Lesion Segmentation

Radiology reports describe kidney lesions by type, size, enhancement, and attenuation, yet existing 3D methods predict only at the patient or organ level. We reformulate kidney CT characterization as a per-lesion set-prediction task: one model emits a variable number of lesions per kidney, each with four clinical attributes. We curated 2,619 CT volumes from 788 patients at one academic medical center, with multi-granularity side- and per-lesion labels, and used KiTS23 (489 cases) for zero-shot external validation. We propose \textbf{LesionDETR}, a DETR-style architecture with size-distance Hungarian matching and a hierarchical loss that aggregates per-slot outputs to side-level objectives. Across four input representations and six encoder initializations, two design choices dominate: a segmentation mask as an input channel, and same-domain abdominal pretraining (SuPreM); generic large-corpus pretraining is no better than random initialization. LesionDETR reaches bilateral side-level abnormality AUC $0.799 \pm 0.009$ on UF-Health and $0.817 \pm 0.072$ on KiTS23. A count-conditioned variant reaches per-lesion mAP $0.190 \pm 0.083$ on cystic lesions; rare solid-lesion AP stays at the noise floor, pointing to targeted data collection, not architecture, as the next bottleneck. The framework yields verified per-lesion predictions for downstream structured report generation.

Placenta Accreta Spectrum (PAS) is a rare but highly dangerous obstetric disease. Early and accurate PAS diagnosis is critical for maternal health. Traditional PAS diagnosis relies on experienced doctors by analyzing the cesarean history and Magnetic Resonance Imaging (MRI) data. However, district-level hospitals often lack the expertise and resources for accurate PAS diagnosis. To address these challenges, we establish the first MRI-based PAS dataset, which includes both fine-grained segmentation and classification annotations. Meanwhile, diagnosing PAS can be significantly enhanced by segmenting lesion areas from MRI images of the uterus. To achieve automatic PAS diagnosis, we propose 3DSAMba, a novel feature learning framework for effective lesion segmentation. More specifically, we first design a 3D Segment Anything Model (SAM) and incorporate medical domain information into the model through an efficient adapter mechanism. In addition, we introduce a Multi-Level Aggregation Mamba (MLAM) to aggregate feature maps across different levels and a Fusion State Space Model (FSSM) to fuse multi-scale features from both the encoder and decoder. Finally, we apply segmentation masks to the original MRI images through element-wise multiplication, effectively isolating lesion areas for more accurate PAS diagnosis. Extensive experiments validate that our framework significantly improves the PAS diagnostic performance. To facilitate further research in PAS diagnosis, we have released the dataset and source code at https://github.com/Drchip61/PASD.

Postoperative pancreatic fistula (POPF) is a serious complication after pancreatic resection, increasing morbidity, hospital stay, and healthcare costs. We present an automatic, end-to-end deep learning pipeline-from pancreatic segmentation to classification-for preoperative POPF risk estimation and stratification using preoperative CT scans. A data set with auto-segmented pancreas volumes and surgical outcomes was used to evaluate multiple architectures, including a custom lightweight 3D CNN baseline (CNN3D), R(2+1)D ResNet-18, and ResNet-MC3-18 models. Evaluation across multiple 3D architectures demonstrated promising predictive performance. This approach offers a clinically valuable tool and a methodological benchmark for pancreas-specific CT classification, supporting improved preoperative decision-making in pancreatic surgery.

Accurate pancreas segmentation is critical for early cancer diagnosis, where annotation scarcity necessitates Semi-Supervised Learning (SSL). However, due to significant inter-sample morphological variability, existing SSL methods face severe generalizability limitations under sparse supervision, leading to the Supervision Bias problem. To address this, we propose Structural Consensus-based KAN Prototype Learning (SCKAN), which constructs the first cross-sample structural consensus learning with Kolmogorov-Arnold Networks (KANs), to achieve more generalizable and accurate segmentation. Specifically, SCKAN contains two key designs: Structure-constrained Prototype Consistency Learning (SPCL), which prompts unbiased structural representation by enforcing cross-sample consistency via prototype-level contrastive optimization, and Consensus-based Kolmogorov-Arnold Fusion (CKaF), which reduces morphology-specific bias by aggregating stable consensus and filtering sample-wise noise via KAN's adaptive B-spline nonlinearity. Extensive experiments on two public pancreas datasets demonstrate the effectiveness of SCKAN. Code is at https://github.com/rhodaliu17/SCKAN.

Liver surface landmark detection is a fundamental prerequisite for anatomical guidance in laparoscopic liver surgery. However, it remains unreliable in practice due to two pervasive challenges: illumination attenuation in underexposed regions and the structural mismatch between pixel-wise localization and continuous curvilinear geometry. To address these limitations, we propose A2ONet, an attenuation-resilient alternating optimization network for robust liver landmark detection. To mitigate illumination attenuation, A2ONet embraces an illumination field compensation (IFC) block that adaptively enhances dark regions while preserving structural consistency. Meanwhile, we introduce a lightweight frequency-orientation selective filter (FOSF) to suppress repetitive texture interference and preserve salient curvilinear cues. Building upon these resilient representations, we design an alternating seg-curve optimization (ASCO) decoder that iteratively couples dense segmentation with explicit curve modeling, enabling mutual guidance to optimize both structural continuity and endpoint localization. Extensive evaluations on L3D-2K, L3D, and P2ILF demonstrate consistent improvements over competitive methods, establishing a more reliable foundation for intraoperative anatomy guidance. Our code will be available at https://github.com/hyperiondk115/A2ONet.

Tracking tumor lesions across serial CT scans is essential for oncological response assessment. Existing automated methods face a fundamental trade-off: end-to-end trackers achieve high automation but offer no opportunity to correct silent tracking failures, while decoupled registration-segmentation pipelines permit user verification yet discard the lesion's prior appearance, limiting accuracy in ambiguous cases. In this work, we propose a Verified Tracking paradigm: a clinician verifies a registration-proposed prompt, which the model leverages alongside the baseline lesion appearance to resolve segmentation ambiguities. We present a unified framework combining early spatial prompt fusion with latent temporal difference weighting for longitudinally-informed segmentation. To address data scarcity, we leverage large-scale synthetic pretraining, proving essential for exploiting longitudinal context, improving performance by up to 4.5 Dice points over training from scratch. Our approach secured first place in the MICCAI autoPET IV challenge. We further curate and release PanTrack, a new longitudinal pancreatic cancer benchmark, to assess out-of-distribution generalization. Experiments show that our model outperforms prior work in both fully automatic and the proposed verified tracking setting offering a clinically safe middle ground between automation and control. Code, model and dataset will be released at https://github.com/MIC-DKFZ/LongiSeg

Accurate segmentation of hepatic and portal vessels in contrast-enhanced computed tomography angiography (CTA) remains challenging due to complex vascular topology, peripheral visibility limitations, and acquisition-induced ambiguities. While existing public datasets offer valuable benchmarks, few include clinically realistic annotation constraints. We introduce VEELA (Vessel Extraction and Extrication for Liver Analysis), a rigorously curated liver vessel dataset derived from 40 CTA scans inherited from the CHAOS grand-challenge cohort. All vessels were manually delineated slice-by-slice under multi-expert consensus, using a strict visibility-driven annotation policy and avoiding anatomically inferred interpolation. This design explicitly captures anatomical variability and imaging-related uncertainty. As a continuation of the CHAOS challenge, VEELA enables reproducible cross-benchmark evaluation while extending the scope to fine-grained hepatic and portal vessel segmentation. We further establish a standardized benchmarking framework and analyze complementary evaluation metrics, including topology-aware (clDice), overlap-based (IoU), boundary-sensitive (NSD), and geometry-aware (area, length) measures. Our results demonstrate that different metrics capture distinct aspects of vascular integrity, underscoring the necessity of multi-perspective evaluation for clinically meaningful vessel segmentation. VEELA is publicly released to facilitate reproducible research and support the development of robust vascular segmentation methods. Researchers can access the evaluation metrics, dataset, and submission platform at https://www.synapse.org/Synapse:syn65471967.

Purpose: To assess whether breast lesion segmentation can be learned directly from acquired MRI k-space, and whether doing so improves robustness when data are accelerated or noisy. Materials and Methods: This retrospective study used public breast dynamic contrast-enhanced MRI (DCE-MRI) datasets with acquired and synthetic k-space, together with a within-dataset synthetic control. We compared four 3D U-Net variants: a hybrid k-space-to-image model, a native k-space model, and magnitude and complex image-space baselines. Models were evaluated under increasing undersampling and added complex Gaussian k-space noise. The primary outcome was patient-level Dice similarity coefficient under cross-validation, with the hybrid model prespecified as the main comparison against the magnitude image-space baseline. Results: At full sampling, the hybrid and image-space models performed similarly. As acceleration increased, the hybrid model retained substantially more segmentation accuracy and significantly outperformed the magnitude image-space baseline across moderate to high undersampling levels. The same pattern was observed when noise was added directly to k-space: the hybrid model degraded more slowly, whereas the image-space baseline failed under heavier noise. This advantage was reproduced in the within-dataset synthetic control. Feature analysis suggested that the k-space stage and image-space stage played complementary roles, with frequency-domain filtering concentrated before image-domain lesion localization. Conclusion: K-space-aware deep learning improves the robustness of breast lesion segmentation under MRI undersampling and k-space noise, while matching image-space methods at full sampling.

The synergistic interpretation of anatomical information from computed tomography (CT) and metabolic information from positron emission tomography (PET) is important to oncologic imaging. However, existing deep learning methods for PET/CT remain largely task-specific, are often trained on single-center cohorts, or adopt dual-branch fusion schemes that delay cross-modal interaction and underutilize early spatial correspondence between PET and CT. To address these limitations, we present an open-source, multi-center, whole-body FDG PET/CT foundation model utilizing 4,997 harmonized scans from four public datasets. Our framework employs hierarchical UNet-shaped backbones with early channel-wise concatenation, enabling anatomical and metabolic features to interact from the first embedding layer onward. We further introduce a masked autoencoding objective based on zero-mean imputation, combined with a weighted global reconstruction loss. This design avoids non-physical intensity discontinuities at masked-region boundaries that arise from learnable mask tokens. On downstream AutoPET lesion segmentation, the proposed models demonstrate strong label efficiency: with only 10% of the labeled training data, they achieve performance comparable to models trained from scratch on the full dataset. Under extreme 5-shot linear probing, joint PET/CT pretraining also achieves higher Dice scores than separated-modality pretraining. This multi-center foundation model demonstrates label efficiency and cross-modality representation learning for PET/CT tumor segmentation. It provides a robust, open-source basis for advancing automated oncologic imaging, significantly reducing the need for large-scale manual annotations in clinical practice.

In recent years, there has been a notable increase in the level of attention that is given to algorithms based on deep learning in the context of medical image segmentation. Nevertheless, the reliability of the field has been hindered due to the absence of a standardized methodology for performance analysis and the utilization of different datasets in previous research. The primary objective of the research is to comprehensively evaluate contemporary segmentation frameworks combined with state-of-the-art pre-trained backbones in order to accurately predict COVID-19 lesions in CT images. Moreover, this evaluation can serve as a point of reference for the segmentation of images in various other imaging scenarios. In order to accomplish this, we integrate four distinct deep learning architectures, namely Unet, PSPNet, Linknet, and FPN, with six pre-trained encoders, including VGG 19, DenseNet 121, Inception ResNet V2, MobileNet V2, SeresNet 101, and EfficientNet B0. This approach enables the development of diverse testing architectures. In the context of image segmentation, our research encompassed both binary and multi-class experimentation. The findings derived from our analysis of three distinct COVID-19 CT segmentation datasets indicate that deep learning architectures yield precise and efficient segmentation outcomes. Significantly, a maximum F1-Score of 98% was attained for binary class segmentation, while multi-class segmentation yielded F1-Scores of 75% and 77% across two separate datasets. The utilization of artificial intelligence and deep learning enhances the diagnostic process for pandemic diseases across multiple dimensions.

Chronic wounds such as diabetic foot ulcers and pressure injuries require accurate tissue-level assessment to guide treatment planning and monitor healing progression. While deep learning methods have advanced automated wound analysis, most existing approaches focus on binary segmentation and inadequately model heterogeneous tissue composition due to high intra-class variability and limited annotated data. Multi-class wound tissue segmentation, therefore, remains a challenging and clinically relevant problem. We propose WoundFormer, a transformer-based framework that enhances hierarchical spatial feature fusion for multi-class wound tissue segmentation. Specifically, we replace the standard SegFormer decoder with a spatially-preserving multi-scale aggregation head that maintains feature topology during cross-scale integration and strengthens contextual interactions through convolutional fusion. This design improves boundary localization and discrimination between visually similar tissue categories while preserving transformer efficiency. We evaluate WoundFormer on the WoundTissueSeg dataset (147 images, six tissue classes) and a second benchmark (DFUTissue dataset). The proposed method achieves an overall Dice score of 81.9%, outperforming strong CNN- and transformer-based baselines by up to 4.3 Dice points on the WoundTissueSeg benchmark, with consistent improvements across minority tissue classes. These results indicate that explicit modeling of hierarchical spatial interactions enhances transformer representations for heterogeneous wound tissue segmentation and supports more reliable quantitative wound assessment.

Automated segmentation of liver lesions on non-contrast computed tomography (NCCT) is clinically important but fundamentally challenging, particularly in low-resource settings across Africa and Asia where contrast agents are frequently unavailable. Progress has been limited by the absence of annotated NCCT benchmarks. Here we describe the TriALS challenge for automated liver lesion segmentation under contrast-limited conditions, supported by a multi-centre dataset of 150 cases with four-phase CT acquisitions (600 volumes) from Egyptian and Chinese institutions. Algorithms were evaluated on 70 cases from three institutions, including an independent external cohort. The top-performing method achieved a mean venous-phase Dice of 0.754, consistent with human-level performance, yet dropped to 0.57 on NCCT. On external validation, the leading method outperformed off-the-shelf models by up to 28% in Dice on NCCT. Algorithm performance was most strongly predicted by training data scale and pre-training strategy. A cross-year comparison exposed a persistent perceptual barrier on NCCT that scaling pre-training alone cannot overcome. Data, annotations, and code are available at https://github.com/xmed-lab/TriALS.

Automated analysis of peripheral blood smears for Acute Lymphoblastic Leukemia (ALL) is hindered by low contrast and substantial variability in cytoplasmic appearance, which complicate conventional membrane-based segmentation. We found that many recent approaches rely on heavy neural architectures and extensive training, but still struggle to generalize across staining and acquisition variability. To address these limitations, we propose the Perinuclear Ring-based Image Segmentation Method (PRISM), which replaces explicit cytoplasmic delineation with adaptive concentric zones constructed around the nucleus. These perinuclear regions enable the extraction of robust cytoplasmic descriptors by integrating color information with texture statistics derived from grey-level co-occurrence patterns, without requiring accurate cell-boundary detection. A calibrated stacking ensemble of traditional classifiers leverages these descriptors to achieve a high performance, with an accuracy of 98.46% and a precision-recall AUC of 0.9937.

Multiple Sclerosis (MS) is a chronic autoimmune disease that can significantly reduce the quality of life of a patient. Existing treatment options can only help slow down the progression of the disease. Therefore, early detection and precise monitoring of disease progression are important. Deep learning offers state-of-the-art models for detecting and segmenting MS lesions in brain MRI scans. However, most of these models are evaluated using the Dice score, without accounting for lesion-wise detection and segmentation performance or other metrics that quantify model performance in cases that are complex or confusing for human annotators, or in cases that are essential for disease detection and progression monitoring. In this paper, we highlight the need to rethink the evaluation of MS lesion segmentation models. In this context, we first present problem fingerprinting in detail to highlight what neurologists look for in brain MRI scans for MS detection and progression monitoring, and which metrics are required to properly quantify model performance in these contexts. Additionally, we present an analysis of state-of-the-art models on two open-source datasets using these metrics to highlight their usability for real-world deployment in hospitals.

Accurate skin lesion segmentation is vital for dermoscopic Computer-Aided Diagnosis. However, visual ambiguity and morphological irregularity often defeat spatial modeling, necessitating multi-domain architectures. Existing paradigms frequently overlook the active use of prediction uncertainty, leading to deterministic frameworks that suffer from blind cross-domain fusion and overfit to label noise. To address these issues, we propose the Uncertainty-Guided Dual-Domain Network (UGDD-Net). UGDD-Net introduces a novel "Glance-and-Gaze" mechanism to transform uncertainty into an active guiding signal. Specifically, the Uncertainty-Guided Bi-directional Feature Fusion (UGBFF) module uses pixel-level uncertainty to modulate spatial-spectral interactions. The Uncertainty-Guided Graph Refinement (UGGR) module constructs a topology-aware graph to propagate reliable semantic consensus and refine uncertain nodes. Finally, the Uncertainty-Guided Margin-Adaptive Loss (UGML) enforces strict constraints on confident pixels while relaxing penalties on uncertain ones to improve statistical calibration. Extensive experiments on ISIC2017, ISIC2018, PH2, and HAM10000 datasets demonstrate that UGDD-Net achieves state-of-the-art performance, especially on "Hard Samples". Our uncertainty maps align with expert inter-observer variability, providing robust interpretability for human-machine collaborative diagnosis.

Multiple sclerosis (MS) expresses substantial clinical and radiological heterogeneity, which poses significant challenges for automatic lesion segmentation. The current deep learning-based SOTA is highly susceptible to changes in both distribution, e.g., changes in scanner; as well as the structure of inputs, evident in the current divide between cross-sectional and longitudinal approaches. We introduce TimeLesSeg, a unified contrast-agnostic framework designed to segment MS lesions regardless of the presence of a temporal dimension in its inputs, with a single convolutional neural network. Our approach models pathological priors through lesion masks, which are processed together with the current scan. Cross-sectional processing is enabled by exposing the model to training cases where no prior information is available, which are modeled with an empty mask, allowing it to operate seamlessly in both scenarios. To overcome the scarcity and inconsistency of longitudinal datasets, we propose a novel generative pipeline in which patterns of lesion evolution are simulated by stochastically deforming each individual lesion with morphological operations, producing realistic prior timepoints. In parallel, we achieve contrast agnosticism through Gaussian mixture model-based domain randomization, enabling the network to experience a wide spectrum of intensity profiles. Results on three publicly available and two in-house datasets show that TimeLesSeg outperforms the contrast-agnostic state of the art on single-modality inputs across overlap- and distance-based metrics. In longitudinal processing, our method outperforms SAMSEG, and captures lesion load dynamics more accurately than both the former and LST-AI. All source code related to the development of TimeLesSeg is available at https://github.com/NeuroADaS-Lab/TimeLesSeg.

Non-alcoholic fatty pancreas disease (NAFPD) is an underdiagnosed condition associated with metabolic syndrome, insulin resistance, and increased risk of pancreatic cancer. Diagnosis typically relies on subjective visual assessment of ultrasound images by clinicians. We propose an end-to-end framework for automatically classifying normal versus fatty pancreas from abdominal ultrasound images. Our method employs a TransUNet-based segmentation architecture with a ResNet encoder and transformer bottleneck to delineate the pancreas and the splenic vein, followed by anatomically-guided patch extraction and patient-level classification through pairwise texture comparison. The feature engineering mimics clinical reasoning by comparing the echogenicity of peri-venous fat to the pancreatic parenchyma, providing an interpretable signal for classification. The segmentation models are initialized via domain-specific transfer learning from a liver segmentation task. We validate the full pipeline on a clinical dataset of 214 abdominal ultrasound images with 107 expert-labeled cases using 5-fold cross-validation. SVM with RBF kernel achieves a mean cross-validated accuracy of 89.7%,$\pm$,1.8% and F1 of 0.898,$\pm$,0.019, while the unsupervised K-Means baseline reaches 87.8% accuracy, demonstrating that the proposed features capture the relevant clinical signal even without labeled training data. To our knowledge, this is the first end-to-end automated framework for fatty pancreas classification from ultrasound using segmentation-guided texture analysis.

Deep learning-based organs/structures-at-risk(OARs) auto-contouring models can improve radiotherapy workflows, but models trained on adult data often underperform in pediatric patients. Developing robust pediatric-specific models is hindered by data scarcity and fragmentation across centers. Federated learning (FL) enables privacy-preserving collaborative training without the need for data sharing. We evaluated the feasibility and performance of FL for developing pediatric-specific OAR segmentation models across two European medical centers. Computed tomography (CT) images from pediatric patients from Utrecht and Heidelberg with a renal tumor or abdominal neuroblastoma were retrospectively collected and locally processed. An nnU-Net-based framework segmented 19 OARs using local and FL schemes. FL was implemented with secure weight exchange on a cloud storage across institutional firewalls. Performance was assessed using the Dice similarity coefficient (DSC), 95th percentile Hausdorff distance, and mean surface distance. Robustness to patient orientation, false-positive segmentation of surgically removed kidneys, and failure cases were identified. A total of 310 postoperative CTs from 272 patients (105 renal tumors, 167 neuroblastomas) were included. Local models performed well on their respective center data but showed significantly reduced cross-center performance for four to seven of the nine evaluated OARs (DSC). In contrast, the FL model matched local performance for at least seven of nine OARs and achieved the best cross-center results across three metrics, with DSC gains of 0.003-0.007 over local models. FL also maintained stable performance across patient orientations and reduced false-positive kidney segmentations. Real-world FL improves cross-center robustness of CT-based OAR segmentation models in pediatric upper abdominal tumors.

We report the design and results of the third autoPET challenge (MICCAI 2024), which benchmarked automated lesion segmentation in whole-body PET/CT under a compositional generalization setting. Training data comprised 1,014 [18F]-FDG PET/CT studies from the University Hospital Tübingen and 597 [18F]/[68Ga]-PSMA PET/CT studies from the LMU University Hospital Munich, constituting the largest publicly available annotated PSMA PET/CT dataset to date. The held-out test set of 200 studies covered four tracer-center combinations, two of which represented unseen compositional pairings. A complementary data-centric award category isolated the contribution of data handling strategies by restricting participants to a fixed baseline model. Seventeen teams submitted 27 algorithms, predominantly nnU-Net-based 3D networks with PET/CT channel concatenation. The top-ranked algorithm achieved a mean DSC of 0.66, FNV of 3.18 mL, and FPV of 2.78 mL across all four test conditions, improving DSC by 8% and reducing the false-negative volume by 5 mL relative to the provided baseline. Ranking was stable across bootstrap resampling and alternative ranking schemes for the top tier. Beyond the benchmark, we provide an in-depth analysis of segmentation performance at the patient and lesion level. Three main conclusions can be drawn: (1) in-domain multitracer PET/CT segmentation is sufficient and probably approaching reader agreement; (2) compositional generalization to unseen tracer-center combinations remains an open problem mainly driven by systematic volume overestimation; (3) heterogeneity and case difficulty drive performance variation substantially more than the choice of algorithm among top-ranked teams.

Although self-supervised pretraining is expected to learn broadly transferable representations, its effectiveness across imaging modalities substantially different from the pretraining domain, and on complex tumor-segmentation tasks, remains understudied. Evaluating CT-pretrained transformers on MRI rectal cancer segmentation, we identified two interacting failure modes in CT-to-MRI transfer: (a) inefficient token usage caused by zero-padding to match pretrained input dimensions, and (b) ineffective feature adaptation. We investigated these vulnerabilities using two primary CT-pretrained hierarchical shifted-window transformer backbones, SMIT and Swin UNETR, together with VoCo as a large-scale-pretrained supporting benchmark; these models differ in pretraining objectives and datasets. Mechanistic analysis leveraged an attention dilution index (ADI), an entropy-based metric quantifying attention diverted toward uninformative padding tokens, and centered kernel alignment (CKA) to measure feature reuse during MRI adaptation. ADI increased with zero-padding, while high feature reuse did not necessarily translate to improved downstream accuracy. To mitigate these issues, we introduced two interventions: a tumor-aware augmentation strategy to expand tumor appearance heterogeneity coverage, and an anisotropic cropping strategy to restore token efficiency. Fine-tuning with these strategies on identical rectal MRI datasets yielded detection rates of 91.1% (225/247) and 88.7% (219/247) for the primary SMIT and Swin UNETR backbones, with the supporting VoCo benchmark reaching 90.3% (223/247), demonstrating significantly improved robustness under CT-to-MRI transfer. This study is among the first to examine when pretrained transformers fail to transfer across imaging modalities and demonstrates how targeted mitigation strategies can systematically overcome cross-modality transfer limitations.

Accurate analysis of histopathological images is critical for disease diagnosis and treatment planning. Whole-slide images (WSIs), which digitize tissue specimens at gigapixel resolution, are fundamental to this process but require aggregating thousands of patches for slide-level predictions. Multiple Instance Learning (MIL) tackles this challenge with a two-stage paradigm, decoupling tile-level embedding and slide-level prediction. However, most existing methods implicitly embed patch representations in homogeneous Euclidean spaces, overlooking the hierarchical organization and regional heterogeneity of pathological tissues. This limits current models' ability to capture global tissue architecture and fine-grained cellular morphology. To address this limitation, we introduce a hybrid hyperbolic-Euclidean representation that embeds WSI features in dual geometric spaces, enabling complementary modeling of hierarchical tissue structures and local morphological details. Building on this formulation, we develop BatMIL, a WSI classification framework that leverages both geometric spaces. To model long-range dependencies among thousands of patches, we employ a structured state space sequence model (S4) backbone that encodes patch sequences with linear computational complexity. Furthermore, to account for regional heterogeneity, we introduce a chunk-level mixture-of-experts (MoE) module that groups patches into regions and dynamically routes them to specialized subnetworks, improving representational capacity while reducing redundant computation. Extensive experiments on seven WSI datasets spanning six cancer types demonstrate that BatMIL consistently outperforms state-of-the-art MIL approaches in slide-level classification tasks. These results indicate that geometry-aware representation learning offers a promising direction for next-generation computational pathology.

Tumor segmentation in whole-body PET/CT imaging is crucial for precise disease evaluation and treatment planning. However, it remains challenging due to variability in lesion size, contrast, and anatomical distribution. Relying on manual segmentation makes the process time-consuming and prone to intra- and inter-observer variability. This work presents a whole-body tumor segmentation method developed for the AutoPET III challenge, where the goal is to build models that generalize across tracers and multi-center data. We employ the nnU-Net framework with a ResNet-based encoder as our baseline and systematically investigate the impact of training strategies, including intensity normalization, batch dice optimization, and data augmentation using CraveMix. Our experiments show that these strategies significantly influence model performance, particularly in reducing false positives and improving robustness to lesion variability. The best-performing configuration achieves a Dice score of up to 0.80 on the preliminary test phase, and our method ranked third in the AutoPET III challenge. The code is publicly available here.

Zero-shot vision-language models (VLMs) offer a promptable alternative to task-specific training for gross tumor volume (GTV) delineation in non-small-cell lung cancer (NSCLC), but the prompt dimensions that govern their spatial behavior remain poorly understood. We study this question by probing alignment directions in VoxTell on a held-out internal NSCLC tumor dataset through sub-prompt decomposition into diagnosis, demographic, staging, anatomical, generic, and irrelevant controls; attribute-wise perturbation robustness; specificity ladders; and cross-case prompt swaps, while benchmarking against fine-tuned and zero-shot baselines using the Dice Similarity Coefficient (DSC) with Wilcoxon signed-rank tests and Benjamini-Hochberg correction. Alignment analyses revealed that anatomical location is the dominant driver of VoxTell's spatial attention: 63.4 percent of location perturbations caused catastrophic drops, prompt specificity improved from generic to full descriptions except for diagnosis-only prompts, irrelevant prompts correctly yielded zero segmentation, and cross-case prompt swaps confirmed patient-specific conditioning (matched DSC 0.906 vs. mismatched 0.406). Histology and stage substitutions had minimal effect, indicating that the model prioritizes "where to look" over "what to look for." In this context, VoxTell, operating fully zero-shot, achieved a mean DSC of 0.613, statistically indistinguishable from nnUNet (0.690, adjusted p = 0.156) and Ahmed et al. (0.675, adjusted p = 0.679), while significantly outperforming all other zero-shot models. Together, these findings argue that segmentation VLMs should be evaluated not only by Dice, but also by the prompt dimensions to which they align.

Accurate lesion segmentation is crucial for clinical diagnosis and treatment planning. However, lesions often resemble surrounding tissues and exhibit ill-defined boundaries, leading to unstable predictions in boundary/transition regions. Moreover, small-lesion cues can be diluted by multi-scale feature extraction, causing under- or over-segmentation. To address these challenges, we propose an Uncertainty-Aware Hypergraph Refinement Network (UHR-Net). First, we introduce an Uncertainty-Oriented Instance Contrastive (UO-IC) pretraining strategy that couples geometry-aware copy-paste augmentation with hard-negative mining of lesion-like background regions to improve instance-level discrimination for small and visually ambiguous lesions. Second, we design an Uncertainty-Guided Hypergraph Refinement (UGHR) block, which derives an entropy-based uncertainty map from a coarse probability map to guide hypergraph refinement. By splitting hyperedge prototypes into foreground and background groups, UGHR decouples higher-order interactions and improves refinement in ambiguous regions. Experiments on five public benchmarks demonstrate consistent gains over strong baselines. Code is available at: https://github.com/CUGfreshman/UHR-Net.

Peritoneal metastases (PM) are staged using the surgically determined Peritoneal Cancer Index (sPCI), which requires invasive laparoscopic assessment. Although CT is routinely used for preoperative evaluation, imaging-based assessment of PM extent remains challenging and is often less structured than surgical PCI scoring. A recent consensus study defined radiological PCI (rPCI) regions for cross-sectional imaging. We present the first deep learning approach to automatically segment 13 rPCI regions on CT. 62 contrast-enhanced CT scans were retrospectively collected across the full PCI range. Each scan was annotated into non-overlapping rPCI regions by one researcher, reviewed by a second, with disagreements resolved by a radiologist. Using five-fold cross-validation, we compared nnU-Net and Swin UNETR with Dice, 95th-percentile Hausdorff distance (HD95) and Average Surface Distance (ASD). We introduce an anatomically constrained pipeline that trains on merged super-regions and splits them during post-processing using TotalSegmentator landmarks at the hips and the ligament of Treitz. On this 62-scan cohort, the baseline nnU-Net reached an overall Dice of 0.81 and outperformed Swin UNETR (0.76). The proposed pipeline improved the overall Dice to 0.84 and reduced boundary error (HD95 13.7 to 11.8 mm; ASD 4.1 to 3.4 mm), with the largest gains in the small-bowel regions, approaching the interobserver Dice of 0.87. Automated rPCI region segmentation on CT is feasible and approaches interobserver agreement. Encoding anatomical boundary constraints substantially improves segmentation quality in the most challenging regions. This provides a reproducible foundation for non-invasive, imaging-based PCI assessment. The main limitations are the single-center cohort and the small interobserver subset.

Surgical resection remains the only potentially curative treatment for pancreatic ductal adenocarcinoma (PDAC), and eligibility depends on accurate assessment of vascular invasion (VI), i.e., tumor extension into adjacent critical vessels. Despite its importance for preoperative staging and surgical planning, computational VI assessment remains underexplored. Two major challenges are the lack of public datasets and the diagnostic ambiguity at the tumor-vessel interface, which leads to substantial inter-rater variability even among expert radiologists. To address these limitations, we introduce the CURVAS-PDACVI Dataset and Challenge, an open benchmark for uncertainty-aware AI in PDAC staging based on a densely annotated dataset with five independent expert annotations per scan. We also propose a multi-metric evaluation framework that extends beyond spatial overlap to include probabilistic calibration and VI assessment. Evaluation of six state-of-the-art methods shows that strong global volumetric overlap does not necessarily translate into reliable performance at clinically critical tumor-vessel interfaces. In particular, methods optimized for binary segmentation perform competitively on average overlap metrics, but often degrade in high-complexity cases with low expert consensus, either collapsing in volume or overextending at uncertain boundaries. In contrast, methods that model inter-rater disagreement produce better calibrated probabilistic maps and show greater robustness in these ambiguous cases. The benchmark highlights the limitations of volumetric accuracy as a proxy for localized surgical utility, motivating uncertainty-aware probabilistic models for preoperative decision-making.

Vision foundation models (VFMs), such as DINOv3, provide rich semantic representations that are promising for computational pathology. However, many current adaptations pair frozen VFMs with lightweight decoders, creating a capacity mismatch that often limits boundary fidelity for infiltrative tumor bulk segmentation. This paper presents Dino-NestedUNet, a framework that couples a pre-trained DINOv3 encoder with a Nested Dense Decoder. Instead of sparse skip connections and linear upsampling, the proposed decoder forms a dense grid of intermediate pathways to enable continuous feature reuse and multi-scale recalibration, aligning high-level semantics with low-level morphological textures during reconstruction. We evaluate Dino-NestedUNet on three histopathology cohorts (multi-center CHTN, institutional OSU, and CAMELYON16) and observe consistent improvements over UNet++ and standard Dino-UNet variants, particularly under cross-domain shift. To further assess external generalization, we perform zero-shot evaluation by training on CHTN and directly testing on unseen TIGER WSIBULK and OSU CRC cohorts without fine-tuning. These results suggest that dense decoding is a key ingredient for unlocking foundation encoders in boundary-sensitive pathology segmentation.

Breast cancer is a leading cause of cancer-related mortality among women worldwide, with mammography as the primary screening tool. While deep learning models have shown strong performance in lesion segmentation, most rely on computationally intensive architectures that limit their use in resource-constrained environments. This study evaluates the performance and efficiency of lightweight models for mammographic lesion segmentation. Architectures including MobileNetV2, EfficientNet Lite, FPN, and Fast-SCNN were compared against a U-Net baseline using the INbreast dataset with 5-fold cross-validation. Performance was assessed using Dice score, Intersection over Union (IoU), and Recall, alongside model complexity. MobileNetV2 with Squeeze-and-Excitation (SCSE) achieved the best performance, with a Dice score of 0.5766 while using approximately 75% fewer parameters than U-Net. Cross-dataset evaluation on the DMID dataset showed reduced accuracy due to domain shift but preserved recall. These results demonstrate that lightweight architectures offer a practical balance between performance and efficiency for deployable CAD systems.

Accurate whole-cell and nuclear segmentation is essential for precision pathology and spatial omics, yet routine hematoxylin and eosin (H&E) staining provides limited cytoplasmic contrast, restricting analyses to nuclei. Multiplex immunofluorescence (mIF) facilitates precise whole-cell delineation but remains constrained by cost and accessibility. We introduce VitaminP, a cross-modal learning framework enabling whole cell segmentation from H&E images. By learning from paired H&E-mIF data, VitaminP transfers molecular boundary information from mIF to overcome cytoplasmic contrast in H&E, establishing cross-modal supervision as a general strategy for recovering missing biological structure. We train VitaminP on 14 public datasets covering 34 cancer types and over 7 million instances, integrating publicly available labels with extensive annotations generated in this study, forming one of the largest resources for segmentation. VitaminP outperforms four state-of-the-art methods and generalizes to unseen datasets, including an in-house dataset spanning 24 rare cancer types. We further developed VitaminPScope, an open-source platform providing an interface for scalable inference and enabling broad adoption.

Deep learning-based nuclei segmentation and classification in pathology images typically rely on large-scale pixel-level manual annotations, which are costly and difficult to obtain across diverse tissues and staining conditions. To address this limitation, we propose a framework that leverages spatial transcriptomics (ST) data as supervision for nuclei segmentation and classification. By incorporating cell-level ST data, we obtain gene expression profiles and corresponding nuclear masks from histopathological images. Gene expression profiles are converted into cell-type labels and used as training data for image-based classification. Because existing gene expression-based cell-type classification methods are not designed for image recognition, we introduce an image-oriented classification approach that bridges gene expression-based cell typing and image-based cell classification. To evaluate generalization, we conduct segmentation experiments on previously unseen organs and compare our method with conventional supervised models. Despite being trained on fewer organ types, our framework achieves higher segmentation accuracy, demonstrating strong transferability. Classification experiments further show consistent improvements over existing approaches.

We present CRC-SAM, a unified framework for colorectal cancer segmentation across colonoscopy, CT, and histopathology images. Unlike prior single-modality methods, CRC-SAM provides consistent, modality-agnostic segmentation throughout the clinical workflow. Built on MedSAM, it incorporates low-rank adaptation (LoRA) layers into a frozen encoder, enabling efficient domain transfer to underrepresented modalities with minimal trainable parameters. Experiments on MSD-Colon, CVC-ClinicDB, and EBHI-Seg demonstrate superior performance across modalities, outperforming state-of-the-art baselines and highlighting the effectiveness of lightweight LoRA adaptation for foundation-model-based colorectal cancer analysis.

Lung adenocarcinoma (LUAD) grading depends on accurately identifying growth patterns, which are indicators of prognosis and can influence treatment decisions. Common deep learning approaches to determine the predominant pattern rely on patch-level classification or segmentation, requiring extensive annotations. This study proposes an attention-based multiple instance learning (ABMIL) framework to predict the predominant LUAD growth pattern at the whole slide level to reduce annotation burden. Our approach integrates pretrained pathology foundation models as patch encoders, used either frozen or fine-tuned on annotated patches, to extract discriminative features that are aggregated through attention mechanisms. Experiments show that fine-tuned encoders improve performance, with Prov-GigaPath achieving the highest agreement (\k{appa} = 0.699) under ABMIL. Compared to simple patch-aggregation baselines, ABMIL yields more robust predictions by leveraging slide-level supervision and spatial attention. Future work will extend this framework to estimate the full distribution of growth patterns and validate performance on external cohorts.

Pancreatic tumor segmentation in contrast-enhanced computed tomography (CT) is clinically important yet technically challenging: lesions are often small, heterogeneous, and easily confused with surrounding soft tissue, and models that perform well on one cohort frequently degrade under cohort shift. Our goal is to improve cross-cohort generalization while keeping the model architecture simple, efficient, and practical for 3D CT segmentation. We introduce PanGuide3D, a cohort-robust architecture with a shared 3D encoder, a pancreas decoder that predicts a probabilistic pancreas map, and a tumor decoder that is explicitly conditioned on this pancreas probability at multiple scales via differentiable soft gating. To capture long-range context under distribution shift, we further add a lightweight Transformer bottleneck in the U-Net bottleneck representation. We evaluate cohort transfer by training on the PanTS (Pancreatic Tumor Segmentation) cohort and testing both in-cohort (PanTS) and out-of-cohort on MSD (Medical Segmentation Decathlon) Task07 Pancreas, using matched preprocessing and training protocols across strong baselines. We collect voxel-level segmentation metrics, patient-level tumor detection, subgroup analyses by tumor size and anatomical location, volume-conditioned performance analyses, and calibration measurements to assess reliability. Across the evaluated models, PanGuide3D achieves the best overall tumor performance and shows improved cross-cohort generalization, particularly for small tumors and challenging anatomical locations, while reducing anatomically implausible false positives. These findings support probabilistic anatomical conditioning as a practical strategy for improving cross-cohort robustness in an end-to-end model and suggest potential utility for contouring support, treatment planning, and multi-institutional studies.

Liver cancer, especially hepatocellular carcinoma (HCC), imposes a substantial global disease burden. Accurate diagnosis and prognostic assessment directly influence treatment selection and patient survival, and pathological examination remains the gold standard for liver cancer diagnosis. Identifying diverse tissue components and pathological subtypes on histopathology slides is crucial for estimating postoperative recurrence risk and overall prognosis. However, most publicly available resources are still provided at the whole-slide image (WSI) level, and well-annotated datasets for fine-grained tissue component identification in liver cancer are scarce, which hinders reproducible model development and the deployment of quantitative analysis tools. To address this gap, we release HepatoBench, a patch-level image database for liver cancer with annotations for seven key tissue categories. Based on HepatoBench, we train and open-source a deep learning classification model as a tissue recognition tool. Furthermore, we train a WSI-level tumor/non-tumor segmentation model to automatically localize lesion regions across entire slides. By integrating the patch-level tissue classifier with the WSI-level segmentation model, we build HepatoQuant, an end-to-end, disease-specific regional quantification tool for liver cancer, enabling a unified workflow from WSIs to tissue composition parsing and quantitative statistics. We also open-source HepatoBench, the benchmarking protocol, and supporting tools, providing a solid foundation for automated regional quantification and fair method comparison in liver cancer pathology.

Recent segmentation models have demonstrated promising efficiency by aggressively reducing parameter counts and computational complexity. However, these models often struggle to accurately delineate fine lesion boundaries and texture patterns essential for early skin cancer diagnosis and treatment planning. In this paper, we propose MambaLiteUNet, a compact yet robust segmentation framework that integrates Mamba state space modeling into a U-Net architecture, along with three key modules: Adaptive Multi-Branch Mamba Feature Fusion (AMF), Local-Global Feature Mixing (LGFM), and Cross-Gated Attention (CGA). These modules are designed to enhance local-global feature interaction, preserve spatial details, and improve the quality of skip connections. MambaLiteUNet achieves an average IoU of 87.12% and average Dice score of 93.09% across ISIC2017, ISIC2018, HAM10000, and PH2 benchmarks, outperforming state-of-the-art models. Compared to U-Net, our model improves average IoU and Dice by 7.72 and 4.61 points, respectively, while reducing parameters by 93.6% and GFLOPs by 97.6%. Additionally, in domain generalization with six unseen lesion categories, MambaLiteUNet achieves 77.61% IoU and 87.23% Dice, performing best among all evaluated models. Our extensive experiments demonstrate that MambaLiteUNet achieves a strong balance between accuracy and efficiency, making it a competitive and practical solution for dermatological image segmentation. Our code is publicly available at: https://github.com/maklachur/MambaLiteUNet.

Automatic pancreas segmentation is fundamental to abdominal MRI analysis, yet deep learning models trained on one MRI sequence often fail catastrophically when applied to another-a challenge that has received little systematic investigation. We introduce CrossPan, a multi-institutional benchmark comprising 1,386 3D scans across three routinely acquired sequences (T1-weighted, T2-weighted, and Out-of-Phase) from eight centers. Our experiments reveal three key findings. First, cross-sequence domain shifts are far more severe than cross-center variability: models achieving Dice scores above 0.85 in-domain collapse to near-zero (<0.02) when transferred across sequences. Second, state-of-the-art domain generalization methods provide negligible benefit under these physics-driven contrast inversions, whereas foundation models like MedSAM2 maintain moderate zero-shot performance through contrast-invariant shape priors. Third, semi-supervised learning offers gains only under stable intensity distributions and becomes unstable on sequences with high intra-organ variability. These results establish cross-sequence generalization-not model architecture or center diversity-as the primary barrier to clinically deployable pancreas MRI segmentation. Dataset and code are available at https://crosspan.netlify.app/.

Automated 3D segmentation of prostate lesions from biparametric MRI (bp-MRI) is essential for reliable algorithmic analysis, but achieving high precision remains challenging. Volumetric methods must combine multiple modalities while ensuring anatomical consistency, but current models struggle to integrate cross-modal information reliably. While vision-language models (VLMs) are replacing the currently used architectural designs, they still lack the fine-grained, lesion-level semantics required for effective localized guidance. To address these limitations, we propose a new multi-encoder U-Net architecture incorporating three key innovations: (1) an alignment loss that enhances foreground text-image similarity to inject lesion semantics; (2) a heatmap loss that calibrates the similarity map and suppresses spurious background activations; and (3) a final-stage, confidence-gated multi-head cross-attention refiner that performs localized boundary edits in high-confidence regions. A phase-scheduled training regime stabilizes the optimization of these components. Our method consistently outperforms prior approaches, establishing a new state-of-the-art on the PI-CAI dataset through enhanced multi-modal fusion and localized text guidance. Our code is available at https://github.com/NUBagciLab/Prostate-Lesion-Segmentation.

Large segmentation foundation models such as the Segment Anything Model (SAM) have reshaped promptable segmentation in natural images, and recent efforts have extended these models to medical images and volumetric settings. However, directly transferring a 3D SAM-style model to lesion segmentation remains challenging due to (i) weak spatial representational capacity for small, irregular targets in intermediate features, and (ii) extreme foreground-background imbalance in 3D volumes.We propose SGP-SAM, a self-gated prompting framework for efficient and effective transfer to 3D lesion segmentation. Our key component, the Self-Gated Prompting Module (SGPM), performs conditional multi-scale spatial enhancement: a lightweight multi-channel gating unit predicts whether the current features require additional multi-scale fusion, and only then activates a Multi-Scale Feature Fusion Block to enrich spatial context. To further address small-lesion learning, we design a Zoom Loss that up-weights lesion-focused supervision by combining Dice and a voxel-balanced focal term.Experiments on MSD Liver Tumor and MSD Brain Tumor (enhancing tumor) show consistent gains over strong transfer baselines based on SAM-Med3D. On MSD Liver Tumor, SGP-SAM improves mDice by 7.3% over fine-tuning.

Robust segmentation of clinically significant prostate cancer (csPCa) on multi-parametric MRI must tolerate frequent degradation of its most informative diffusion sequences. Multi-modal fusion commonly employs learned modality gating under the assumption that gates implement per-sample modality quality routing -- rarely tested directly. We ask how gating behaves across backbone architectures. We systematically analyze modality-isolated gated fusion (MIGF) for csPCa segmentation on two backbones (nnU-Net and Mamba) using PI-CAI (n=1500), with cross-cohort validation on Prostate158 (n=158): a factorial ablation over gating, modality dropout, and deep supervision under 5-fold cross-validation (180 trained models), plus a gate-weight and counterfactual analysis of 30 trained gating models. Modality gating is backbone-conditional. On nnU-Net, adding gating reduces the ranking score (marginal effect -0.037; gating configurations p<0.05), whereas on Mamba the gating-plus-dropout configuration improves it (+0.024, p=0.037). Gate-weight analysis explains this: nnU-Net gates collapse into a near-static modality prior (across-case SD 0.0033), while Mamba gates retain sample-dependent variation (0.0365, ~11x larger, non-overlapping); replacing per-sample gates with their training-set mean leaves nnU-Net unchanged but degrades Mamba. Modality dropout is the only component beneficial on both backbones. Under cross-cohort shift, convolutional backbones collapse to case-level specificity near zero, whereas Mamba retains it (MIGF-Mamba highest, 0.31). Learned modality gates do not universally perform per-sample quality routing; their effective behavior is conditional on the backbone's inherent modality awareness. Among tested configurations, MIGF-Mamba is the most cross-cohort robust, and training-time modality dropout is the only component beneficial across both backbones.

Whole slide image (WSI) analysis heavily relies on multiple instance learning (MIL). While recent methods benefit from large-scale foundation models and advanced sequence modeling to capture long-range dependencies, they still struggle with two critical issues. First, directly applying frozen, task-agnostic features often leads to suboptimal separability due to the domain gap with specific histological tasks. Second, relying solely on global aggregators can cause over-smoothing, where sparse but critical diagnostic signals are overshadowed by the dominant background context. In this paper, we present ReconMIL, a novel framework designed to bridge this domain gap and balance global-local feature aggregation. Our approach introduces a Latent Space Reconstruction module that adaptively projects generic features into a compact, task-specific manifold, improving boundary delineation. To prevent information dilution, we develop a bi-stream architecture combining a Mamba-based global stream for contextual priors and a CNN-based local stream to preserve subtle morphological anomalies. A scale-adaptive selection mechanism dynamically fuses these two streams, determining when to rely on overall architecture versus local saliency. Evaluations across multiple diagnostic and survival prediction benchmarks show that ReconMIL consistently outperforms current state-of-the-art methods, effectively localizing fine-grained diagnostic regions while suppressing background noise. Visualization results confirm the models superior ability to localize diagnostic regions by effectively balancing global structure and local granularity.

Background and Objective: Precise and scalable instance segmentation of cell nuclei is a fundamental prerequisite for computational pathology, yet gigapixel whole-slide images (WSIs) pose significant computational challenges. While patch-based processing is standard during training, existing methods are often limited to small tile sizes during inference due to architectural bottlenecks or reliance on computationally expensive post-processing for instance separation. We introduce a faster, scalable, and end-to-end framework capable of processing large-scale image tiles while accurately modeling biologically realistic overlapping nuclei. Methods: We propose LSP-DETR (Local Star Polygon DEtection TRansformer). The model represents nuclei as star-convex polygons and employs a lightweight transformer with linear complexity, enabling the processing of high-resolution images in a single forward pass. A novel radial distance loss accommodates annotation uncertainty, allowing the segmentation of overlapping nuclei to emerge naturally without explicit overlap labels. Results: LSP-DETR achieves state-of-the-art efficiency, with an inference time of 0.45 s/mm^2, a 3.2x speedup over StarDist, the next-fastest method. On PanNuke, the model achieves competitive accuracy (67.5 bPQ), while yielding an F$_1$-score of 0.964 in polygon overlap when evaluated against consensus annotations from two expert pathologists. Furthermore, it outperforms larger models such as LKCell in generalization robustness, reaching an F1-score of 85.0 on MoNuSeg. Conclusions: LSP-DETR bridges the gap between high-fidelity segmentation and practical clinical requirements by eliminating heuristic post-processing. By providing a scalable, linear-complexity solution that naturally handles overlaps between nuclei, this framework sets a new direction for efficient high-throughput WSI analysis in digital pathology.

While foundation models in radiology are expected to be applied to various clinical tasks, computational cost constraints remain a major challenge when training on 3D-CT volumetric data. In this study, we propose TotalFM, a radiological foundation model that efficiently learns the correspondence between 3D-CT images and linguistic expressions based on the concept of organ separation, utilizing a large-scale dataset of 140,000 series. By automating the creation of organ volume and finding-sentence pairs through segmentation techniques and Large Language Model (LLM)-based radiology report processing, and by combining self-supervised pre-training via VideoMAE with contrastive learning using volume-text pairs, we aimed to balance computational efficiency and representation capability. In zero-shot organ-wise lesion classification tasks, the proposed model achieved higher F1 scores in 83% (5/6) of organs compared to CT-CLIP and 64% (9/14) of organs compared to Merlin. These results suggest that the proposed model exhibits high generalization performance in a clinical evaluation setting using actual radiology report sentences. Furthermore, in zero-shot finding-wise lesion classification tasks, our model achieved a higher AUROC in 83% (25/30) of finding categories compared to Merlin. We also confirmed performance comparable to existing Vision-Language Models (VLMs) in radiology report generation tasks. Our results demonstrate that the organ-separated learning framework can serve as a realistic and effective design guideline for the practical implementation of 3D-CT foundation models. The source code and pretrained models are publicly available at https://github.com/jichi-labo/TotalFM.

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

Peripheral neuroblastic tumors (pNTs) are among the most common extracranial solid tumors in children, and accurate pathological subtyping is important for risk stratification and treatment planning. However, pNT subtyping on hematoxylin-eosin whole-slide images (WSIs) remains challenging because of limited pediatric tumor cohorts, marked histological heterogeneity, inter-observer variability, and the computational burden of existing WSI classifiers. To address these challenges, we propose CoPath, a framework consisting of CoHisNet and PathVote. CoHisNet is a lightweight multi-scale feature-fusion network for patch-level histopathological classification. By replacing the multilayer perceptron components in Swin Transformer blocks and the classification head with Kolmogorov-Arnold Network layers, CoHisNet improves nonlinear feature modeling under a compact architecture. Its multi-scale interaction and contrast-driven feature-enhancement design enables the model to capture both tissue-level structures and fine-grained cellular morphology. PathVote further incorporates pathology-informed tissue-component priors to aggregate patch-level predictions into WSI-level decisions. We validated CoPath on a private two-branch PpNTs cohort and the public BreakHis breast cancer histopathology dataset. Experimental results show that CoPath achieves competitive or superior performance compared with general image classifiers, pathology foundation models under linear probing, and pathology-specific classification models, while maintaining substantially lower computational complexity. The source code is available at https://github.com/JSLiam94/CoPath.

Cancer survival prediction from whole slide images (WSIs) is a challenging task in computational pathology due to the large size, irregular shape, and high granularity of the WSIs. These characteristics make it difficult to capture the full spectrum of patterns, from subtle cellular abnormalities to complex tissue interactions, which are crucial for accurate prognosis. To address this, we propose CrossFusion, a novel multi-scale feature integration framework that extracts and fuses information from patches across different magnification levels. By effectively modeling both scale-specific patterns and their interactions, CrossFusion generates a rich feature set that enhances survival prediction accuracy. We validate our approach across six cancer types from public datasets, demonstrating significant improvements over existing state-of-the-art methods. Moreover, when coupled with domain-specific feature extraction backbones, our method shows further gains in prognostic performance compared to general-purpose backbones. The source code is available at: https://github.com/RustinS/CrossFusion

Accurate segmentation of pulmonary lesions is essential for effective clinical diagnosis and treatment strategies. Existing segmentation approaches often lack task-specific semantic guidance, as text-based annotations typically offer coarse localization of lesions, leading to inadequate delineation of lesion boundaries and poor performance on small-scale lesions. To address this, we propose CGSM, a Concept-Guided Segmentation Model that integrates LLM-generated and clinically reviewed concepts into the segmentation process. Specifically, we design a Concept-Visual Alignment Module (CVAM) to activate relevant tokens within the concepts that align with visual features, enhancing the interaction between textual and visual information. In addition, we introduce a Concept Modulated Decoder (CM-Decoder), which uses concepts from CVAM as modulation signals to facilitate the adaptive fusion of image and text features, improving the segmentation accuracy. Extensive experiments on two public datasets show that CGSM achieves state-of-the-art performance, with results of 91.59% Dice and 84.49% mIoU on the QaTa-COV19 dataset, demonstrating its effectiveness in pulmonary lesion segmentation.

Accurate wound classification (WC) and boundary segmentation are essential for guiding clinical decisions in chronic and acute wound management. However, most existing artificial intelligence (AI) models are limited, focusing on a narrow set of wound types, limited variations in wound severity, or a single task (segmentation or classification), which reduces their clinical applicability. This study presents two dedicated instance segmentation models based on You Only Look Once (YOLO)v11 that perform wound boundary segmentation (WBS) and WC across five clinically relevant wound types: burn injury (BI), pressure injury, diabetic foot ulcer, vascular ulcer, and surgical wound. A wound-type balanced dataset of 2,963 annotated images was created to train the models for both tasks, using five-fold cross-validation. Models trained on the original, non-augmented dataset performed consistently across folds, though BI detection accuracy was relatively low; augmenting the dataset with rotation, flipping, and variations in brightness, saturation, and exposure significantly improved performance, particularly for visually subtle BI cases. Among the tested variants, YOLOv11x achieved the best WBS performance (F1-score: 0.9341; mAP50: 0.9629). For WC, YOLOv11m achieved the highest mAP50 (0.9194) and mAP50-95 (0.6950), whereas YOLOv11l achieved the highest F1-score (0.8797). The lightweight YOLOv11n provided comparable accuracy at lower computational cost, making it suitable for resource-constrained deployments. Supported by confusion matrices and visual detection outputs, the results confirm robustness against complex backgrounds and high intra-class variability, demonstrating the potential of YOLOv11-based architectures for accurate, real-time wound analysis in clinical and remote care settings.