segmentation. The I-MSA module utilizes the preprocessed features to efficiently response to the annotator inputs in real-time. The experiments on several datasets demonstrate the effectiveness of InterFormer, which outperforms previous interactive segmentation models in terms of computational efficiency and segmentation quality, achieve real-time high-quality interactive segmentation on CPU-only devices. The code is available at https://github.com/YouHuang67/InterFormer.

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

Collecting large-scale medical datasets with fully annotated samples for training of deep networks is prohibitively expensive, especially for 3D volume data. Recent breakthroughs in self-supervised learning (SSL) offer the ability to overcome the lack of labeled training samples by learning feature representations from unlabeled data. However, most current SSL techniques in the medical field have been designed for either 2D images or 3D volumes. In practice, this restricts the capability to fully leverage unlabeled data from numerous sources, which may include both 2D and 3D data. Additionally, the use of these pre-trained networks is constrained to downstream tasks with compatible data dimensions. In this paper, we propose a novel framework for unsupervised joint learning on 2D and 3D data modalities. Given a set of 2D images or 2D slices extracted from 3D volumes, we construct an SSL task based on a 2D contrastive clustering problem for distinct classes. The 3D volumes are exploited by computing vectored embedding at each slice and then assembling a holistic feature through deformable self-attention mechanisms in Transformer, allowing incorporating long-range dependencies between slices inside 3D volumes. These holistic features are further utilized to define a novel 3D clustering agreement-based SSL task and masking embedding prediction inspired by pre-trained language models. Experiments on downstream tasks, such as 3D brain segmentation, lung nodule detection, 3D heart structures segmentation, and abnormal chest X-ray detection, demonstrate the effectiveness of our joint 2D and 3D SSL approach. We improve plain 2D Deep-ClusterV2 and SwAV by a significant margin and also surpass various modern 2D and 3D SSL approaches.

Although the preservation of shape continuity and physiological anatomy is a natural assumption in the segmentation of medical images, it is often neglected by deep learning methods that mostly aim for the statistical modeling of input data as pixels rather than interconnected structures. In biological structures, however, organs are not separate entities; for example, in reality, a severed vessel is an indication of an underlying problem, but traditional segmentation models are not designed to strictly enforce the continuity of anatomy, potentially leading to inaccurate medical diagnoses. To address this issue, we propose a graph-based approach that enforces the continuity and connectivity of anatomical topology in medical images. Our method encodes the continuity of shapes as a graph constraint, ensuring that the network's predictions maintain this continuity. We evaluate our method on two public benchmarks on retinal vessel segmentation, showing significant improvements in connectivity metrics compared to traditional methods while getting better or on-par performance on segmentation metrics.

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

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

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.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.