Dominic LaBella

Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu et al.

Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children. The five-year survival rate for high-grade glioma in children is less than 20%. The development of new treatments is dependent upon multi-institutional collaborative clinical trials requiring reproducible and accurate centralized response assessment. We present the results of the BraTS-PEDs 2023 challenge, the first Brain Tumor Segmentation (BraTS) challenge focused on pediatric brain tumors. This challenge utilized data acquired from multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. BraTS-PEDs 2023 aimed to evaluate volumetric segmentation algorithms for pediatric brain gliomas from magnetic resonance imaging using standardized quantitative performance evaluation metrics employed across the BraTS 2023 challenges. The top-performing AI approaches for pediatric tumor analysis included ensembles of nnU-Net and Swin UNETR, Auto3DSeg, or nnU-Net with a self-supervised framework. The BraTSPEDs 2023 challenge fostered collaboration between clinicians (neuro-oncologists, neuroradiologists) and AI/imaging scientists, promoting faster data sharing and the development of automated volumetric analysis techniques. These advancements could significantly benefit clinical trials and improve the care of children with brain tumors.

Mohamed Sobhi Jabal, Jikai Zhang, Dominic LaBella et al.

The Brain Tumor Reporting and Data System (BT-RADS) standardizes post-treatment MRI response assessment in patients with diffuse gliomas but requires complex integration of imaging trends, medication effects, and radiation timing. This study evaluates an end-to-end multi-agent large language model (LLM) and convolutional neural network (CNN) system for automated BT-RADS classification. A multi-agent LLM system combined with automated CNN-based tumor segmentation was retrospectively evaluated on 509 consecutive post-treatment glioma MRI examinations from a single high-volume center. An extractor agent identified clinical variables (steroid status, bevacizumab status, radiation date) from unstructured clinical notes, while a scorer agent applied BT-RADS decision logic integrating extracted variables with volumetric measurements. Expert reference standard classifications were established by an independent board-certified neuroradiologist. Of 509 examinations, 492 met inclusion criteria. The system achieved 374/492 (76.0%; 95% CI, 72.1%-79.6%) accuracy versus 283/492 (57.5%; 95% CI, 53.1%-61.8%) for initial clinical assessments (+18.5 percentage points; P<.001). Context-dependent categories showed high sensitivity (BT-1b 100%, BT-1a 92.7%, BT-3a 87.5%), while threshold-dependent categories showed moderate sensitivity (BT-3c 74.8%, BT-2 69.2%, BT-4 69.3%, BT-3b 57.1%). For BT-4, positive predictive value was 92.9%. The multi-agent LLM system achieved higher BT-RADS classification agreement with expert reference standard compared to initial clinical scoring, with high accuracy for context-dependent scores and high positive predictive value for BT-4 detection.

Florian Kofler, Marcel Rosier, Mehdi Astaraki et al.

The Brain Tumor Segmentation (BraTS) cluster of challenges has significantly advanced brain tumor image analysis by providing large, curated datasets and addressing clinically relevant tasks. However, despite its success and popularity, algorithms and models developed through BraTS have seen limited adoption in both scientific and clinical communities. To accelerate their dissemination, we introduce BraTS orchestrator, an open-source Python package that provides seamless access to state-of-the-art segmentation and synthesis algorithms for diverse brain tumors from the BraTS challenge ecosystem. Available on GitHub (https://github.com/BrainLesion/BraTS), the package features intuitive tutorials designed for users with minimal programming experience, enabling both researchers and clinicians to easily deploy winning BraTS algorithms for inference. By abstracting the complexities of modern deep learning, BraTS orchestrator democratizes access to the specialized knowledge developed within the BraTS community, making these advances readily available to broader neuro-radiology and neuro-oncology audiences.

Kaiyuan Yang, Fabio Musio, Yihui Ma et al.

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 neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building.

Dominic LaBella, Ujjwal Baid, Omaditya Khanna et al.

We describe the design and results from the BraTS 2023 Intracranial Meningioma Segmentation Challenge. The BraTS Meningioma Challenge differed from prior BraTS Glioma challenges in that it focused on meningiomas, which are typically benign extra-axial tumors with diverse radiologic and anatomical presentation and a propensity for multiplicity. Nine participating teams each developed deep-learning automated segmentation models using image data from the largest multi-institutional systematically expert annotated multilabel multi-sequence meningioma MRI dataset to date, which included 1000 training set cases, 141 validation set cases, and 283 hidden test set cases. Each case included T2, FLAIR, T1, and T1Gd brain MRI sequences with associated tumor compartment labels delineating enhancing tumor, non-enhancing tumor, and surrounding non-enhancing FLAIR hyperintensity. Participant automated segmentation models were evaluated and ranked based on a scoring system evaluating lesion-wise metrics including dice similarity coefficient (DSC) and 95% Hausdorff Distance. The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0.976, 0.976, and 0.964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0.899, 0.904, and 0.871, respectively. These results serve as state-of-the-art benchmarks for future pre-operative meningioma automated segmentation algorithms. Additionally, we found that 1286 of 1424 cases (90.3%) had at least 1 compartment voxel abutting the edge of the skull-stripped image edge, which requires further investigation into optimal pre-processing face anonymization steps.

Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu et al.

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge, focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors.

Xuan Qi, Dominic Labella, Thomas Sanford et al.

We tackle atypical versus normal mitosis classification in the MIDOG 2025 challenge using EfficientViT-L2, a hybrid CNN--ViT architecture optimized for accuracy and efficiency. A unified dataset of 13,938 nuclei from seven cancer types (MIDOG++ and AMi-Br) was used, with atypical mitoses comprising ~15. To assess domain generalization, we applied leave-one-cancer-type-out cross-validation with 5-fold ensembles, using stain-deconvolution for image augmentation. For challenge submissions, we trained an ensemble with the same 5-fold split but on all cancer types. In the preliminary evaluation phase, this model achieved balanced accuracy of 0.859, ROC AUC of 0.942, and raw accuracy of 0.85, demonstrating competitive and well-balanced performance across metrics.

Keshav Jha, William Sharp, Dominic LaBella

Accurate delineation of pancreatic tumors is critical for diagnosis, treatment planning, and outcome assessment, yet automated segmentation remains challenging due to anatomical variability and limited dataset availability. In this study, SegResNet models, as part of the Auto3DSeg architecture, were trained and evaluated on two MRI-based pancreatic tumor segmentation tasks as part of the 2025 PANTHER Challenge. Algorithm methodology included 5-fold cross-validation with STAPLE ensembling after focusing on an anatomically relevant region-of-interest. The Pancreatic Tumor Segmentation on Diagnostic MRI task 1 training set included 91 T1-weighted arterial contrast-enhanced MRI with expert annotated pancreas and tumor labels. The Pancreatic Tumor Segmentation on MR-Linac task 2 training set used 50 T2-weighted MR-Linac cases with expert annotated pancreas and tumor labels. Algorithm-automated segmentation performance of pancreatic tumor was assessed using Dice Similarity Coefficient (DSC), 5 mm DSC, 95th percentile Hausdorff Distance (HD95), Mean Average Surface Distance (MASD), and Root Mean Square Error (RMSE). For Task 1, the algorithm achieved a DSC of 0.56, 5 mm DSC of 0.73, HD95 of 41.1 mm, MASD of 26.0 mm, and RMSE of 5164 mm. For Task 2, performance decreased, with a DSC of 0.33, 5 mm DSC of 0.50, HD95 of 20.1 mm, MASD of 7.2 mm, and RMSE of 17,203 mm. These findings illustrate the challenges of MRI-based pancreatic tumor segmentation with small datasets, highlighting variability introduced by different MRI sequences. Despite modest performance, the results demonstrate potential for automated delineation and emphasize the need for larger, standardized MRI datasets to improve model robustness and clinical utility.

Dominic LaBella, Keshav Jha, Jared Robbins et al.

Cone-beam computed tomography (CBCT) has become an invaluable imaging modality in dentistry, enabling 3D visualization of teeth and surrounding structures for diagnosis and treatment planning. Automated segmentation of dental structures in CBCT can efficiently assist in identifying pathology (e.g., pulpal or periapical lesions) and facilitate radiation therapy planning in head and neck cancer patients. We describe the DLaBella29 team's approach for the MICCAI 2025 ToothFairy3 Challenge, which involves a deep learning pipeline for multi-class tooth segmentation. We utilized the MONAI Auto3DSeg framework with a 3D SegResNet architecture, trained on a subset of the ToothFairy3 dataset (63 CBCT scans) with 5-fold cross-validation. Key preprocessing steps included image resampling to 0.6 mm isotropic resolution and intensity clipping. We applied an ensemble fusion using Multi-Label STAPLE on the 5-fold predictions to infer a Phase 1 segmentation and then conducted tight cropping around the easily segmented Phase 1 mandible to perform Phase 2 segmentation on the smaller nerve structures. Our method achieved an average Dice of 0.87 on the ToothFairy3 challenge out-of-sample validation set. This paper details the clinical context, data preparation, model development, results of our approach, and discusses the relevance of automated dental segmentation for improving patient care in radiation oncology.

Maruf Adewole, Jeffrey D. Rudie, Anu Gbadamosi et al.

Gliomas are the most common type of primary brain tumors. Although gliomas are relatively rare, they are among the deadliest types of cancer, with a survival rate of less than 2 years after diagnosis. Gliomas are challenging to diagnose, hard to treat and inherently resistant to conventional therapy. Years of extensive research to improve diagnosis and treatment of gliomas have decreased mortality rates across the Global North, while chances of survival among individuals in low- and middle-income countries (LMICs) remain unchanged and are significantly worse in Sub-Saharan Africa (SSA) populations. Long-term survival with glioma is associated with the identification of appropriate pathological features on brain MRI and confirmation by histopathology. Since 2012, the Brain Tumor Segmentation (BraTS) Challenge have evaluated state-of-the-art machine learning methods to detect, characterize, and classify gliomas. However, it is unclear if the state-of-the-art methods can be widely implemented in SSA given the extensive use of lower-quality MRI technology, which produces poor image contrast and resolution and more importantly, the propensity for late presentation of disease at advanced stages as well as the unique characteristics of gliomas in SSA (i.e., suspected higher rates of gliomatosis cerebri). Thus, the BraTS-Africa Challenge provides a unique opportunity to include brain MRI glioma cases from SSA in global efforts through the BraTS Challenge to develop and evaluate computer-aided-diagnostic (CAD) methods for the detection and characterization of glioma in resource-limited settings, where the potential for CAD tools to transform healthcare are more likely.

Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu et al.

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20\%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. The MICCAI Brain Tumor Segmentation (BraTS) Challenge is a landmark community benchmark event with a successful history of 12 years of resource creation for the segmentation and analysis of adult glioma. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge, which represents the first BraTS challenge focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The BraTS-PEDs 2023 challenge focuses on benchmarking the development of volumentric segmentation algorithms for pediatric brain glioma through standardized quantitative performance evaluation metrics utilized across the BraTS 2023 cluster of challenges. Models gaining knowledge from the BraTS-PEDs multi-parametric structural MRI (mpMRI) training data will be evaluated on separate validation and unseen test mpMRI dataof high-grade pediatric glioma. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors.

Hongwei Bran Li, Gian Marco Conte, Qingqiao Hu et al.

Automated brain tumor segmentation methods have become well-established and reached performance levels offering clear clinical utility. These methods typically rely on four input magnetic resonance imaging (MRI) modalities: T1-weighted images with and without contrast enhancement, T2-weighted images, and FLAIR images. However, some sequences are often missing in clinical practice due to time constraints or image artifacts, such as patient motion. Consequently, the ability to substitute missing modalities and gain segmentation performance is highly desirable and necessary for the broader adoption of these algorithms in the clinical routine. In this work, we present the establishment of the Brain MR Image Synthesis Benchmark (BraSyn) in conjunction with the Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2023. The primary objective of this challenge is to evaluate image synthesis methods that can realistically generate missing MRI modalities when multiple available images are provided. The ultimate aim is to facilitate automated brain tumor segmentation pipelines. The image dataset used in the benchmark is diverse and multi-modal, created through collaboration with various hospitals and research institutions.

Florian Kofler, Felix Meissen, Felix Steinbauer et al.

A myriad of algorithms for the automatic analysis of brain MR images is available to support clinicians in their decision-making. For brain tumor patients, the image acquisition time series typically starts with an already pathological scan. This poses problems, as many algorithms are designed to analyze healthy brains and provide no guarantee for images featuring lesions. Examples include, but are not limited to, algorithms for brain anatomy parcellation, tissue segmentation, and brain extraction. To solve this dilemma, we introduce the BraTS inpainting challenge. Here, the participants explore inpainting techniques to synthesize healthy brain scans from lesioned ones. The following manuscript contains the task formulation, dataset, and submission procedure. Later, it will be updated to summarize the findings of the challenge. The challenge is organized as part of the ASNR-BraTS MICCAI challenge.

Dominic LaBella, Maruf Adewole, Michelle Alonso-Basanta et al.

Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality. Radiologists, neurosurgeons, neuro-oncologists, and radiation oncologists rely on multiparametric MRI (mpMRI) for diagnosis, treatment planning, and longitudinal treatment monitoring; yet automated, objective, and quantitative tools for non-invasive assessment of meningiomas on mpMRI are lacking. The BraTS meningioma 2023 challenge will provide a community standard and benchmark for state-of-the-art automated intracranial meningioma segmentation models based on the largest expert annotated multilabel meningioma mpMRI dataset to date. Challenge competitors will develop automated segmentation models to predict three distinct meningioma sub-regions on MRI including enhancing tumor, non-enhancing tumor core, and surrounding nonenhancing T2/FLAIR hyperintensity. Models will be evaluated on separate validation and held-out test datasets using standardized metrics utilized across the BraTS 2023 series of challenges including the Dice similarity coefficient and Hausdorff distance. The models developed during the course of this challenge will aid in incorporation of automated meningioma MRI segmentation into clinical practice, which will ultimately improve care of patients with meningioma.