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Found 60 papers, 29 papers with code
BraTS orchestrator : Democratizing and Disseminating state-of-the-art brain tumor image analysis
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.
Analysis of the MICCAI Brain Tumor Segmentation -- Metastases (BraTS-METS) 2025 Lighthouse Challenge: Brain Metastasis Segmentation on Pre- and Post-treatment MRI
The BraTS-METS 2025 Lighthouse Challenge aims to address this critical need by establishing inter-rater and intra-rater variability in dataset annotation by generating high quality annotated datasets from four individual instances of segmentation by neuroradiologists while being recorded on video (two instances doing "from scratch" and two instances after AI pre-segmentation).
Efficient Deep Learning-based Forward Solvers for Brain Tumor Growth Models
Glioblastoma, a highly aggressive brain tumor, poses major challenges due to its poor prognosis and high morbidity rates.
Spatial Brain Tumor Concentration Estimation for Individualized Radiotherapy Planning
Biophysical modeling of brain tumors has emerged as a promising strategy for personalizing radiotherapy planning by estimating the otherwise hidden distribution of tumor cells within the brain.
FedPID: An Aggregation Method for Federated 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.
MultiOrg: A Multi-rater Organoid-detection Dataset
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.
Physics-Regularized Multi-Modal Image Assimilation for Brain Tumor Localization
Physical models in the form of partial differential equations serve as important priors for many under-constrained problems.
Neural Network Surrogate and Projected Gradient Descent for Fast and Reliable Finite Element Model Calibration: a Case Study on an Intervertebral Disc
The proposed method is evaluated against SOTA Genetic Algorithm and inverse model baselines on synthetic and in vitro experimental datasets.
BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023
Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children.
Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge
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.
The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children.
A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge
We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge.
QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge
The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets.
Cross-domain and Cross-dimension Learning for Image-to-Graph Transformers
We propose (1) a regularized edge sampling loss to effectively learn object relations in multiple domains with different numbers of edges, (2) a domain adaptation framework for image-to-graph transformers aligning image- and graph-level features from different domains, and (3) a projection function that allows using 2D data for training 3D transformers.
A Learnable Prior Improves Inverse Tumor Growth Modeling
Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients.
Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA
The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology.
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.
Personalized Predictions of Glioblastoma Infiltration: Mathematical Models, Physics-Informed Neural Networks and Multimodal Scans
This work proposes a method that uses Physics-Informed Neural Networks (PINNs) to estimate patient-specific parameters of a reaction-diffusion PDE model of GBM growth from a single 3D structural MRI snapshot.
A skeletonization algorithm for gradient-based optimization
Finally, we demonstrate the utility of our algorithm by integrating it with two medical image processing applications that use gradient-based optimization: deep-learning-based blood vessel segmentation, and multimodal registration of the mandible in computed tomography and magnetic resonance images.
Framing image registration as a landmark detection problem for label-noise-aware task representation (HitR)
Accurate image registration is pivotal in biomedical image analysis, where selecting suitable registration algorithms demands careful consideration.
The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI
Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children.
The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting
The challenge is organized as part of the ASNR-BraTS MICCAI challenge.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn)
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 ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma
Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality.
FedPIDAvg: A PID controller inspired aggregation method for Federated Learning
Another key challenge was the vastly varying size of data samples per center.
Primitive Simultaneous Optimization of Similarity Metrics for Image Registration
Even though simultaneous optimization of similarity metrics is a standard procedure in the field of semantic segmentation, surprisingly, this is much less established for image registration.
Why is the winner the best?
The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning.
Identifying chromophore fingerprints of brain tumor tissue on hyperspectral imaging using principal component analysis
In this article, we perform a statistical analysis of the brain tumor patients' HSI scans from the HELICoiD dataset with the aim of identifying the correlation between reflectance spectra and absorption spectra of tissue chromophores.
Clustering disease trajectories in contrastive feature space for biomarker discovery in age-related macular degeneration
Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly.
Approaching Peak Ground Truth
Machine learning models are typically evaluated by computing similarity with reference annotations and trained by maximizing similarity with such.
Automated analysis of diabetic retinopathy using vessel segmentation maps as inductive bias
Recent studies suggest that early stages of diabetic retinopathy (DR) can be diagnosed by monitoring vascular changes in the deep vascular complex.
Landmark-free Statistical Shape Modeling via Neural Flow Deformations
Statistical shape modeling aims at capturing shape variations of an anatomical structure that occur within a given population.
Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021
This challenge aimed to promote the development of methods for automated detection and segmentation of small and sparse imaging markers of cerebral small vessel disease, namely enlarged perivascular spaces (EPVS) (Task 1), cerebral microbleeds (Task 2) and lacunes of presumed vascular origin (Task 3) while leveraging weak and noisy labels.
ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset
The test dataset will be used for model validation only and will not be released to the public.
Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings
To approximate human quality ratings on scarce expert data, we train surrogate quality estimation models.
blob loss: instance imbalance aware loss functions for semantic segmentation
\emph{Blob loss} is designed for semantic segmentation problems where detecting multiple instances matters.
Federated Learning Enables Big Data for Rare Cancer Boundary Detection
Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data.
Relationformer: A Unified Framework for Image-to-Graph Generation
We leverage direct set-based object prediction and incorporate the interaction among the objects to learn an object-relation representation jointly.
A unified 3D framework for Organs at Risk Localization and Segmentation for Radiation Therapy Planning
Automatic localization and segmentation of organs-at-risk (OAR) in CT are essential pre-processing steps in medical image analysis tasks, such as radiation therapy planning.
Generalized Wasserstein Dice Loss, Test-time Augmentation, and Transformers for the BraTS 2021 challenge
Importantly, we explore the inclusion of a transformer in the bottleneck of the U-Net architecture.
FedCostWAvg: A new averaging for better Federated Learning
We propose a simple new aggregation strategy for federated learning that won the MICCAI Federated Tumor Segmentation Challenge 2021 (FETS), the first ever challenge on Federated Learning in the Machine Learning community.
Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling
Current treatment planning of patients diagnosed with a brain tumor, such as glioma, could significantly benefit by accessing the spatial distribution of tumor cell concentration.
Semi-Implicit Neural Solver for Time-dependent Partial Differential Equations
In this paper, we propose a neural solver to learn an optimal iterative scheme in a data-driven fashion for any class of PDEs.
Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience (VesselGraph)
Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset.
clDice - A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation
Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research.
METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy
Novel multimodal imaging methods are capable of generating extensive, super high resolution datasets for preclinical research.
Are we using appropriate segmentation metrics? Identifying correlates of human expert perception for CNN training beyond rolling the DICE coefficient
It is often unclear how to optimize abstract metrics, such as human expert perception, in convolutional neural network (CNN) training.
Imbalance-Aware Self-Supervised Learning for 3D Radiomic Representations
Radiomic representations can quantify properties of regions of interest in medical image data.
The MICCAI Hackathon on reproducibility, diversity, and selection of papers at the MICCAI conference
With this growth, however, come new challenges for the community.
An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset
It is critical to quantitatively analyse the developing human fetal brain in order to fully understand neurodevelopment in both normal fetuses and those with congenital disorders.
A distance-based loss for smooth and continuous skin layer segmentation in optoacoustic images
Raster-scan optoacoustic mesoscopy (RSOM) is a powerful, non-invasive optical imaging technique for functional, anatomical, and molecular skin and tissue analysis.
Red-GAN: Attacking class imbalance via conditioned generation. Yet another perspective on medical image synthesis for skin lesion dermoscopy and brain tumor MRI
Exploiting learning algorithms under scarce data regimes is a limitation and a reality of the medical imaging field.
clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation
Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research.
Red-GAN: Attacking class imbalance via conditioned generation. Yet another medical imaging perspective
Exploiting learning algorithms under scarce data regimes is a limitation and a reality of the medical imaging field.
VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images
Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf. io/nqjyw/, https://osf. io/t98fz/).
Implicit Neural Solver for Time-dependent Linear PDEs with Convergence Guarantee
The existing implicit schemes are usually iterative and employ a general-purpose solver which may be sub-optimal for a specific class of PDEs.
Shape-Aware Complementary-Task Learning for Multi-Organ Segmentation
Multi-organ segmentation in whole-body computed tomography (CT) is a constant pre-processing step which finds its application in organ-specific image retrieval, radiotherapy planning, and interventional image analysis.
Neural parameters estimation for brain tumor growth modeling
In this work, we propose a learning-based technique for the estimation of tumor growth model parameters from medical scans.
The Liver Tumor Segmentation Benchmark (LiTS)
In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018.
