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Towards Affordable Tumor Segmentation and Visualization for 3D Breast MRI Using SAM2

Solha Kang, Eugene Kim, Joris Vankerschaver, Utku Ozbulak

arxiv logopreprintJul 31 2025
Breast MRI provides high-resolution volumetric imaging critical for tumor assessment and treatment planning, yet manual interpretation of 3D scans remains labor-intensive and subjective. While AI-powered tools hold promise for accelerating medical image analysis, adoption of commercial medical AI products remains limited in low- and middle-income countries due to high license costs, proprietary software, and infrastructure demands. In this work, we investigate whether the Segment Anything Model 2 (SAM2) can be adapted for low-cost, minimal-input 3D tumor segmentation in breast MRI. Using a single bounding box annotation on one slice, we propagate segmentation predictions across the 3D volume using three different slice-wise tracking strategies: top-to-bottom, bottom-to-top, and center-outward. We evaluate these strategies across a large cohort of patients and find that center-outward propagation yields the most consistent and accurate segmentations. Despite being a zero-shot model not trained for volumetric medical data, SAM2 achieves strong segmentation performance under minimal supervision. We further analyze how segmentation performance relates to tumor size, location, and shape, identifying key failure modes. Our results suggest that general-purpose foundation models such as SAM2 can support 3D medical image analysis with minimal supervision, offering an accessible and affordable alternative for resource-constrained settings.

Consistent Point Matching

Halid Ziya Yerebakan, Gerardo Hermosillo Valadez

arxiv logopreprintJul 31 2025
This study demonstrates that incorporating a consistency heuristic into the point-matching algorithm \cite{yerebakan2023hierarchical} improves robustness in matching anatomical locations across pairs of medical images. We validated our approach on diverse longitudinal internal and public datasets spanning CT and MRI modalities. Notably, it surpasses state-of-the-art results on the Deep Lesion Tracking dataset. Additionally, we show that the method effectively addresses landmark localization. The algorithm operates efficiently on standard CPU hardware and allows configurable trade-offs between speed and robustness. The method enables high-precision navigation between medical images without requiring a machine learning model or training data.

Thin-slice 2D MR Imaging of the Shoulder Joint Using Denoising Deep Learning Reconstruction Provides Higher Image Quality Than 3D MR Imaging.

Kakigi T, Sakamoto R, Arai R, Yamamoto A, Kuriyama S, Sano Y, Imai R, Numamoto H, Miyake KK, Saga T, Matsuda S, Nakamoto Y

pubmed logopapersJul 31 2025
This study was conducted to evaluate whether thin-slice 2D fat-saturated proton density-weighted images of the shoulder joint in three imaging planes combined with parallel imaging, partial Fourier technique, and denoising approach with deep learning-based reconstruction (dDLR) are more useful than 3D fat-saturated proton density multi-planar voxel images. Eighteen patients who underwent MRI of the shoulder joint at 3T were enrolled. The denoising effect of dDLR in 2D was evaluated using coefficient of variation (CV). Qualitative evaluation of anatomical structures, noise, and artifacts in 2D after dDLR and 3D was performed by two radiologists using a five-point Likert scale. All were analyzed statistically. Gwet's agreement coefficients were also calculated. The CV of 2D after dDLR was significantly lower than that before dDLR (P < 0.05). Both radiologists rated 2D higher than 3D for all anatomical structures and noise (P < 0.05), except for artifacts. Both Gwet's agreement coefficients of anatomical structures, noise, and artifacts in 2D and 3D produced nearly perfect agreement between the two radiologists. The evaluation of 2D tended to be more reproducible than 3D. 2D with parallel imaging, partial Fourier technique, and dDLR was proved to be superior to 3D for depicting shoulder joint structures with lower noise.

DICOM De-Identification via Hybrid AI and Rule-Based Framework for Scalable, Uncertainty-Aware Redaction

Kyle Naddeo, Nikolas Koutsoubis, Rahul Krish, Ghulam Rasool, Nidhal Bouaynaya, Tony OSullivan, Raj Krish

arxiv logopreprintJul 31 2025
Access to medical imaging and associated text data has the potential to drive major advances in healthcare research and patient outcomes. However, the presence of Protected Health Information (PHI) and Personally Identifiable Information (PII) in Digital Imaging and Communications in Medicine (DICOM) files presents a significant barrier to the ethical and secure sharing of imaging datasets. This paper presents a hybrid de-identification framework developed by Impact Business Information Solutions (IBIS) that combines rule-based and AI-driven techniques, and rigorous uncertainty quantification for comprehensive PHI/PII removal from both metadata and pixel data. Our approach begins with a two-tiered rule-based system targeting explicit and inferred metadata elements, further augmented by a large language model (LLM) fine-tuned for Named Entity Recognition (NER), and trained on a suite of synthetic datasets simulating realistic clinical PHI/PII. For pixel data, we employ an uncertainty-aware Faster R-CNN model to localize embedded text, extract candidate PHI via Optical Character Recognition (OCR), and apply the NER pipeline for final redaction. Crucially, uncertainty quantification provides confidence measures for AI-based detections to enhance automation reliability and enable informed human-in-the-loop verification to manage residual risks. This uncertainty-aware deidentification framework achieves robust performance across benchmark datasets and regulatory standards, including DICOM, HIPAA, and TCIA compliance metrics. By combining scalable automation, uncertainty quantification, and rigorous quality assurance, our solution addresses critical challenges in medical data de-identification and supports the secure, ethical, and trustworthy release of imaging data for research.

Topology Optimization in Medical Image Segmentation with Fast Euler Characteristic

Liu Li, Qiang Ma, Cheng Ouyang, Johannes C. Paetzold, Daniel Rueckert, Bernhard Kainz

arxiv logopreprintJul 31 2025
Deep learning-based medical image segmentation techniques have shown promising results when evaluated based on conventional metrics such as the Dice score or Intersection-over-Union. However, these fully automatic methods often fail to meet clinically acceptable accuracy, especially when topological constraints should be observed, e.g., continuous boundaries or closed surfaces. In medical image segmentation, the correctness of a segmentation in terms of the required topological genus sometimes is even more important than the pixel-wise accuracy. Existing topology-aware approaches commonly estimate and constrain the topological structure via the concept of persistent homology (PH). However, these methods are difficult to implement for high dimensional data due to their polynomial computational complexity. To overcome this problem, we propose a novel and fast approach for topology-aware segmentation based on the Euler Characteristic ($\chi$). First, we propose a fast formulation for $\chi$ computation in both 2D and 3D. The scalar $\chi$ error between the prediction and ground-truth serves as the topological evaluation metric. Then we estimate the spatial topology correctness of any segmentation network via a so-called topological violation map, i.e., a detailed map that highlights regions with $\chi$ errors. Finally, the segmentation results from the arbitrary network are refined based on the topological violation maps by a topology-aware correction network. Our experiments are conducted on both 2D and 3D datasets and show that our method can significantly improve topological correctness while preserving pixel-wise segmentation accuracy.

Hybrid optimization enabled Eff-FDMNet for Parkinson's disease detection and classification in federated learning.

Subramaniam S, Balakrishnan U

pubmed logopapersJul 31 2025
Parkinson's Disease (PD) is a progressive neurodegenerative disorder and the early diagnosis is crucial for managing symptoms and slowing disease progression. This paper proposes a framework named Federated Learning Enabled Waterwheel Shuffled Shepherd Optimization-based Efficient-Fuzzy Deep Maxout Network (FedL_WSSO based Eff-FDMNet) for PD detection and classification. In local training model, the input image from the database "Image and Data Archive (IDA)" is given for preprocessing that is performed using Gaussian filter. Consequently, image augmentation takes place and feature extraction is conducted. These processes are executed for every input image. Therefore, the collected outputs of images are used for PD detection using Shepard Convolutional Neural Network Fuzzy Zeiler and Fergus Net (ShCNN-Fuzzy-ZFNet). Then, PD classification is accomplished using Eff-FDMNet, which is trained using WSSO. At last, based on CAViaR, local updation and aggregation are changed in server. The developed method obtained highest accuracy as 0.927, mean average precision as 0.905, lowest false positive rate (FPR) as 0.082, loss as 0.073, Mean Squared Error (MSE) as 0.213, and Root Mean Squared Error (RMSE) as 0.461. The high accuracy and low error rates indicate that the potent framework can enhance patient outcomes by enabling more reliable and personalized diagnosis.

Effect of spatial resolution on the diagnostic performance of machine-learning radiomics model in lung adenocarcinoma: comparisons between normal- and high-spatial-resolution imaging for predicting invasiveness.

Yanagawa M, Nagatani Y, Hata A, Sumikawa H, Moriya H, Iwano S, Tsuchiya N, Iwasawa T, Ohno Y, Tomiyama N

pubmed logopapersJul 31 2025
To construct two machine learning radiomics (MLR) for invasive adenocarcinoma (IVA) prediction using normal-spatial-resolution (NSR) and high-spatial-resolution (HSR) training cohorts, and to validate models (model-NSR and -HSR) in another test cohort while comparing independent radiologists' (R1, R2) performance with and without model-HSR. In this retrospective multicenter study, all CT images were reconstructed using NSR data (512 matrix, 0.5-mm thickness) and HSR data (2048 matrix, 0.25-mm thickness). Nodules were divided into training (n = 61 non-IVA, n = 165 IVA) and test sets (n = 36 non-IVA, n = 203 IVA). Two MLR models were developed with 18 significant factors for the NSR model and 19 significant factors for the HSR model from 172 radiomics features using random forest. Area under the receiver operator characteristic curves (AUC) was analyzed using DeLong's test in the test set. Accuracy (acc), sensitivity (sen), and specificity (spc) of R1 and R2 with and without model-HSR were compared using McNemar test. 437 patients (70 ± 9 years, 203 men) had 465 nodules (n = 368, IVA). Model-HSR AUCs were significantly higher than model-NSR in training (0.839 vs. 0.723) and test sets (0.863 vs. 0.718) (p < 0.05). R1's acc (87.2%) and sen (93.1%) with model-HSR were significantly higher than without (77.0% and 79.3%) (p < 0.0001). R2's acc (83.7%) and sen (86.7%) with model-HSR might be equal or higher than without (83.7% and 85.7%, respectively), but not significant (p > 0.50). Spc of R1 (52.8%) and R2 (66.7%) with model-HSR might be lower than without (63.9% and 72.2%, respectively), but not significant (p > 0.21). HSR-based MLR model significantly increased IVA diagnostic performance compared to NSR, supporting radiologists without compromising accuracy and sensitivity. However, this benefit came at the cost of reduced specificity, potentially increasing false positives, which may lead to unnecessary examinations or overtreatment in clinical settings.

Generative artificial intelligence for counseling of fetal malformations following ultrasound diagnosis.

Grünebaum A, Chervenak FA

pubmed logopapersJul 31 2025
To explore the potential role of generative artificial intelligence (GenAI) in enhancing patient counseling following prenatal ultrasound diagnosis of fetal malformations, with an emphasis on clinical utility, patient comprehension, and ethical implementation. The detection of fetal anomalies during the mid-trimester ultrasound is emotionally distressing for patients and presents significant challenges in communication and decision-making. Generative AI tools, such as GPT-4 and similar models, offer novel opportunities to support clinicians in delivering accurate, empathetic, and accessible counseling while preserving the physician's central role. We present a narrative review and applied framework illustrating how GenAI can assist obstetricians before, during, and after the fetal anomaly scan. Use cases include lay summaries, visual aids, anticipatory guidance, multilingual translation, and emotional support. Tables and sample prompts demonstrate practical applications across a range of anomalies.

A Trust-Guided Approach to MR Image Reconstruction with Side Information.

Atalik A, Chopra S, Sodickson DK

pubmed logopapersJul 31 2025
Reducing MRI scan times can improve patient care and lower healthcare costs. Many acceleration methods are designed to reconstruct diagnostic-quality images from sparse k-space data, via an ill-posed or ill-conditioned linear inverse problem (LIP). To address the resulting ambiguities, it is crucial to incorporate prior knowledge into the optimization problem, e.g., in the form of regularization. Another form of prior knowledge less commonly used in medical imaging is the readily available auxiliary data (a.k.a. side information) obtained from sources other than the current acquisition. In this paper, we present the Trust-Guided Variational Network (TGVN), an end-to-end deep learning framework that effectively and reliably integrates side information into LIPs. We demonstrate its effectiveness in multi-coil, multi-contrast MRI reconstruction, where incomplete or low-SNR measurements from one contrast are used as side information to reconstruct high-quality images of another contrast from heavily under-sampled data. TGVN is robust across different contrasts, anatomies, and field strengths. Compared to baselines utilizing side information, TGVN achieves superior image quality while preserving subtle pathological features even at challenging acceleration levels, drastically speeding up acquisition while minimizing hallucinations. Source code and dataset splits are available on github.com/sodicksonlab/TGVN.

Label-free estimation of clinically relevant performance metrics under distribution shifts

Tim Flühmann, Alceu Bissoto, Trung-Dung Hoang, Lisa M. Koch

arxiv logopreprintJul 30 2025
Performance monitoring is essential for safe clinical deployment of image classification models. However, because ground-truth labels are typically unavailable in the target dataset, direct assessment of real-world model performance is infeasible. State-of-the-art performance estimation methods address this by leveraging confidence scores to estimate the target accuracy. Despite being a promising direction, the established methods mainly estimate the model's accuracy and are rarely evaluated in a clinical domain, where strong class imbalances and dataset shifts are common. Our contributions are twofold: First, we introduce generalisations of existing performance prediction methods that directly estimate the full confusion matrix. Then, we benchmark their performance on chest x-ray data in real-world distribution shifts as well as simulated covariate and prevalence shifts. The proposed confusion matrix estimation methods reliably predicted clinically relevant counting metrics on medical images under distribution shifts. However, our simulated shift scenarios exposed important failure modes of current performance estimation techniques, calling for a better understanding of real-world deployment contexts when implementing these performance monitoring techniques for postmarket surveillance of medical AI models.
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