vesselFM: A Foundation Model for Universal 3D Blood Vessel Segmentation

Segmenting 3D blood vessels is a critical yet challenging task in medical image analysis. This is due to significant imaging modality-specific variations in artifacts, vascular patterns and scales, signal-to-noise ratios, and background tissues. These variations, along with domain gaps arising from varying imaging protocols, limit the generalization of existing supervised learning-based methods, requiring tedious voxel-level annotations for each dataset separately. While foundation models promise to alleviate this limitation, they typically fail to generalize to the task of blood vessel segmentation, posing a unique, complex problem. In this work, we present vesselFM, a foundation model designed specifically for the broad task of 3D blood vessel segmentation. Unlike previous models, vesselFM can effortlessly generalize to unseen domains. To achieve zero-shot generalization, we train vesselFM on three heterogeneous data sources: a large, curated annotated dataset, data generated by a domain randomization scheme, and data sampled from a flow matching-based generative model. Extensive evaluations show that vesselFM outperforms state-of-the-art medical image segmentation foundation models across four (pre-)clinically relevant imaging modalities in zero-, one-, and few-shot scenarios, therefore providing a universal solution for 3D blood vessel segmentation.

FedPID: An Aggregation Method for Federated Learning

This paper presents FedPID, our submission to the Federated Tumor Segmentation Challenge 2024 (FETS24). Inspired by FedCostWAvg and FedPIDAvg, our winning contributions to FETS21 and FETS2022, we propose an improved aggregation strategy for federated and collaborative learning. FedCostWAvg is a method that averages results by considering both the number of training samples in each group and how much the cost function decreased in the last round of training. This is similar to how the derivative part of a PID controller works. In FedPIDAvg, we also included the integral part that was missing. Another challenge we faced were vastly differing dataset sizes at each center. We solved this by assuming the sizes follow a Poisson distribution and adjusting the training iterations for each center accordingly. Essentially, this part of the method controls that outliers that require too much training time are less frequently used. Based on these contributions we now adapted FedPIDAvg by changing how the integral part is computed. Instead of integrating the loss function we measure the global drop in cost since the first round.

3D Vessel Graph Generation Using Denoising Diffusion

Blood vessel networks, represented as 3D graphs, help predict disease biomarkers, simulate blood flow, and aid in synthetic image generation, relevant in both clinical and pre-clinical settings. However, generating realistic vessel graphs that correspond to an anatomy of interest is challenging. Previous methods aimed at generating vessel trees mostly in an autoregressive style and could not be applied to vessel graphs with cycles such as capillaries or specific anatomical structures such as the Circle of Willis. Addressing this gap, we introduce the first application of \textit{denoising diffusion models} in 3D vessel graph generation. Our contributions include a novel, two-stage generation method that sequentially denoises node coordinates and edges. We experiment with two real-world vessel datasets, consisting of microscopic capillaries and major cerebral vessels, and demonstrate the generalizability of our method for producing diverse, novel, and anatomically plausible vessel graphs.

Whole Heart 3D+T Representation Learning Through Sparse 2D Cardiac MR Images

Cardiac Magnetic Resonance (CMR) imaging serves as the gold-standard for evaluating cardiac morphology and function. Typically, a multi-view CMR stack, covering short-axis (SA) and 2/3/4-chamber long-axis (LA) views, is acquired for a thorough cardiac assessment. However, efficiently streamlining the complex, high-dimensional 3D+T CMR data and distilling compact, coherent representation remains a challenge. In this work, we introduce a whole-heart self-supervised learning framework that utilizes masked imaging modeling to automatically uncover the correlations between spatial and temporal patches throughout the cardiac stacks. This process facilitates the generation of meaningful and well-clustered heart representations without relying on the traditionally required, and often costly, labeled data. The learned heart representation can be directly used for various downstream tasks. Furthermore, our method demonstrates remarkable robustness, ensuring consistent representations even when certain CMR planes are missing/flawed. We train our model on 14,000 unlabeled CMR data from UK BioBank and evaluate it on 1,000 annotated data. The proposed method demonstrates superior performance to baselines in tasks that demand comprehensive 3D+T cardiac information, e.g. cardiac phenotype (ejection fraction and ventricle volume) prediction and multi-plane/multi-frame CMR segmentation, highlighting its effectiveness in extracting comprehensive cardiac features that are both anatomically and pathologically relevant.

Enhancing Interpretability of Vertebrae Fracture Grading using Human-interpretable Prototypes

Vertebral fracture grading classifies the severity of vertebral fractures, which is a challenging task in medical imaging and has recently attracted Deep Learning (DL) models. Only a few works attempted to make such models human-interpretable despite the need for transparency and trustworthiness in critical use cases like DL-assisted medical diagnosis. Moreover, such models either rely on post-hoc methods or additional annotations. In this work, we propose a novel interpretable-by-design method, ProtoVerse, to find relevant sub-parts of vertebral fractures (prototypes) that reliably explain the model's decision in a human-understandable way. Specifically, we introduce a novel diversity-promoting loss to mitigate prototype repetitions in small datasets with intricate semantics. We have experimented with the VerSe'19 dataset and outperformed the existing prototype-based method. Further, our model provides superior interpretability against the post-hoc method. Importantly, expert radiologists validated the visual interpretability of our results, showing clinical applicability.

A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

Topologically faithful multi-class segmentation in medical images

Topological accuracy in medical image segmentation is a highly important property for downstream applications such as network analysis and flow modeling in vessels or cell counting. Recently, significant methodological advancements have brought well-founded concepts from algebraic topology to binary segmentation. However, these approaches have been underexplored in multi-class segmentation scenarios, where topological errors are common. We propose a general loss function for topologically faithful multi-class segmentation extending the recent Betti matching concept, which is based on induced matchings of persistence barcodes. We project the N-class segmentation problem to N single-class segmentation tasks, which allows us to use 1-parameter persistent homology making training of neural networks computationally feasible. We validate our method on a comprehensive set of four medical datasets with highly variant topological characteristics. Our loss formulation significantly enhances topological correctness in cardiac, cell, artery-vein, and Circle of Willis segmentation.

Cross-domain and Cross-dimension Learning for Image-to-Graph Transformers

Direct image-to-graph transformation is a challenging task that solves object detection and relationship prediction in a single model. Due to the complexity of this task, large training datasets are rare in many domains, which makes the training of large networks challenging. This data sparsity necessitates the establishment of pre-training strategies akin to the state-of-the-art in computer vision. In this work, we introduce a set of methods enabling cross-domain and cross-dimension transfer learning for image-to-graph transformers. We propose (1) a regularized edge sampling loss for sampling the optimal number of object relationships (edges) across domains, (2) a domain adaptation framework for image-to-graph transformers that aligns features from different domains, and (3) a simple projection function that allows us to pretrain 3D transformers on 2D input data. We demonstrate our method's utility in cross-domain and cross-dimension experiments, where we pretrain our models on 2D satellite images before applying them to vastly different target domains in 2D and 3D. Our method consistently outperforms a series of baselines on challenging benchmarks, such as retinal or whole-brain vessel graph extraction.

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset and invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. TopCoW dataset was the first public dataset with voxel-level annotations for CoW's 13 vessel components, made possible by virtual-reality (VR) technology. It was also the first dataset with paired MRA and CTA from the same patients. TopCoW challenge aimed to tackle the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant's topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically.

Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps

This paper introduces panoptica, a versatile and performance-optimized package designed for computing instance-wise segmentation quality metrics from 2D and 3D segmentation maps. panoptica addresses the limitations of existing metrics and provides a modular framework that complements the original intersection over union-based panoptic quality with other metrics, such as the distance metric Average Symmetric Surface Distance. The package is open-source, implemented in Python, and accompanied by comprehensive documentation and tutorials. panoptica employs a three-step metrics computation process to cover diverse use cases. The efficacy of panoptica is demonstrated on various real-world biomedical datasets, where an instance-wise evaluation is instrumental for an accurate representation of the underlying clinical task. Overall, we envision panoptica as a valuable tool facilitating in-depth evaluation of segmentation methods.