Scaling nnU-Net for CBCT Segmentation

This paper presents our approach to scaling the nnU-Net framework for multi-structure segmentation on Cone Beam Computed Tomography (CBCT) images, specifically in the scope of the ToothFairy2 Challenge. We leveraged the nnU-Net ResEnc L model, introducing key modifications to patch size, network topology, and data augmentation strategies to address the unique challenges of dental CBCT imaging. Our method achieved a mean Dice coefficient of 0.9253 and HD95 of 18.472 on the test set, securing a mean rank of 4.6 and with it the first place in the ToothFairy2 challenge. The source code is publicly available, encouraging further research and development in the field.

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

From FDG to PSMA: A Hitchhiker's Guide to Multitracer, Multicenter Lesion Segmentation in PET/CT Imaging

Automated lesion segmentation in PET/CT scans is crucial for improving clinical workflows and advancing cancer diagnostics. However, the task is challenging due to physiological variability, different tracers used in PET imaging, and diverse imaging protocols across medical centers. To address this, the autoPET series was created to challenge researchers to develop algorithms that generalize across diverse PET/CT environments. This paper presents our solution for the autoPET III challenge, targeting multitracer, multicenter generalization using the nnU-Net framework with the ResEncL architecture. Key techniques include misalignment data augmentation and multi-modal pretraining across CT, MR, and PET datasets to provide an initial anatomical understanding. We incorporate organ supervision as a multitask approach, enabling the model to distinguish between physiological uptake and tracer-specific patterns, which is particularly beneficial in cases where no lesions are present. Compared to the default nnU-Net, which achieved a Dice score of 57.61, or the larger ResEncL (65.31) our model significantly improved performance with a Dice score of 68.40, alongside a reduction in false positive (FPvol: 7.82) and false negative (FNvol: 10.35) volumes. These results underscore the effectiveness of combining advanced network design, augmentation, pretraining, and multitask learning for PET/CT lesion segmentation. Code is publicly available at https://github.com/MIC-DKFZ/autopet-3-submission.

Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures

Accurately segmenting thin tubular structures, such as vessels, nerves, roads or concrete cracks, is a crucial task in computer vision. Standard deep learning-based segmentation loss functions, such as Dice or Cross-Entropy, focus on volumetric overlap, often at the expense of preserving structural connectivity or topology. This can lead to segmentation errors that adversely affect downstream tasks, including flow calculation, navigation, and structural inspection. Although current topology-focused losses mark an improvement, they introduce significant computational and memory overheads. This is particularly relevant for 3D data, rendering these losses infeasible for larger volumes as well as increasingly important multi-class segmentation problems. To mitigate this, we propose a novel Skeleton Recall Loss, which effectively addresses these challenges by circumventing intensive GPU-based calculations with inexpensive CPU operations. It demonstrates overall superior performance to current state-of-the-art approaches on five public datasets for topology-preserving segmentation, while substantially reducing computational overheads by more than 90%. In doing so, we introduce the first multi-class capable loss function for thin structure segmentation, excelling in both efficiency and efficacy for topology-preservation.

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.

atTRACTive: Semi-automatic white matter tract segmentation using active learning

Accurately identifying white matter tracts in medical images is essential for various applications, including surgery planning and tract-specific analysis. Supervised machine learning models have reached state-of-the-art solving this task automatically. However, these models are primarily trained on healthy subjects and struggle with strong anatomical aberrations, e.g. caused by brain tumors. This limitation makes them unsuitable for tasks such as preoperative planning, wherefore time-consuming and challenging manual delineation of the target tract is typically employed. We propose semi-automatic entropy-based active learning for quick and intuitive segmentation of white matter tracts from whole-brain tractography consisting of millions of streamlines. The method is evaluated on 21 openly available healthy subjects from the Human Connectome Project and an internal dataset of ten neurosurgical cases. With only a few annotations, the proposed approach enables segmenting tracts on tumor cases comparable to healthy subjects (dice=0.71), while the performance of automatic methods, like TractSeg dropped substantially (dice=0.34) in comparison to healthy subjects. The method is implemented as a prototype named atTRACTive in the freely available software MITK Diffusion. Manual experiments on tumor data showed higher efficiency due to lower segmentation times compared to traditional ROI-based segmentation.