Daily Papers

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

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

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

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://medicaldecathlon.com/. In addition, both data and online evaluation are accessible via www.lits-challenge.com.

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

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

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.

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.

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

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

The non-invasive assessment of increasingly incidentally discovered renal masses is a critical challenge in urologic oncology, where diagnostic uncertainty frequently leads to the overtreatment of benign or indolent tumors. In this study, we developed and validated RenalCLIP using a dataset of 27,866 CT scans from 8,809 patients across nine Chinese medical centers and the public TCIA cohort, a visual-language foundation model for characterization, diagnosis and prognosis of renal mass. The model was developed via a two-stage pre-training strategy that first enhances the image and text encoders with domain-specific knowledge before aligning them through a contrastive learning objective, to create robust representations for superior generalization and diagnostic precision. RenalCLIP achieved better performance and superior generalizability across 10 core tasks spanning the full clinical workflow of kidney cancer, including anatomical assessment, diagnostic classification, and survival prediction, compared with other state-of-the-art general-purpose CT foundation models. Especially, for complicated task like recurrence-free survival prediction in the TCIA cohort, RenalCLIP achieved a C-index of 0.726, representing a substantial improvement of approximately 20% over the leading baselines. Furthermore, RenalCLIP's pre-training imparted remarkable data efficiency; in the diagnostic classification task, it only needs 20% training data to achieve the peak performance of all baseline models even after they were fully fine-tuned on 100% of the data. Additionally, it achieved superior performance in report generation, image-text retrieval and zero-shot diagnosis tasks. Our findings establish that RenalCLIP provides a robust tool with the potential to enhance diagnostic accuracy, refine prognostic stratification, and personalize the management of patients with kidney cancer.

Recently, bladder cancer has been significantly increased in terms of incidence and mortality. Currently, two subtypes are known based on tumour growth: non-muscle invasive (NMIBC) and muscle-invasive bladder cancer (MIBC). In this work, we focus on the MIBC subtype because it is of the worst prognosis and can spread to adjacent organs. We present a self-learning framework to grade bladder cancer from histological images stained via immunohistochemical techniques. Specifically, we propose a novel Deep Convolutional Embedded Attention Clustering (DCEAC) which allows classifying histological patches into different severity levels of the disease, according to the patterns established in the literature. The proposed DCEAC model follows a two-step fully unsupervised learning methodology to discern between non-tumour, mild and infiltrative patterns from high-resolution samples of 512x512 pixels. Our system outperforms previous clustering-based methods by including a convolutional attention module, which allows refining the features of the latent space before the classification stage. The proposed network exceeds state-of-the-art approaches by 2-3% across different metrics, achieving a final average accuracy of 0.9034 in a multi-class scenario. Furthermore, the reported class activation maps evidence that our model is able to learn by itself the same patterns that clinicians consider relevant, without incurring prior annotation steps. This fact supposes a breakthrough in muscle-invasive bladder cancer grading which bridges the gap with respect to train the model on labelled data.

Pan-cancer screening in large-scale CT scans remains challenging for existing AI methods, primarily due to the difficulty of localizing diverse types of tiny lesions in large CT volumes. The extreme foreground-background imbalance significantly hinders models from focusing on diseased regions, while redundant focus on healthy regions not only decreases the efficiency but also increases false positives. Inspired by radiologists' glance and focus diagnostic strategy, we introduce GF-Screen, a Glance and Focus reinforcement learning framework for pan-cancer screening. GF-Screen employs a Glance model to localize the diseased regions and a Focus model to precisely segment the lesions, where segmentation results of the Focus model are leveraged to reward the Glance model via Reinforcement Learning (RL). Specifically, the Glance model crops a group of sub-volumes from the entire CT volume and learns to select the sub-volumes with lesions for the Focus model to segment. Given that the selecting operation is non-differentiable for segmentation training, we propose to employ the segmentation results to reward the Glance model. To optimize the Glance model, we introduce a novel group relative learning paradigm, which employs group relative comparison to prioritize high-advantage predictions and discard low-advantage predictions within sub-volume groups, not only improving efficiency but also reducing false positives. In this way, for the first time, we effectively extend cutting-edge RL techniques to tackle the specific challenges in pan-cancer screening. Extensive experiments on 16 internal and 7 external datasets across 9 lesion types demonstrated the effectiveness of GF-Screen. Notably, GF-Screen leads the public validation leaderboard of MICCAI FLARE25 pan-cancer challenge, surpassing the FLARE24 champion solution by a large margin (+25.6% DSC and +28.2% NSD).

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.

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.

Clinical monitoring of metastatic disease to the brain can be a laborious and time-consuming process, especially in cases involving multiple metastases when the assessment is performed manually. The Response Assessment in Neuro-Oncology Brain Metastases (RANO-BM) guideline, which utilizes the unidimensional longest diameter, is commonly used in clinical and research settings to evaluate response to therapy in patients with brain metastases. However, accurate volumetric assessment of the lesion and surrounding peri-lesional edema holds significant importance in clinical decision-making and can greatly enhance outcome prediction. The unique challenge in performing segmentations of brain metastases lies in their common occurrence as small lesions. Detection and segmentation of lesions that are smaller than 10 mm in size has not demonstrated high accuracy in prior publications. The brain metastases challenge sets itself apart from previously conducted MICCAI challenges on glioma segmentation due to the significant variability in lesion size. Unlike gliomas, which tend to be larger on presentation scans, brain metastases exhibit a wide range of sizes and tend to include small lesions. We hope that the BraTS-METS dataset and challenge will advance the field of automated brain metastasis detection and segmentation.

We demonstrate that AI models can accurately segment liver tumors without the need for manual annotation by using synthetic tumors in CT scans. Our synthetic tumors have two intriguing advantages: (I) realistic in shape and texture, which even medical professionals can confuse with real tumors; (II) effective for training AI models, which can perform liver tumor segmentation similarly to the model trained on real tumors -- this result is exciting because no existing work, using synthetic tumors only, has thus far reached a similar or even close performance to real tumors. This result also implies that manual efforts for annotating tumors voxel by voxel (which took years to create) can be significantly reduced in the future. Moreover, our synthetic tumors can automatically generate many examples of small (or even tiny) synthetic tumors and have the potential to improve the success rate of detecting small liver tumors, which is critical for detecting the early stages of cancer. In addition to enriching the training data, our synthesizing strategy also enables us to rigorously assess the AI robustness.

Pancreatic ductal adenocarcinoma (PDAC) segmentation on contrast-enhanced CT is inherently ambiguous: inter-rater disagreement among experts reflects genuine uncertainty rather than annotation noise. Standard deep learning approaches assume a single ground truth, producing probabilistic outputs that can be poorly calibrated and difficult to interpret under such ambiguity. We present TwinTrack, a framework that addresses this gap through post-hoc calibration of ensemble segmentation probabilities to the empirical mean human response (MHR) -the fraction of expert annotators labeling a voxel as tumor. Calibrated probabilities are thus directly interpretable as the expected proportion of annotators assigning the tumor label, explicitly modeling inter-rater disagreement. The proposed post-hoc calibration procedure is simple and requires only a small multi-rater calibration set. It consistently improves calibration metrics over standard approaches when evaluated on the MICCAI 2025 CURVAS-PDACVI multi-rater benchmark.

Precise delineation of meningiomas is crucial for effective radiotherapy (RT) planning, directly influencing treatment efficacy and preservation of adjacent healthy tissues. While automated deep learning approaches have demonstrated considerable potential, achieving consistently accurate clinical segmentation remains challenging due to tumor heterogeneity. Interactive Medical Image Segmentation (IMIS) addresses this challenge by integrating advanced AI techniques with clinical input. However, generic segmentation tools, despite widespread applicability, often lack the specificity required for clinically critical and disease-specific tasks like meningioma RT planning. To overcome these limitations, we introduce Interactive-MEN-RT, a dedicated IMIS tool specifically developed for clinician-assisted 3D meningioma segmentation in RT workflows. The system incorporates multiple clinically relevant interaction methods, including point annotations, bounding boxes, lasso tools, and scribbles, enhancing usability and clinical precision. In our evaluation involving 500 contrast-enhanced T1-weighted MRI scans from the BraTS 2025 Meningioma RT Segmentation Challenge, Interactive-MEN-RT demonstrated substantial improvement compared to other segmentation methods, achieving Dice similarity coefficients of up to 77.6\% and Intersection over Union scores of 64.8\%. These results emphasize the need for clinically tailored segmentation solutions in critical applications such as meningioma RT planning. The code is publicly available at: https://github.com/snuh-rad-aicon/Interactive-MEN-RT

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.

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

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.

Several Deep Learning (DL) methods have recently been proposed for an automated identification of kidney stones during an ureteroscopy to enable rapid therapeutic decisions. Even if these DL approaches led to promising results, they are mainly appropriate for kidney stone types for which numerous labelled data are available. However, only few labelled images are available for some rare kidney stone types. This contribution exploits Deep Metric Learning (DML) methods i) to handle such classes with few samples, ii) to generalize well to out of distribution samples, and iii) to cope better with new classes which are added to the database. The proposed Guided Deep Metric Learning approach is based on a novel architecture which was designed to learn data representations in an improved way. The solution was inspired by Few-Shot Learning (FSL) and makes use of a teacher-student approach. The teacher model (GEMINI) generates a reduced hypothesis space based on prior knowledge from the labeled data, and is used it as a guide to a student model (i.e., ResNet50) through a Knowledge Distillation scheme. Extensive tests were first performed on two datasets separately used for the recognition, namely a set of images acquired for the surfaces of the kidney stone fragments, and a set of images of the fragment sections. The proposed DML-approach improved the identification accuracy by 10% and 12% in comparison to DL-methods and other DML-approaches, respectively. Moreover, model embeddings from the two dataset types were merged in an organized way through a multi-view scheme to simultaneously exploit the information of surface and section fragments. Test with the resulting mixed model improves the identification accuracy by at least 3% and up to 30% with respect to DL-models and shallow machine learning methods, respectively.

The ODELIA Breast MRI Challenge 2025 addresses a critical issue in breast cancer screening: improving early detection through more efficient and accurate interpretation of breast MRI scans. Even though methods for general-purpose whole-body lesion segmentation as well as multi-time-point analysis exist, breast cancer detection remains highly challenging, largely due to the limited availability of high-quality segmentation labels. Therefore, developing robust classification-based approaches is crucial for the future of early breast cancer detection, particularly in applications such as large-scale screening. In this write-up, we provide a comprehensive overview of our approach to the challenge. We begin by detailing the underlying concept and foundational assumptions that guided our work. We then describe the iterative development process, highlighting the key stages of experimentation, evaluation, and refinement that shaped the evolution of our solution. Finally, we present the reasoning and evidence that informed the design choices behind our final submission, with a focus on performance, robustness, and clinical relevance. We release our full implementation publicly at https://github.com/MIC-DKFZ/MeisenMeister

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

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

One of the primary challenges in brain tumor segmentation arises from the uncertainty of voxels close to tumor boundaries. However, the conventional process of generating ground truth segmentation masks fails to treat such uncertainties properly. Those "hard labels" with 0s and 1s conceptually influenced the majority of prior studies on brain image segmentation. As a result, tumor segmentation is often solved through voxel classification. In this work, we instead view this problem as a voxel-level regression, where the ground truth represents a certainty mapping from any pixel to the border of the tumor. We propose a novel ground truth label transformation, which is based on a signed geodesic transform, to capture the uncertainty in brain tumors' vicinity. We combine this idea with a Focal-like regression L1-loss that enables effective regression learning in high-dimensional output space by appropriately weighting voxels according to their difficulty. We thoroughly conduct an experimental evaluation to validate the components of our proposed method, compare it to a diverse array of state-of-the-art segmentation models, and show that it is architecture-agnostic. The code of our method is made publicly available (https://github.com/Oulu-IMEDS/SiNGR/).

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.

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.

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.

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

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

Accurate tumor size measurement is a cornerstone of evaluating cancer treatment response. The most widely adopted standard for this purpose is the Response Evaluation Criteria in Solid Tumors (RECIST) v1.1, which relies on measuring the longest tumor diameter in a single plane. However, volumetric measurements have been shown to provide a more reliable assessment of treatment effect. Their clinical adoption has been limited, though, due to the labor-intensive nature of manual volumetric annotation. In this paper, we present Lite ENSAM, a lightweight adaptation of the ENSAM architecture designed for efficient volumetric tumor segmentation from CT scans annotated with RECIST annotations. Lite ENSAM was submitted to the MICCAI FLARE 2025 Task 1: Pan-cancer Segmentation in CT Scans, Subtask 2, where it achieved a Dice Similarity Coefficient (DSC) of 60.7% and a Normalized Surface Dice (NSD) of 63.6% on the hidden test set, and an average total RAM time of 50.6 GBs and an average inference time of 14.4 s on CPU on the public validation dataset.

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

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.

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.

Medical image and video segmentation is a critical task for precision medicine, which has witnessed considerable progress in developing task or modality-specific and generalist models for 2D images. However, there have been limited studies on building general-purpose models for 3D images and videos with comprehensive user studies. Here, we present MedSAM2, a promptable segmentation foundation model for 3D image and video segmentation. The model is developed by fine-tuning the Segment Anything Model 2 on a large medical dataset with over 455,000 3D image-mask pairs and 76,000 frames, outperforming previous models across a wide range of organs, lesions, and imaging modalities. Furthermore, we implement a human-in-the-loop pipeline to facilitate the creation of large-scale datasets resulting in, to the best of our knowledge, the most extensive user study to date, involving the annotation of 5,000 CT lesions, 3,984 liver MRI lesions, and 251,550 echocardiogram video frames, demonstrating that MedSAM2 can reduce manual costs by more than 85%. MedSAM2 is also integrated into widely used platforms with user-friendly interfaces for local and cloud deployment, making it a practical tool for supporting efficient, scalable, and high-quality segmentation in both research and healthcare environments.

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

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

Accurate and efficient segmentation of brain tumors is critical for diagnosis, treatment planning, and monitoring in clinical practice. In this study, we present an enhanced ResUNet architecture for automatic brain tumor segmentation, integrating an EfficientNetB0 encoder, a channel attention mechanism, and an Atrous Spatial Pyramid Pooling (ASPP) module. The EfficientNetB0 encoder leverages pre-trained features to improve feature extraction efficiency, while the channel attention mechanism enhances the model's focus on tumor-relevant features. ASPP enables multiscale contextual learning, crucial for handling tumors of varying sizes and shapes. The proposed model was evaluated on two benchmark datasets: TCGA LGG and BraTS 2020. Experimental results demonstrate that our method consistently outperforms the baseline ResUNet and its EfficientNet variant, achieving Dice coefficients of 0.903 and 0.851 and HD95 scores of 9.43 and 3.54 for whole tumor and tumor core regions on the BraTS 2020 dataset, respectively. compared with state-of-the-art methods, our approach shows competitive performance, particularly in whole tumor and tumor core segmentation. These results indicate that combining a powerful encoder with attention mechanisms and ASPP can significantly enhance brain tumor segmentation performance. The proposed approach holds promise for further optimization and application in other medical image segmentation tasks.

AI-driven tumor analysis has garnered increasing attention in healthcare. However, its progress is significantly hindered by the lack of annotated tumor cases, which requires radiologists to invest a lot of effort in collecting and annotation. In this paper, we introduce a highly practical solution for robust tumor synthesis and segmentation, termed FreeTumor, which refers to annotation-free synthetic tumors and our desire to free patients that suffering from tumors. Instead of pursuing sophisticated technical synthesis modules, we aim to design a simple yet effective tumor synthesis paradigm to unleash the power of large-scale data. Specifically, FreeTumor advances existing methods mainly from three aspects: (1) Existing methods only leverage small-scale labeled data for synthesis training, which limits their ability to generalize well on unseen data from different sources. To this end, we introduce the adversarial training strategy to leverage large-scale and diversified unlabeled data in synthesis training, significantly improving tumor synthesis. (2) Existing methods largely ignored the negative impact of low-quality synthetic tumors in segmentation training. Thus, we employ an adversarial-based discriminator to automatically filter out the low-quality synthetic tumors, which effectively alleviates their negative impact. (3) Existing methods only used hundreds of cases in tumor segmentation. In FreeTumor, we investigate the data scaling law in tumor segmentation by scaling up the dataset to 11k cases. Extensive experiments demonstrate the superiority of FreeTumor, e.g., on three tumor segmentation benchmarks, average +8.9% DSC over the baseline that only using real tumors and +6.6% DSC over the state-of-the-art tumor synthesis method. Code will be available.

Application of deep learning on histopathological whole slide images (WSIs) holds promise of improving diagnostic efficiency and reproducibility but is largely dependent on the ability to write computer code or purchase commercial solutions. We present a code-free pipeline utilizing free-to-use, open-source software (QuPath, DeepMIB, and FastPathology) for creating and deploying deep learning-based segmentation models for computational pathology. We demonstrate the pipeline on a use case of separating epithelium from stroma in colonic mucosa. A dataset of 251 annotated WSIs, comprising 140 hematoxylin-eosin (HE)-stained and 111 CD3 immunostained colon biopsy WSIs, were developed through active learning using the pipeline. On a hold-out test set of 36 HE and 21 CD3-stained WSIs a mean intersection over union score of 96.6% and 95.3% was achieved on epithelium segmentation. We demonstrate pathologist-level segmentation accuracy and clinical acceptable runtime performance and show that pathologists without programming experience can create near state-of-the-art segmentation solutions for histopathological WSIs using only free-to-use software. The study further demonstrates the strength of open-source solutions in its ability to create generalizable, open pipelines, of which trained models and predictions can seamlessly be exported in open formats and thereby used in external solutions. All scripts, trained models, a video tutorial, and the full dataset of 251 WSIs with ~31k epithelium annotations are made openly available at https://github.com/andreped/NoCodeSeg to accelerate research in the field.

Histopathological cancer diagnostics has become more complex, and the increasing number of biopsies is a challenge for most pathology laboratories. Thus, development of automatic methods for evaluation of histopathological cancer sections would be of value. In this study, we used 624 whole slide images (WSIs) of breast cancer from a Norwegian cohort. We propose a cascaded convolutional neural network design, called H2G-Net, for semantic segmentation of gigapixel histopathological images. The design involves a detection stage using a patch-wise method, and a refinement stage using a convolutional autoencoder. To validate the design, we conducted an ablation study to assess the impact of selected components in the pipeline on tumour segmentation. Guiding segmentation, using hierarchical sampling and deep heatmap refinement, proved to be beneficial when segmenting the histopathological images. We found a significant improvement when using a refinement network for postprocessing the generated tumour segmentation heatmaps. The overall best design achieved a Dice score of 0.933 on an independent test set of 90 WSIs. The design outperformed single-resolution approaches, such as cluster-guided, patch-wise high-resolution classification using MobileNetV2 (0.872) and a low-resolution U-Net (0.874). In addition, segmentation on a representative x400 WSI took ~58 seconds, using only the CPU. The findings demonstrate the potential of utilizing a refinement network to improve patch-wise predictions. The solution is efficient and does not require overlapping patch inference or ensembling. Furthermore, we showed that deep neural networks can be trained using a random sampling scheme that balances on multiple different labels simultaneously, without the need of storing patches on disk. Future work should involve more efficient patch generation and sampling, as well as improved clustering.

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

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge, focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors.

Accurate segmentation of brain tumors plays a key role in the diagnosis and treatment of brain tumor diseases. It serves as a critical technology for quantifying tumors and extracting their features. With the increasing application of deep learning methods, the computational burden has become progressively heavier. To achieve a lightweight model with good segmentation performance, this study proposes the MBDRes-U-Net model using the three-dimensional (3D) U-Net codec framework, which integrates multibranch residual blocks and fused attention into the model. The computational burden of the model is reduced by the branch strategy, which effectively uses the rich local features in multimodal images and enhances the segmentation performance of subtumor regions. Additionally, during encoding, an adaptive weighted expansion convolution layer is introduced into the multi-branch residual block, which enriches the feature expression and improves the segmentation accuracy of the model. Experiments on the Brain Tumor Segmentation (BraTS) Challenge 2018 and 2019 datasets show that the architecture could maintain a high precision of brain tumor segmentation while considerably reducing the calculation overhead.Our code is released at https://github.com/Huaibei-normal-university-cv-laboratory/mbdresunet

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

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

Mitotic figure (MF) detection in histopathology images is challenging due to large variations in slide scanners, staining protocols, tissue types, and the presence of artifacts. This paper presents a collection of training techniques - a bag of tricks - that enable robust, real-time MF detection across diverse domains. We build on the efficient RTMDet single stage object detector to achieve high inference speed suitable for clinical deployment. Our method addresses scanner variability and tumor heterogeneity via extensive multi-domain training data, balanced sampling, and careful augmentation. Additionally, we employ targeted, hard negative mining on necrotic and debris tissue to reduce false positives. In a grouped 5-fold cross-validation across multiple MF datasets, our model achieves an F1 score between 0.78 and 0.84. On the preliminary test set of the MItosis DOmain Generalization (MIDOG) 2025 challenge, our single-stage RTMDet-S based approach reaches an F1 of 0.81, outperforming larger models and demonstrating adaptability to new, unfamiliar domains. The proposed solution offers a practical trade-off between accuracy and speed, making it attractive for real-world clinical adoption.

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

In this work, we address the TrackRAD2025 challenge of real-time tumor tracking in cine-MRI sequences of the thoracic and abdominal regions under strong data scarcity constraints. Two complementary strategies were explored: (i) unsupervised registration with the IMPACT similarity metric and (ii) foundation model-based segmentation leveraging SAM 2.1 and its recent variants through prompt-based interaction. Due to the one-second runtime constraint, the SAM-based method was ultimately selected. The final configuration used SAM2.1 b+ with mask-based prompts from the first annotated slice, fine-tuned solely on the small labeled subset from TrackRAD2025. Training was configured to minimize overfitting, using 1024x1024 patches (batch size 1), standard augmentations, and a balanced Dice + IoU loss. A low uniform learning rate (0.0001) was applied to all modules (prompt encoder, decoder, Hiera backbone) to preserve generalization while adapting to annotator-specific styles. Training lasted 300 epochs (~12h on RTX A6000, 48GB). The same inference strategy was consistently applied across all anatomical sites and MRI field strengths. Test-time augmentation was considered but ultimately discarded due to negligible performance gains. The final model was selected based on the highest Dice Similarity Coefficient achieved on the validation set after fine-tuning. On the hidden test set, the model reached a Dice score of 0.8794, ranking 6th overall in the TrackRAD2025 challenge. These results highlight the strong potential of foundation models for accurate and real-time tumor tracking in MRI-guided radiotherapy.

In this paper, we present a novel approach for segmenting pediatric brain tumors using a deep learning architecture, inspired by expert radiologists' segmentation strategies. Our model delineates four distinct tumor labels and is benchmarked on a held-out PED BraTS 2024 test set (i.e., pediatric brain tumor datasets introduced by BraTS). Furthermore, we evaluate our model's performance against the state-of-the-art (SOTA) model using a new external dataset of 30 patients from CBTN (Children's Brain Tumor Network), labeled in accordance with the PED BraTS 2024 guidelines and 2023 BraTS Adult Glioma dataset. We compare segmentation outcomes with the winning algorithm from the PED BraTS 2023 challenge as the SOTA model. Our proposed algorithm achieved an average Dice score of 0.642 and an HD95 of 73.0 mm on the CBTN test data, outperforming the SOTA model, which achieved a Dice score of 0.626 and an HD95 of 84.0 mm. Moreover, our model exhibits strong generalizability, attaining a 0.877 Dice score in whole tumor segmentation on the BraTS 2023 Adult Glioma dataset, surpassing existing SOTA. Our results indicate that the proposed model is a step towards providing more accurate segmentation for pediatric brain tumors, which is essential for evaluating therapy response and monitoring patient progress. Our source code is available at https://github.com/NUBagciLab/Pediatric-Brain-Tumor-Segmentation-Model.

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.

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.

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

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

Head and neck tumor segmentation challenge (HECKTOR) 2022 offers a platform for researchers to compare their solutions to segmentation of tumors and lymph nodes from 3D CT and PET images. In this work, we describe our solution to HECKTOR 2022 segmentation task. We re-sample all images to a common resolution, crop around head and neck region, and train SegResNet semantic segmentation network from MONAI. We use 5-fold cross validation to select best model checkpoints. The final submission is an ensemble of 15 models from 3 runs. Our solution (team name NVAUTO) achieves the 1st place on the HECKTOR22 challenge leaderboard with an aggregated dice score of 0.78802.

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

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

When developing deep neural networks for segmenting intraoperative ultrasound images, several practical issues are encountered frequently, such as the presence of ultrasound frames that do not contain regions of interest and the high variance in ground-truth labels. In this study, we evaluate the utility of a pre-screening classification network prior to the segmentation network. Experimental results demonstrate that such a classifier, minimising frame classification errors, was able to directly impact the number of false positive and false negative frames. Importantly, the segmentation accuracy on the classifier-selected frames, that would be segmented, remains comparable to or better than those from standalone segmentation networks. Interestingly, the efficacy of the pre-screening classifier was affected by the sampling methods for training labels from multiple observers, a seemingly independent problem. We show experimentally that a previously proposed approach, combining random sampling and consensus labels, may need to be adapted to perform well in our application. Furthermore, this work aims to share practical experience in developing a machine learning application that assists highly variable interventional imaging for prostate cancer patients, to present robust and reproducible open-source implementations, and to report a set of comprehensive results and analysis comparing these practical, yet important, options in a real-world clinical application.

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

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

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

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.

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.

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

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

As lung cancer evolves, the presence of enlarged and potentially malignant lymph nodes must be assessed to properly estimate disease progression and select the best treatment strategy. Following the clinical guidelines, estimation of short-axis diameter and mediastinum station are paramount for correct diagnosis. A method for accurate and automatic segmentation is hence decisive for quantitatively describing lymph nodes. In this study, the use of 3D convolutional neural networks, either through slab-wise schemes or the leveraging of downsampled entire volumes, is investigated. Furthermore, the potential impact from simple ensemble strategies is considered. As lymph nodes have similar attenuation values to nearby anatomical structures, we suggest using the knowledge of other organs as prior information to guide the segmentation task. To assess the segmentation and instance detection performances, a 5-fold cross-validation strategy was followed over a dataset of 120 contrast-enhanced CT volumes. For the 1178 lymph nodes with a short-axis diameter geq10 mm, our best performing approach reached a patient-wise recall of 92%, a false positive per patient ratio of 5, and a segmentation overlap of 80.5%. The method performs similarly well across all stations. Fusing a slab-wise and a full volume approach within an ensemble scheme generated the best performances. The anatomical priors guiding strategy is promising, yet a larger set than four organs appears needed to generate an optimal benefit. A larger dataset is also mandatory, given the wide range of expressions a lymph node can exhibit (i.e., shape, location, and attenuation), and contrast uptake variations.

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

Background: Pancreatic cancer is one of the most aggressive cancers, with poor survival rates. Endoscopic ultrasound (EUS) is a key diagnostic modality, but its effectiveness is constrained by operator subjectivity. This study evaluates a Vision Transformer-based deep learning segmentation model for pancreatic tumors. Methods: A segmentation model using the USFM framework with a Vision Transformer backbone was trained and validated with 17,367 EUS images (from two public datasets) in 5-fold cross-validation. The model was tested on an independent dataset of 350 EUS images from another public dataset, manually segmented by radiologists. Preprocessing included grayscale conversion, cropping, and resizing to 512x512 pixels. Metrics included Dice similarity coefficient (DSC), intersection over union (IoU), sensitivity, specificity, and accuracy. Results: In 5-fold cross-validation, the model achieved a mean DSC of 0.651 +/- 0.738, IoU of 0.579 +/- 0.658, sensitivity of 69.8%, specificity of 98.8%, and accuracy of 97.5%. For the external validation set, the model achieved a DSC of 0.657 (95% CI: 0.634-0.769), IoU of 0.614 (95% CI: 0.590-0.689), sensitivity of 71.8%, and specificity of 97.7%. Results were consistent, but 9.7% of cases exhibited erroneous multiple predictions. Conclusions: The Vision Transformer-based model demonstrated strong performance for pancreatic tumor segmentation in EUS images. However, dataset heterogeneity and limited external validation highlight the need for further refinement, standardization, and prospective studies.

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

Computer vision techniques have advanced significantly in recent years, finding diverse and impactful applications within the medical field. In this paper, we introduce a new framework for the detection of Bethesda cells in Pap smear images, developed for Track B of the Riva Cytology Challenge held in association with the International Symposium on Biomedical Imaging (ISBI). This work focuses on enhancing computer vision models for cell detection, with performance evaluated using the mAP50-95 metric. We propose a solution based on an ensemble of YOLO and U-Net architectures, followed by a refinement stage utilizing overlap removal techniques and a binary classifier. Our framework achieved second place with a mAP50-95 score of 0.5909 in the competition. The implementation and source code are available at the following repository: github.com/martinamster/riva-trackb

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.

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

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.

We present the 2017 DAVIS Challenge on Video Object Segmentation, a public dataset, benchmark, and competition specifically designed for the task of video object segmentation. Following the footsteps of other successful initiatives, such as ILSVRC and PASCAL VOC, which established the avenue of research in the fields of scene classification and semantic segmentation, the DAVIS Challenge comprises a dataset, an evaluation methodology, and a public competition with a dedicated workshop co-located with CVPR 2017. The DAVIS Challenge follows up on the recent publication of DAVIS (Densely-Annotated VIdeo Segmentation), which has fostered the development of several novel state-of-the-art video object segmentation techniques. In this paper we describe the scope of the benchmark, highlight the main characteristics of the dataset, define the evaluation metrics of the competition, and present a detailed analysis of the results of the participants to the challenge.

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

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.

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

Accurate lesion segmentation is essential in medical image analysis, yet most existing methods are designed for specific anatomical sites or imaging modalities, limiting their generalizability. Recent vision-language foundation models enable concept-driven segmentation in natural images, offering a promising direction for more flexible medical image analysis. However, concept-prompt-based lesion segmentation, particularly with the latest Segment Anything Model 3 (SAM3), remains underexplored. In this work, we present a systematic evaluation of SAM3 for lesion segmentation. We assess its performance using geometric bounding boxes and concept-based text and image prompts across multiple modalities, including multiparametric MRI, CT, ultrasound, dermoscopy, and endoscopy. To improve robustness, we incorporate additional prior knowledge, such as adjacent-slice predictions, multiparametric information, and prior annotations. We further compare different fine-tuning strategies, including partial module tuning, adapter-based methods, and full-model optimization. Experiments on 13 datasets covering 11 lesion types demonstrate that SAM3 achieves strong cross-modality generalization, reliable concept-driven segmentation, and accurate lesion delineation. These results highlight the potential of concept-based foundation models for scalable and practical medical image segmentation. Code and trained models will be released at: https://github.com/apple1986/lesion-sam3

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

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.

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD) - a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to non AI experts.

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

Identifying key pathological features in brain MRIs is crucial for the long-term survival of glioma patients. However, manual segmentation is time-consuming, requiring expert intervention and is susceptible to human error. Therefore, significant research has been devoted to developing machine learning methods that can accurately segment tumors in 3D multimodal brain MRI scans. Despite their progress, state-of-the-art models are often limited by the data they are trained on, raising concerns about their reliability when applied to diverse populations that may introduce distribution shifts. Such shifts can stem from lower quality MRI technology (e.g., in sub-Saharan Africa) or variations in patient demographics (e.g., children). The BraTS-2024 challenge provides a platform to address these issues. This study presents our methodology for segmenting tumors in the BraTS-2024 SSA and Pediatric Tumors tasks using MedNeXt, comprehensive model ensembling, and thorough postprocessing. Our approach demonstrated strong performance on the unseen validation set, achieving an average Dice Similarity Coefficient (DSC) of 0.896 on the BraTS-2024 SSA dataset and an average DSC of 0.830 on the BraTS Pediatric Tumor dataset. Additionally, our method achieved an average Hausdorff Distance (HD95) of 14.682 on the BraTS-2024 SSA dataset and an average HD95 of 37.508 on the BraTS Pediatric dataset. Our GitHub repository can be accessed here: Project Repository : https://github.com/python-arch/BioMbz-Optimizing-Brain-Tumor-Segmentation-with-MedNeXt-BraTS-2024-SSA-and-Pediatrics

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

In mainstream computer vision and machine learning, public datasets such as ImageNet, COCO and KITTI have helped drive enormous improvements by enabling researchers to understand the strengths and limitations of different algorithms via performance comparison. However, this type of approach has had limited translation to problems in robotic assisted surgery as this field has never established the same level of common datasets and benchmarking methods. In 2015 a sub-challenge was introduced at the EndoVis workshop where a set of robotic images were provided with automatically generated annotations from robot forward kinematics. However, there were issues with this dataset due to the limited background variation, lack of complex motion and inaccuracies in the annotation. In this work we present the results of the 2017 challenge on robotic instrument segmentation which involved 10 teams participating in binary, parts and type based segmentation of articulated da Vinci robotic instruments.

Brain tumors, particularly gliomas, pose significant chall-enges due to their complex growth patterns, infiltrative nature, and the variability in brain structure across individuals, which makes accurate diagnosis and monitoring difficult. Deep learning models have been developed to accurately delineate these tumors. However, most of these models were trained on relatively homogenous high-resource datasets, limiting their robustness when deployed in underserved regions. In this study, we performed segmentation-aware offline data augmentation on the BraTS-Africa dataset to increase the data sample size and diversity to enhance generalization. We further constructed an ensemble of three distinct architectures, MedNeXt, SegMamba, and Residual-Encoder U-Net, to leverage their complementary strengths. Our best-performing model, MedNeXt, was trained on 1000 epochs and achieved the highest average lesion-wise dice and normalized surface distance scores of 0.86 and 0.81 respectively. However, the ensemble model trained for 500 epochs produced the most balanced segmentation performance across the tumour subregions. This work demonstrates that a combination of advanced augmentation and model ensembling can improve segmentation accuracy and robustness on diverse and underrepresented datasets. Code available at: https://github.com/SPARK-Academy-2025/SPARK-2025/tree/main/SPARK2025_BraTs_MODELS/SPARK_NeuroAshanti

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

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.

Over the past decade, U-Net has been the dominant architecture in medical image segmentation, leading to the development of thousands of U-shaped variants. Despite its widespread adoption, there is still no comprehensive benchmark to systematically evaluate their performance and utility, largely because of insufficient statistical validation and limited consideration of efficiency and generalization across diverse datasets. To bridge this gap, we present U-Bench, the first large-scale, statistically rigorous benchmark that evaluates 100 U-Net variants across 28 datasets and 10 imaging modalities. Our contributions are threefold: (1) Comprehensive Evaluation: U-Bench evaluates models along three key dimensions: statistical robustness, zero-shot generalization, and computational efficiency. We introduce a novel metric, U-Score, which jointly captures the performance-efficiency trade-off, offering a deployment-oriented perspective on model progress. (2) Systematic Analysis and Model Selection Guidance: We summarize key findings from the large-scale evaluation and systematically analyze the impact of dataset characteristics and architectural paradigms on model performance. Based on these insights, we propose a model advisor agent to guide researchers in selecting the most suitable models for specific datasets and tasks. (3) Public Availability: We provide all code, models, protocols, and weights, enabling the community to reproduce our results and extend the benchmark with future methods. In summary, U-Bench not only exposes gaps in previous evaluations but also establishes a foundation for fair, reproducible, and practically relevant benchmarking in the next decade of U-Net-based segmentation models. The project can be accessed at: https://fenghetan9.github.io/ubench. Code is available at: https://github.com/FengheTan9/U-Bench.

Medical image segmentation involves partitioning medical images into meaningful regions, with a focus on identifying anatomical structures and lesions. It has broad applications in healthcare, and deep learning methods have enabled significant advancements in automating this process. Recently, the introduction of the Segmentation Anything Model (SAM), the first foundation model for segmentation task, has prompted researchers to adapt it for the medical domain to improve performance across various tasks. However, SAM's large model size and high GPU requirements hinder its scalability and development in the medical domain. In this work, we propose MCP-MedSAM, a powerful and lightweight medical SAM model designed to be trainable on a single A100 GPU with 40GB of memory within one day while delivering superior segmentation performance. Recognizing the significant internal differences between modalities and the need for direct segmentation target information within bounding boxes, we introduce two kinds of prompts: the modality prompt and the content prompt. After passing through the prompt encoder, their embedding representations can further improve the segmentation performance by incorporating more relevant information without adding significant training overhead. Additionally, we adopt an effective modality-based data sampling strategy to address data imbalance between modalities, ensuring more balanced performance across all modalities. Our method was trained and evaluated using a large-scale challenge dataset, compared to top-ranking methods on the challenge leaderboard, MCP-MedSAM achieved superior performance while requiring only one day of training on a single GPU. The code is publicly available at blue{https://github.com/dong845/MCP-MedSAM}.}

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

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

This work summarizes the results of the largest skin image analysis challenge in the world, hosted by the International Skin Imaging Collaboration (ISIC), a global partnership that has organized the world's largest public repository of dermoscopic images of skin. The challenge was hosted in 2018 at the Medical Image Computing and Computer Assisted Intervention (MICCAI) conference in Granada, Spain. The dataset included over 12,500 images across 3 tasks. 900 users registered for data download, 115 submitted to the lesion segmentation task, 25 submitted to the lesion attribute detection task, and 159 submitted to the disease classification task. Novel evaluation protocols were established, including a new test for segmentation algorithm performance, and a test for algorithm ability to generalize. Results show that top segmentation algorithms still fail on over 10% of images on average, and algorithms with equal performance on test data can have different abilities to generalize. This is an important consideration for agencies regulating the growing set of machine learning tools in the healthcare domain, and sets a new standard for future public challenges in healthcare.

Unsupervised domain adaptation for medical image segmentation remains a significant challenge due to substantial domain shifts across imaging modalities, such as CT and MRI. While recent vision-language representation learning methods have shown promise, their potential in UDA segmentation tasks remains underexplored. To address this gap, we propose TCSA-UDA, a Text-driven Cross-Semantic Alignment framework that leverages domain-invariant textual class descriptions to guide visual representation learning. Our approach introduces a vision-language covariance cosine loss to directly align image encoder features with inter-class textual semantic relations, encouraging semantically meaningful and modality-invariant feature representations. Additionally, we incorporate a prototype alignment module that aligns class-wise pixel-level feature distributions across domains using high-level semantic prototypes. This mitigates residual category-level discrepancies and enhances cross-modal consistency. Extensive experiments on challenging cross-modality cardiac, abdominal, and brain tumor segmentation benchmarks demonstrate that our TCSA-UDA framework significantly reduces domain shift and consistently outperforms state-of-the-art UDA methods, establishing a new paradigm for integrating language-driven semantics into domain-adaptive medical image analysis.

We propose Uncertainty Augmented Context Attention network (UACANet) for polyp segmentation which consider a uncertain area of the saliency map. We construct a modified version of U-Net shape network with additional encoder and decoder and compute a saliency map in each bottom-up stream prediction module and propagate to the next prediction module. In each prediction module, previously predicted saliency map is utilized to compute foreground, background and uncertain area map and we aggregate the feature map with three area maps for each representation. Then we compute the relation between each representation and each pixel in the feature map. We conduct experiments on five popular polyp segmentation benchmarks, Kvasir, CVC-ClinicDB, ETIS, CVC-ColonDB and CVC-300, and achieve state-of-the-art performance. Especially, we achieve 76.6% mean Dice on ETIS dataset which is 13.8% improvement compared to the previous state-of-the-art method. Source code is publicly available at https://github.com/plemeri/UACANet

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.

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

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

In this work, we present LesionLocator, a framework for zero-shot longitudinal lesion tracking and segmentation in 3D medical imaging, establishing the first end-to-end model capable of 4D tracking with dense spatial prompts. Our model leverages an extensive dataset of 23,262 annotated medical scans, as well as synthesized longitudinal data across diverse lesion types. The diversity and scale of our dataset significantly enhances model generalizability to real-world medical imaging challenges and addresses key limitations in longitudinal data availability. LesionLocator outperforms all existing promptable models in lesion segmentation by nearly 10 dice points, reaching human-level performance, and achieves state-of-the-art results in lesion tracking, with superior lesion retrieval and segmentation accuracy. LesionLocator not only sets a new benchmark in universal promptable lesion segmentation and automated longitudinal lesion tracking but also provides the first open-access solution of its kind, releasing our synthetic 4D dataset and model to the community, empowering future advancements in medical imaging. Code is available at: www.github.com/MIC-DKFZ/LesionLocator

Automated segmentation of brain tumors from 3D magnetic resonance images (MRIs) is necessary for the diagnosis, monitoring, and treatment planning of the disease. Manual delineation practices require anatomical knowledge, are expensive, time consuming and can be inaccurate due to human error. Here, we describe a semantic segmentation network for tumor subregion segmentation from 3D MRIs based on encoder-decoder architecture. Due to a limited training dataset size, a variational auto-encoder branch is added to reconstruct the input image itself in order to regularize the shared decoder and impose additional constraints on its layers. The current approach won 1st place in the BraTS 2018 challenge.

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

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.

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.

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

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

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

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

The applicability of current lesion segmentation models for chest X-rays (CXRs) has been limited both by a small number of target labels and the reliance on long, detailed expert-level text inputs, creating a barrier to practical use. To address these limitations, we introduce a new paradigm: instruction-guided lesion segmentation (ILS), which is designed to segment diverse lesion types based on simple, user-friendly instructions. Under this paradigm, we construct MIMIC-ILS, the first large-scale instruction-answer dataset for CXR lesion segmentation, using our fully automated multimodal pipeline that generates annotations from chest X-ray images and their corresponding reports. MIMIC-ILS contains 1.1M instruction-answer pairs derived from 192K images and 91K unique segmentation masks, covering seven major lesion types. To empirically demonstrate its utility, we introduce ROSALIA, a vision-language model fine-tuned on MIMIC-ILS. ROSALIA can segment diverse lesions and provide textual explanations in response to user instructions. The model achieves high segmentation and textual accuracy in our newly proposed task, highlighting the effectiveness of our pipeline and the value of MIMIC-ILS as a foundational resource for pixel-level CXR lesion grounding.

This paper presents the winning solution of task 1 and the third-placed solution of task 3 of the BraTS challenge. The use of automated tools in clinical practice has increased due to the development of more and more sophisticated and reliable algorithms. However, achieving clinical standards and developing tools for real-life scenarios is a major challenge. To this end, BraTS has organised tasks to find the most advanced solutions for specific purposes. In this paper, we propose the use of synthetic data to train state-of-the-art frameworks in order to improve the segmentation of adult gliomas in a post-treatment scenario, and the segmentation of meningioma for radiotherapy planning. Our results suggest that the use of synthetic data leads to more robust algorithms, although the synthetic data generation pipeline is not directly suited to the meningioma task. In task 1, we achieved a DSC of 0.7900, 0.8076, 0.7760, 0.8926, 0.7874, 0.8938 and a HD95 of 35.63, 30.35, 44.58, 16.87, 38.19, 17.95 for ET, NETC, RC, SNFH, TC and WT, respectively and, in task 3, we achieved a DSC of 0.801 and HD95 of 38.26, in the testing phase. The code for these tasks is available at https://github.com/ShadowTwin41/BraTS_2023_2024_solutions.

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

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

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

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

Lung cancer remains the leading cause of cancer-related mortality worldwide, and early detection through low-dose computed tomography (LDCT) has shown significant promise in reducing death rates. With the growing integration of artificial intelligence (AI) into medical imaging, the development and evaluation of robust AI models require access to large, well-annotated datasets. In this study, we introduce the utility of Duke Lung Cancer Screening (DLCS) Dataset, the largest open-access LDCT dataset with over 2,000 scans and 3,000 expert-verified nodules. We benchmark deep learning models for both 3D nodule detection and lung cancer classification across internal and external datasets including LUNA16, LUNA25, and NLST-3D+. For detection, we develop two MONAI-based RetinaNet models (DLCSDmD and LUNA16-mD), evaluated using the Competition Performance Metric (CPM). For classification, we compare five models, including state-of-the-art pretrained models (Models Genesis, Med3D), a selfsupervised foundation model (FMCB), a randomly initialized ResNet50, and proposed a novel Strategic Warm-Start++ (SWS++) model. SWS++ uses curated candidate patches to pretrain a classification backbone within the same detection pipeline, enabling task-relevant feature learning. Our models demonstrated strong generalizability, with SWS++ achieving comparable or superior performance to existing foundational models across multiple datasets (AUC: 0.71 to 0.90). All code, models, and data are publicly released to promote reproducibility and collaboration. This work establishes a standardized benchmarking resource for lung cancer AI research, supporting future efforts in model development, validation, and clinical translation.

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

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

In the radiation therapy of nasopharyngeal carcinoma (NPC), clinicians typically delineate the gross tumor volume (GTV) using non-contrast planning computed tomography to ensure accurate radiation dose delivery. However, the low contrast between tumors and adjacent normal tissues necessitates that radiation oncologists manually delineate the tumors, often relying on diagnostic MRI for guidance. % In this study, we propose a novel approach to directly segment NPC gross tumors on non-contrast planning CT images, circumventing potential registration errors when aligning MRI or MRI-derived tumor masks to planning CT. To address the low contrast issues between tumors and adjacent normal structures in planning CT, we introduce a 3D Semantic Asymmetry Tumor segmentation (SATs) method. Specifically, we posit that a healthy nasopharyngeal region is characteristically bilaterally symmetric, whereas the emergence of nasopharyngeal carcinoma disrupts this symmetry. Then, we propose a Siamese contrastive learning segmentation framework that minimizes the voxel-wise distance between original and flipped areas without tumor and encourages a larger distance between original and flipped areas with tumor. Thus, our approach enhances the sensitivity of features to semantic asymmetries. % Extensive experiments demonstrate that the proposed SATs achieves the leading NPC GTV segmentation performance in both internal and external testing, e.g., with at least 2\% absolute Dice score improvement and 12\% average distance error reduction when compared to other state-of-the-art methods in the external testing.