Deep learning-based 3-dimensional (3D) shape reconstruction from 2-dimensional (2D) magnetic resonance imaging (MRI) has become increasingly important in medical disease diagnosis, treatment planning, and computational modeling. This review surveys the methodological landscape of 3D MRI reconstruction, focusing on 4 primary approaches: point cloud, mesh-based, shape-aware, and volumetric models. For each category, we analyze the current state-of-the-art techniques, their methodological foundation, limitations, and applications across anatomical structures. We provide an extensive overview ranging from cardiac to neurological to lung imaging. We also focus on the clinical applicability of models to diseased anatomy, and the influence of their training and testing data. We examine publicly available datasets, computational demands, and evaluation metrics. Finally, we highlight the emerging research directions including multimodal integration and cross-modality frameworks. This review aims to provide researchers with a structured overview of current 3D reconstruction methodologies to identify opportunities for advancing deep learning towards more robust, generalizable, and clinically impactful solutions.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

Robot-assisted surgeries rely on accurate and real-time scene understanding to safely guide surgical instruments. However, segmentation models trained on static datasets face key limitations when deployed in these dynamic and evolving surgical environments. Class-incremental semantic segmentation (CISS) allows models to continually adapt to new classes while avoiding catastrophic forgetting of prior knowledge, without training on previous data. In this work, we build upon the recently introduced Taxonomy-Oriented Poincaré-regularized Incremental Class Segmentation (TOPICS) approach and propose an enhanced variant, termed TOPICS+, specifically tailored for robust segmentation of surgical scenes. Concretely, we incorporate the Dice loss into the hierarchical loss formulation to handle strong class imbalances, introduce hierarchical pseudo-labeling, and design tailored label taxonomies for robotic surgery environments. We also propose six novel CISS benchmarks designed for robotic surgery environments including multiple incremental steps and several semantic categories to emulate realistic class-incremental settings in surgical environments. In addition, we introduce a refined set of labels with more than 144 classes on the Syn-Mediverse synthetic dataset, hosted online as an evaluation benchmark. We make the code and trained models publicly available at http://topics.cs.uni-freiburg.de.

Accurate motion estimation in cardiac computed tomography (CT) imaging is critical for assessing cardiac function and surgical planning. Data-driven methods have become the standard approach for dense motion estimation, but they rely on vast amounts of labeled data with dense ground-truth (GT) motion annotations, which are often unfeasible to obtain. To address this limitation, we present a novel approach that synthesizes realistically looking pairs of cardiac CT frames enriched with dense 3D flow field annotations. Our method leverages a conditional Variational Autoencoder (CVAE), which incorporates a novel multi-scale feature conditioning mechanism and is trained to generate 3D flow fields conditioned on a single CT frame. By applying the generated flow field to warp the given frame, we create pairs of frames that simulate realistic myocardium deformations across the cardiac cycle. These pairs serve as fully annotated data samples, providing optical flow GT annotations. Our data generation pipeline could enable the training and validation of more complex and accurate myocardium motion models, allowing for substantially reducing reliance on manual annotations. Our code, along with animated generated samples and additional material, is available on our project page: https://shaharzuler.github.io/GenerativeCardiacMotion_Page.

Accurate classification of computed tomography (CT) images is essential for diagnosis and treatment planning, but existing methods often struggle with the subtle and spatially diverse nature of pathological features. Current approaches typically process images uniformly, limiting their ability to detect localized abnormalities that require focused analysis. We introduce UGPL, an uncertainty-guided progressive learning framework that performs a global-to-local analysis by first identifying regions of diagnostic ambiguity and then conducting detailed examination of these critical areas. Our approach employs evidential deep learning to quantify predictive uncertainty, guiding the extraction of informative patches through a non-maximum suppression mechanism that maintains spatial diversity. This progressive refinement strategy, combined with an adaptive fusion mechanism, enables UGPL to integrate both contextual information and fine-grained details. Experiments across three CT datasets demonstrate that UGPL consistently outperforms state-of-the-art methods, achieving improvements of 3.29%, 2.46%, and 8.08% in accuracy for kidney abnormality, lung cancer, and COVID-19 detection, respectively. Our analysis shows that the uncertainty-guided component provides substantial benefits, with performance dramatically increasing when the full progressive learning pipeline is implemented. Our code is available at: https://github.com/shravan-18/UGPL

Dental diagnosis relies on two primary imaging modalities: panoramic radiographs (PX) providing 2D oral cavity representations, and Cone-Beam Computed Tomography (CBCT) offering detailed 3D anatomical information. While PX images are cost-effective and accessible, their lack of depth information limits diagnostic accuracy. CBCT addresses this but presents drawbacks including higher costs, increased radiation exposure, and limited accessibility. Existing reconstruction models further complicate the process by requiring CBCT flattening or prior dental arch information, often unavailable clinically. We introduce ViT-NeBLa, a vision transformer-based Neural Beer-Lambert model enabling accurate 3D reconstruction directly from single PX. Our key innovations include: (1) enhancing the NeBLa framework with Vision Transformers for improved reconstruction capabilities without requiring CBCT flattening or prior dental arch information, (2) implementing a novel horseshoe-shaped point sampling strategy with non-intersecting rays that eliminates intermediate density aggregation required by existing models due to intersecting rays, reducing sampling point computations by $52 \%$, (3) replacing CNN-based U-Net with a hybrid ViT-CNN architecture for superior global and local feature extraction, and (4) implementing learnable hash positional encoding for better higher-dimensional representation of 3D sample points compared to existing Fourier-based dense positional encoding. Experiments demonstrate that ViT-NeBLa significantly outperforms prior state-of-the-art methods both quantitatively and qualitatively, offering a cost-effective, radiation-efficient alternative for enhanced dental diagnostics.

Registration of histological and mass spectrometry imaging (MSI) allows for more precise identification of structural changes and chemical interactions in tissue. With histology and MSI having entirely different image formation processes and dimensionalities, registration of the two modalities remains an ongoing challenge. This work proposes a solution that synthesises histological images from MSI, using a pix2pix model, to effectively enable unimodal registration. Preliminary results show promising synthetic histology images with limited artifacts, achieving increases in mutual information (MI) and structural similarity index measures (SSIM) of +0.924 and +0.419, respectively, compared to a baseline U-Net model. Our source code is available on GitHub: https://github.com/kimberley/MIUA2025.

Existing semi-supervised medical segmentation co-learning frameworks have realized that model performance can be diminished by the biases in model recognition caused by low-quality pseudo-labels. Due to the averaging nature of their pseudo-label integration strategy, they fail to explore the reliability of pseudo-labels from different sources. In this paper, we propose a mutual evidential deep learning (MEDL) framework that offers a potentially viable solution for pseudo-label generation in semi-supervised learning from two perspectives. First, we introduce networks with different architectures to generate complementary evidence for unlabeled samples and adopt an improved class-aware evidential fusion to guide the confident synthesis of evidential predictions sourced from diverse architectural networks. Second, utilizing the uncertainty in the fused evidence, we design an asymptotic Fisher information-based evidential learning strategy. This strategy enables the model to initially focus on unlabeled samples with more reliable pseudo-labels, gradually shifting attention to samples with lower-quality pseudo-labels while avoiding over-penalization of mislabeled classes in high data uncertainty samples. Additionally, for labeled data, we continue to adopt an uncertainty-driven asymptotic learning strategy, gradually guiding the model to focus on challenging voxels. Extensive experiments on five mainstream datasets have demonstrated that MEDL achieves state-of-the-art performance.

Deep learning can help uncover patterns in resting-state functional Magnetic Resonance Imaging (rs-fMRI) associated with psychiatric disorders and personal traits. Yet the problem of interpreting deep learning findings is rarely more evident than in fMRI analyses, as the data is sensitive to scanning effects and inherently difficult to visualize. We propose a simple approach to mitigate these challenges grounded on sparsification and self-supervision. Instead of extracting post-hoc feature attributions to uncover functional connections that are important to the target task, we identify a small subset of highly informative connections during training and occlude the rest. To this end, we jointly train a (1) sparse input mask, (2) variational autoencoder (VAE), and (3) downstream classifier in an end-to-end fashion. While we need a portion of labeled samples to train the classifier, we optimize the sparse mask and VAE with unlabeled data from additional acquisition sites, retaining only the input features that generalize well. We evaluate our method - Sparsely Reconstructed Graphs (SpaRG) - on the public ABIDE dataset for the task of sex classification, training with labeled cases from 18 sites and adapting the model to two additional out-of-distribution sites with a portion of unlabeled samples. For a relatively coarse parcellation (64 regions), SpaRG utilizes only 1% of the original connections while improving the classification accuracy across domains. Our code can be found at github.com/yanismiraoui/SpaRG.

Manually annotating nuclei from the gigapixel Hematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features. But due to high intra- and inter-class variability of nuclei morphological and chromatic features, as well as H&E-stains susceptibility to artefacts, state-of-the-art algorithms cannot correctly detect and classify instances with the necessary performance. In this work, we hypothesise context and attention inductive biases in artificial neural networks (ANNs) could increase the generalization of algorithms for cell nuclei instance segmentation and classification. We conduct a thorough survey on context and attention methods for cell nuclei instance segmentation and classification from H&E-stained microscopy imaging, while providing a comprehensive discussion of the challenges being tackled with context and attention. Besides, we illustrate some limitations of current approaches and present ideas for future research. As a case study, we extend both a general instance segmentation and classification method (Mask-RCNN) and a tailored cell nuclei instance segmentation and classification model (HoVer-Net) with context- and attention-based mechanisms, and do a comparative analysis on a multi-centre colon nuclei identification and counting dataset. Although pathologists rely on context at multiple levels while paying attention to specific Regions of Interest (RoIs) when analysing and annotating WSIs, our findings suggest translating that domain knowledge into algorithm design is no trivial task, but to fully exploit these mechanisms, the scientific understanding of these methods should be addressed.