Caterina Fuster-Barceló

Wanlu Lei, Caterina Fuster-Barceló, Gabriel Reder et al.

We present the BioImage$.$IO Chatbot, an AI assistant powered by Large Language Models and supported by a community-driven knowledge base and toolset. This chatbot is designed to cater to a wide range of user needs through a flexible extension mechanism that spans from information retrieval to AI-enhanced analysis and microscopy control. Embracing open-source principles, the chatbot is designed to evolve through community contributions. By simplifying navigation through the intricate bioimaging landscape, the BioImage$.$IO Chatbot empowers life sciences to progress by leveraging the collective expertise and innovation of its users.

Caterina Fuster-Barceló, Carmen Cámara, Pedro Peris-López

Over the course of the past two decades, a substantial body of research has substantiated the viability of utilising cardiac signals as a biometric modality. This paper presents a novel approach for patient identification in healthcare systems using electrocardiogram signals. A convolutional neural network (CNN) is employed to classify users based on electrocardiomatrices, a specific type of image derived from ECG signals. The proposed identification system is evaluated in multiple databases, achieving up to 99.84\% accuracy on healthy subjects, 97.09\% on patients with cardiovascular diseases, and 97.89% on mixed populations including both healthy and arrhythmic patients. The system also performs robustly under varying activity conditions, achieving 91.32% accuracy in scenarios involving different physical activities. These consistent and reliable results, with low error rates such as a FAR of 0.01% and FRR of 0.157% in the best cases, demonstrate the method's significant advancement in subject identification within healthcare systems. By considering patients' cardiovascular conditions and activity levels, the proposed approach addresses gaps in the existing literature, positioning it as a strong candidate for practical applications in real-world healthcare settings.

Caterina Fuster-Barceló, Claudia Castrillón, Laura Rodrigo-Muñoz et al.

We present OREHAS (Optimized Recognition & Evaluation of volumetric Hydrops in the Auditory System), the first fully automatic pipeline for volumetric quantification of endolymphatic hydrops (EH) from routine 3D-SPACE-MRC and 3D-REAL-IR MRI. The system integrates three components -- slice classification, inner ear localization, and sequence-specific segmentation -- into a single workflow that computes per-ear endolymphatic-to-vestibular volume ratios (ELR) directly from whole MRI volumes, eliminating the need for manual intervention. Trained with only 3 to 6 annotated slices per patient, OREHAS generalized effectively to full 3D volumes, achieving Dice scores of 0.90 for SPACE-MRC and 0.75 for REAL-IR. In an external validation cohort with complete manual annotations, OREHAS closely matched expert ground truth (VSI = 74.3%) and substantially outperformed the clinical syngo.via software (VSI = 42.5%), which tended to overestimate endolymphatic volumes. Across 19 test patients, vestibular measurements from OREHAS were consistent with syngo.via, while endolymphatic volumes were systematically smaller and more physiologically realistic. These results show that reliable and reproducible EH quantification can be achieved from standard MRI using limited supervision. By combining efficient deep-learning-based segmentation with a clinically aligned volumetric workflow, OREHAS reduces operator dependence, ensures methodological consistency. Besides, the results are compatible with established imaging protocols. The approach provides a robust foundation for large-scale studies and for recalibrating clinical diagnostic thresholds based on accurate volumetric measurements of the inner ear.

Caterina Fuster-Barceló, Virginie Uhlmann

Although vision foundation models (VFMs) are increasingly reused for biomedical image analysis, it remains unclear whether the latent representations they provide are general enough to support effective transfer and reuse across heterogeneous microscopy image datasets. Here, we study this question for the problem of mitochondria segmentation in electron microscopy (EM) images, using two popular public EM datasets (Lucchi++ and VNC) and three recent representative VFMs (DINOv2, DINOv3, and OpenCLIP). We evaluate two practical model adaptation regimes: a frozen-backbone setting in which only a lightweight segmentation head is trained on top of the VFM, and parameter-efficient fine-tuning (PEFT) via Low-Rank Adaptation (LoRA) in which the VFM is fine-tuned in a targeted manner to a specific dataset. Across all backbones, we observe that training on a single EM dataset yields good segmentation performance (quantified as foreground Intersection-over-Union), and that LoRA consistently improves in-domain performance. In contrast, training on multiple EM datasets leads to severe performance degradation for all models considered, with only marginal gains from PEFT. Exploration of the latent representation space through various techniques (PCA, Fréchet Dinov2 distance, and linear probes) reveals a pronounced and persistent domain mismatch between the two considered EM datasets in spite of their visual similarity, which is consistent with the observed failure of paired training. These results suggest that, while VFMs can deliver competitive results for EM segmentation within a single domain under lightweight adaptation, current PEFT strategies are insufficient to obtain a single robust model across heterogeneous EM datasets without additional domain-alignment mechanisms.