Foundation models for volumetric medical image segmentation have emerged as powerful tools in clinical workflows, enabling radiologists to delineate regions of interest through intuitive clicks. While these models demonstrate promising capabilities in segmenting previously unseen anatomical structures, their performance is strongly influenced by prompt quality. In clinical settings, radiologists often provide suboptimal prompts, which affects segmentation reliability and accuracy. To address this limitation, we present SafeClick, an error-tolerant interactive segmentation approach for medical volumes based on hierarchical expert consensus. SafeClick operates as a plug-and-play module compatible with foundation models including SAM 2 and MedSAM 2. The framework consists of two key components: a collaborative expert layer (CEL) that generates diverse feature representations through specialized transformer modules, and a consensus reasoning layer (CRL) that performs cross-referencing and adaptive integration of these features. This architecture transforms the segmentation process from a prompt-dependent operation to a robust framework capable of producing accurate results despite imperfect user inputs. Extensive experiments across 15 public datasets demonstrate that our plug-and-play approach consistently improves the performance of base foundation models, with particularly significant gains when working with imperfect prompts. The source code is available at https://github.com/yifangao112/SafeClick.

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

Deep learning-based medical image classification techniques are rapidly advancing in medical image analysis, making it crucial to develop accurate and trustworthy models that can be efficiently deployed across diverse clinical scenarios. Concept Bottleneck Models (CBMs), which first predict a set of explainable concepts from images and then perform classification based on these concepts, are increasingly being adopted for explainable medical image classification. However, the inherent explainability of CBMs introduces new challenges when deploying trained models to new environments. Variations in imaging protocols and staining methods may induce concept-level shifts, such as alterations in color distribution and scale. Furthermore, since CBM training requires explicit concept annotations, fine-tuning models solely with image-level labels could compromise concept prediction accuracy and faithfulness - a critical limitation given the high cost of acquiring expert-annotated concept labels in medical domains. To address these challenges, we propose a training-free confusion concept identification strategy. By leveraging minimal new data (e.g., 4 images per class) with only image-level labels, our approach enhances out-of-domain performance without sacrificing source domain accuracy through two key operations: masking misactivated confounding concepts and amplifying under-activated discriminative concepts. The efficacy of our method is validated on both skin and white blood cell images. Our code is available at: https://github.com/riverback/TF-TTI-XMed.

Synthetic data has recently reached a level of visual fidelity that makes it nearly indistinguishable from real data, offering great promise for privacy-preserving data sharing in medical imaging. However, fully synthetic datasets still suffer from significant limitations: First and foremost, the legal aspect of sharing synthetic data is often neglected and data regulations, such as the GDPR, are largley ignored. Secondly, synthetic models fall short of matching the performance of real data, even for in-domain downstream applications. Recent methods for image generation have focused on maximising image diversity instead of fidelity solely to improve the mode coverage and therefore the downstream performance of synthetic data. In this work, we shift perspective and highlight how maximizing diversity can also be interpreted as protecting natural persons from being singled out, which leads to predicate singling-out (PSO) secure synthetic datasets. Specifically, we propose a generalisable framework for training diffusion models on personal data which leads to unpersonal synthetic datasets achieving performance within one percentage point of real-data models while significantly outperforming state-of-the-art methods that do not ensure privacy. Our code is available at https://github.com/MischaD/Trichotomy.

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

PurposeTo develop a deep learning model - Cornea nnU-Net Extractor (CUNEX) - for full-thickness corneal segmentation of anterior segment optical coherence tomography (AS-OCT) images and evaluate its utility in artificial intelligence (AI) research. MethodsWe trained and evaluated CUNEX using nnU-Net on 600 AS-OCT images (CSO MS-39) from 300 patients: 100 normal, 100 keratoconus (KC), and 100 Fuchs endothelial corneal dystrophy (FECD) eyes. To assess generalizability, we externally validated CUNEX on 1,168 AS-OCT images from an infectious keratitis dataset acquired from a different device (Casia SS-1000). We benchmarked CUNEX against two recent models, CorneaNet and ScLNet. We then applied CUNEX to our dataset of 194,599 scans from 37,499 patients as preprocessing for a classification model evaluating whether segmentation improves AI prediction, including age, sex, and disease staging (KC and FECD). ResultsCUNEX achieved Dice similarity coefficient (DSC) and intersection over union (IoU) scores ranging from 94-95% and 90-99%, respectively, across healthy, KC, and FECD eyes. This was similar to ScLNet (within 3%) but better than CorneaNet (8-35% lower). On external validation, CUNEX maintained high performance (DSC 83%; IoU 71%) while ScLNet (DSC 14%; IoU 8%) and CorneaNet (DSC 16%; IoU 9%) failed to generalize. Unexpectedly, segmentation minimally impacted classification accuracy except for sex prediction, where accuracy dropped from 81 to 68%, suggesting sex-related features may lie outside the cornea. ConclusionCUNEX delivers the first open-source generalizable corneal segmentation model using the latest framework, supporting its use in clinical analysis and AI workflows across diseases and imaging platforms. It is available at https://github.com/lkandakji/CUNEX.

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

In clinical practice, imaging modalities with functional characteristics, such as positron emission tomography (PET) and fractional anisotropy (FA), are often aligned with a structural reference (e.g., MRI, CT) for accurate interpretation or group analysis, necessitating multi-modal deformable image registration (DIR). However, due to the extreme heterogeneity of these modalities compared to standard structural scans, conventional unsupervised DIR methods struggle to learn reliable spatial mappings and often distort images. We find that the similarity metrics guiding these models fail to capture alignment between highly disparate modalities. To address this, we propose M2M-Reg (Multi-to-Mono Registration), a novel framework that trains multi-modal DIR models using only mono-modal similarity while preserving the established architectural paradigm for seamless integration into existing models. We also introduce GradCyCon, a regularizer that leverages M2M-Reg's cyclic training scheme to promote diffeomorphism. Furthermore, our framework naturally extends to a semi-supervised setting, integrating pre-aligned and unaligned pairs only, without requiring ground-truth transformations or segmentation masks. Experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate that M2M-Reg achieves up to 2x higher DSC than prior methods for PET-MRI and FA-MRI registration, highlighting its effectiveness in handling highly heterogeneous multi-modal DIR. Our code is available at https://github.com/MICV-yonsei/M2M-Reg.

Medical report generation from imaging data remains a challenging task in clinical practice. While large language models (LLMs) show great promise in addressing this challenge, their effective integration with medical imaging data still deserves in-depth exploration. In this paper, we present MRG-LLM, a novel multimodal large language model (MLLM) that combines a frozen LLM with a learnable visual encoder and introduces a dynamic prompt customization mechanism. Our key innovation lies in generating instance-specific prompts tailored to individual medical images through conditional affine transformations derived from visual features. We propose two implementations: prompt-wise and promptbook-wise customization, enabling precise and targeted report generation. Extensive experiments on IU X-ray and MIMIC-CXR datasets demonstrate that MRG-LLM achieves state-of-the-art performance in medical report generation. Our code will be made publicly available.

Objective: Our study aimed to evaluate and validate PanSegNet, a deep learning (DL) algorithm for pediatric pancreas segmentation on MRI in children with acute pancreatitis (AP), chronic pancreatitis (CP), and healthy controls. Methods: With IRB approval, we retrospectively collected 84 MRI scans (1.5T/3T Siemens Aera/Verio) from children aged 2-19 years at Gazi University (2015-2024). The dataset includes healthy children as well as patients diagnosed with AP or CP based on clinical criteria. Pediatric and general radiologists manually segmented the pancreas, then confirmed by a senior pediatric radiologist. PanSegNet-generated segmentations were assessed using Dice Similarity Coefficient (DSC) and 95th percentile Hausdorff distance (HD95). Cohen's kappa measured observer agreement. Results: Pancreas MRI T2W scans were obtained from 42 children with AP/CP (mean age: 11.73 +/- 3.9 years) and 42 healthy children (mean age: 11.19 +/- 4.88 years). PanSegNet achieved DSC scores of 88% (controls), 81% (AP), and 80% (CP), with HD95 values of 3.98 mm (controls), 9.85 mm (AP), and 15.67 mm (CP). Inter-observer kappa was 0.86 (controls), 0.82 (pancreatitis), and intra-observer agreement reached 0.88 and 0.81. Strong agreement was observed between automated and manual volumes (R^2 = 0.85 in controls, 0.77 in diseased), demonstrating clinical reliability. Conclusion: PanSegNet represents the first validated deep learning solution for pancreatic MRI segmentation, achieving expert-level performance across healthy and diseased states. This tool, algorithm, along with our annotated dataset, are freely available on GitHub and OSF, advancing accessible, radiation-free pediatric pancreatic imaging and fostering collaborative research in this underserved domain.