Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data.

High-throughput image analysis in the biomedical domain has gained significant attention in recent years, driving advancements in drug discovery, disease prediction, and personalized medicine. Organoids, specifically, are an active area of research, providing excellent models for human organs and their functions. Automating the quantification of organoids in microscopy images would provide an effective solution to overcome substantial manual quantification bottlenecks, particularly in high-throughput image analysis. However, there is a notable lack of open biomedical datasets, in contrast to other domains, such as autonomous driving, and, notably, only few of them have attempted to quantify annotation uncertainty. In this work, we present MultiOrg a comprehensive organoid dataset tailored for object detection tasks with uncertainty quantification. This dataset comprises over 400 high-resolution 2d microscopy images and curated annotations of more than 60,000 organoids. Most importantly, it includes three label sets for the test data, independently annotated by two experts at distinct time points. We additionally provide a benchmark for organoid detection, and make the best model available through an easily installable, interactive plugin for the popular image visualization tool Napari, to perform organoid quantification.

Graph neural network (GNN) has powerful representation ability, but optimal configurations of GNN are non-trivial to obtain due to diversity of graph structure and cascaded nonlinearities. This paper aims to understand some properties of GNN from a computer vision (CV) perspective. In mathematical analysis, we propose an adaptive GNN model by recursive definition, and derive its relation with two basic operations in CV: filtering and propagation operations. The proposed GNN model is formulated as a label propagation system with guided map, graph Laplacian and node weight. It reveals that 1) the guided map and node weight determine whether a GNN leads to filtering or propagation diffusion, and 2) the kernel of graph Laplacian controls diffusion pattern. In practical verification, we design a new regularization structure with guided feature to produce GNN-based filtering and propagation diffusion to tackle the ill-posed inverse problems of quotient image analysis (QIA), which recovers the reflectance ratio as a signature for image analysis or adjustment. A flexible QIA-GNN framework is constructed to achieve various image-based editing tasks, like face illumination synthesis and low-light image enhancement. Experiments show the effectiveness of the QIA-GNN, and provide new insights of GNN for image analysis and editing.

For many applications in image analysis, learning models that are invariant to translations and rotations is paramount. This is the case, for example, in medical imaging where the objects of interest can appear at arbitrary positions, with arbitrary orientations. As of today, Convolutional Neural Networks (CNN) are one of the most powerful tools for image analysis. They achieve, thanks to convolutions, an invariance with respect to translations. In this work, we present a new type of convolutional layer that takes advantage of Bessel functions, well known in physics, to build Bessel-CNNs (B-CNNs) that are invariant to all the continuous set of possible rotation angles by design.

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Leukemia diagnosis and monitoring rely increasingly on high-throughput image data, yet conventional clustering methods lack the flexibility to accommodate evolving cellular patterns and quantify uncertainty in real time. We introduce Adaptive and Dynamic Neuro-Fuzzy Clustering, a novel streaming-capable framework that combines Convolutional Neural Network-based feature extraction with an online fuzzy clustering engine. ADNF initializes soft partitions via Fuzzy C-Means, then continuously updates micro-cluster centers, densities, and fuzziness parameters using a Fuzzy Temporal Index (FTI) that measures entropy evolution. A topology refinement stage performs density-weighted merging and entropy-guided splitting to guard against over- and under-segmentation. On the C-NMC leukemia microscopy dataset, our tool achieves a silhouette score of 0.51, demonstrating superior cohesion and separation over static baselines. The method's adaptive uncertainty modeling and label-free operation hold immediate potential for integration within the INFANT pediatric oncology network, enabling scalable, up-to-date support for personalized leukemia management.

This paper presents a comprehensive comparative model analysis on a novel gastrointestinal medical imaging dataset, comprised of 4,000 endoscopic images spanning four critical disease classes: Diverticulosis, Neoplasm, Peritonitis, and Ureters. Leveraging state-of-the-art deep learning techniques, the study confronts common endoscopic challenges such as variable lighting, fluctuating camera angles, and frequent imaging artifacts. The best performing models, VGG16 and MobileNetV2, each achieved a test accuracy of 96.5%, while Xception reached 94.24%, establishing robust benchmarks and baselines for automated disease classification. In addition to strong classification performance, the approach includes explainable AI via Grad-CAM visualization, enabling identification of image regions most influential to model predictions and enhancing clinical interpretability. Experimental results demonstrate the potential for robust, accurate, and interpretable medical image analysis even in complex real-world conditions. This work contributes original benchmarks, comparative insights, and visual explanations, advancing the landscape of gastrointestinal computer-aided diagnosis and underscoring the importance of diverse, clinically relevant datasets and model explainability in medical AI research.

Due to the high cost of annotation or the rarity of some diseases, medical image segmentation is often limited by data scarcity and the resulting overfitting problem. Self-supervised learning and semi-supervised learning can mitigate the data scarcity challenge to some extent. However, both of these paradigms are complex and require either hand-crafted pretexts or well-defined pseudo-labels. In contrast, data augmentation represents a relatively simple and straightforward approach to addressing data scarcity issues. It has led to significant improvements in image recognition tasks. However, the effectiveness of local image editing augmentation techniques in the context of segmentation has been less explored. We propose HSMix, a novel approach to local image editing data augmentation involving hard and soft mixing for medical semantic segmentation. In our approach, a hard-augmented image is created by combining homogeneous regions (superpixels) from two source images. A soft mixing method further adjusts the brightness of these composed regions with brightness mixing based on locally aggregated pixel-wise saliency coefficients. The ground-truth segmentation masks of the two source images undergo the same mixing operations to generate the associated masks for the augmented images. Our method fully exploits both the prior contour and saliency information, thus preserving local semantic information in the augmented images while enriching the augmentation space with more diversity. Our method is a plug-and-play solution that is model agnostic and applicable to a range of medical imaging modalities. Extensive experimental evidence has demonstrated its effectiveness in a variety of medical segmentation tasks. The source code is available in https://github.com/DanielaPlusPlus/HSMix.

Convolutional neural networks are increasingly used outside the domain of image analysis, in particular in various areas of the natural sciences concerned with spatial data. Such networks often work out-of-the box, and in some cases entire model architectures from image analysis can be carried over to other problem domains almost unaltered. Unfortunately, this convenience does not trivially extend to data in non-euclidean spaces, such as spherical data. In this paper, we introduce two strategies for conducting convolutions on the sphere, using either a spherical-polar grid or a grid based on the cubed-sphere representation. We investigate the challenges that arise in this setting, and extend our discussion to include scenarios of spherical volumes, with several strategies for parameterizing the radial dimension. As a proof of concept, we conclude with an assessment of the performance of spherical convolutions in the context of molecular modelling, by considering structural environments within proteins. We show that the models are capable of learning non-trivial functions in these molecular environments, and that our spherical convolutions generally outperform standard 3D convolutions in this setting. In particular, despite the lack of any domain specific feature-engineering, we demonstrate performance comparable to state-of-the-art methods in the field, which build on decades of domain-specific knowledge.

Foundation models (FMs) are changing the way medical images are analyzed by learning from large collections of unlabeled data. Instead of relying on manually annotated examples, FMs are pre-trained to learn general-purpose visual features that can later be adapted to specific clinical tasks with little additional supervision. In this review, we examine how FMs are being developed and applied in pathology, radiology, and ophthalmology, drawing on evidence from over 150 studies. We explain the core components of FM pipelines, including model architectures, self-supervised learning methods, and strategies for downstream adaptation. We also review how FMs are being used in each imaging domain and compare design choices across applications. Finally, we discuss key challenges and open questions to guide future research.