Accurate fetal brain tissue segmentation and biometric measurement are essential for monitoring neurodevelopment and detecting abnormalities in utero. The Fetal Tissue Annotation (FeTA) Challenges have established robust multi-center benchmarks for evaluating state-of-the-art segmentation methods. This paper presents the results of the 2024 challenge edition, which introduced three key innovations. First, we introduced a topology-aware metric based on the Euler characteristic difference (ED) to overcome the performance plateau observed with traditional metrics like Dice or Hausdorff distance (HD), as the performance of the best models in segmentation surpassed the inter-rater variability. While the best teams reached similar scores in Dice (0.81-0.82) and HD95 (2.1-2.3 mm), ED provided greater discriminative power: the winning method achieved an ED of 20.9, representing roughly a 50% improvement over the second-and third-ranked teams despite comparable Dice scores. Second, we introduced a new 0.55T low-field MRI test set, which, when paired with high-quality super-resolution reconstruction, achieved the highest segmentation performance across all test cohorts (Dice=0.86, HD95=1.69, ED=6.26). This provides the first quantitative evidence that low-cost, low-field MRI can match or surpass high-field systems in automated fetal brain segmentation. Third, the new biometry estimation task exposed a clear performance gap: although the best model reached a mean average percentage error (MAPE) of 7.72%, most submissions failed to outperform a simple gestational-age-based linear regression model (MAPE=9.56%), and all remained above inter-rater variability with a MAPE of 5.38%. Finally, by analyzing the top-performing models from FeTA 2024 alongside those from previous challenge editions, we identify ensembles of 3D nnU-Net trained on both real and synthetic data with both image-and anatomy-level augmentations as the most effective approaches for fetal brain segmentation. Our quantitative analysis reveals that acquisition site, super-resolution strategy, and image quality are the primary sources of domain shift, informing recommendations to enhance the robustness and generalizability of automated fetal brain analysis methods.

Segmentation is a critical step in analyzing the developing human fetal brain. There have been vast improvements in automatic segmentation methods in the past several years, and the Fetal Brain Tissue Annotation (FeTA) Challenge 2021 helped to establish an excellent standard of fetal brain segmentation. However, FeTA 2021 was a single center study, and the generalizability of algorithms across different imaging centers remains unsolved, limiting real-world clinical applicability. The multi-center FeTA Challenge 2022 focuses on advancing the generalizability of fetal brain segmentation algorithms for magnetic resonance imaging (MRI). In FeTA 2022, the training dataset contained images and corresponding manually annotated multi-class labels from two imaging centers, and the testing data contained images from these two imaging centers as well as two additional unseen centers. The data from different centers varied in many aspects, including scanners used, imaging parameters, and fetal brain super-resolution algorithms applied. 16 teams participated in the challenge, and 17 algorithms were evaluated. Here, a detailed overview and analysis of the challenge results are provided, focusing on the generalizability of the submissions. Both in- and out of domain, the white matter and ventricles were segmented with the highest accuracy, while the most challenging structure remains the cerebral cortex due to anatomical complexity. The FeTA Challenge 2022 was able to successfully evaluate and advance generalizability of multi-class fetal brain tissue segmentation algorithms for MRI and it continues to benchmark new algorithms. The resulting new methods contribute to improving the analysis of brain development in utero.

Deep learning-based medical image segmentation techniques have shown promising results when evaluated based on conventional metrics such as the Dice score or Intersection-over-Union. However, these fully automatic methods often fail to meet clinically acceptable accuracy, especially when topological constraints should be observed, e.g., continuous boundaries or closed surfaces. In medical image segmentation, the correctness of a segmentation in terms of the required topological genus sometimes is even more important than the pixel-wise accuracy. Existing topology-aware approaches commonly estimate and constrain the topological structure via the concept of persistent homology (PH). However, these methods are difficult to implement for high dimensional data due to their polynomial computational complexity. To overcome this problem, we propose a novel and fast approach for topology-aware segmentation based on the Euler Characteristic (χ). First, we propose a fast formulation for χ computation in both 2D and 3D. The scalar χ error between the prediction and ground-truth serves as the topological evaluation metric. Then we estimate the spatial topology correctness of any segmentation network via a so-called topological violation map, i.e., a detailed map that highlights regions with χ errors. Finally, the segmentation results from the arbitrary network are refined based on the topological violation maps by a topology-aware correction network. Our experiments are conducted on both 2D and 3D datasets and show that our method can significantly improve topological correctness while preserving pixel-wise segmentation accuracy.

Reconstructing temporally coherent 3D meshes of the beating heart from multi-view MR images is an important but challenging problem. The challenge is entangled by the complexity in integrating multi-view data, the sparse coverage of a 3D geometry by 2D image slices, and the interplay between geometry and motion. Current approaches often treat mesh reconstruction and motion estimation as two separate problems. Here we propose Mesh4D, a novel motion-aware method that jointly learns cardiac shape and motion, directly from multi-view MR image sequences. The method introduces three key innovations: (1) A cross-attention encoder that fuses multi-view image information, (2) A transformer-based variational autoencoder (VAE) that jointly model the image feature and motion, and (3) A deformation decoder that generates continuous deformation fields and temporally smooth 3D+t cardiac meshes. Incorporating geometric regularisation and motion consistency constraints, Mesh4D can reconstruct high-quality 3D+t meshes (7,698 vertices, 15,384 faces) of the heart ventricles across 50 time frames, within less than 3 s. When compared to existing approaches, Mesh4D achieves notable improvements in reconstruction accuracy and motion smoothness, offering an efficient image-to-mesh solution for quantifying shape and motion of the heart and creating digital heart models.

Although existing medical image segmentation methods provide impressive pixel-wise accuracy, they often neglect topological correctness, making their segmentations unusable for many downstream tasks. One option is to retrain such models whilst including a topology-driven loss component. However, this is computationally expensive and often impractical. A better solution would be to have a versatile plug-and-play topology refinement method that is compatible with any domain-specific segmentation pipeline. Directly training a post-processing model to mitigate topological errors often fails as such models tend to be biased towards the topological errors of a target segmentation network. The diversity of these errors is confined to the information provided by a labelled training set, which is especially problematic for small datasets. Our method solves this problem by training a model-agnostic topology refinement network with synthetic segmentations that cover a wide variety of topological errors. Inspired by the Stone-Weierstrass theorem, we synthesize topology-perturbation masks with randomly sampled coefficients of orthogonal polynomial bases, which ensures a complete and unbiased representation. Practically, we verified the efficiency and effectiveness of our methods as being compatible with multiple families of polynomial bases, and show evidence that our universal plug-and-play topology refinement network outperforms both existing topology-driven learning-based and post-processing methods. We also show that combining our method with learning-based models provides an effortless add-on, which can further improve the performance of existing approaches.

Existing learning-based cortical surface reconstruction approaches heavily rely on the supervision of pseudo ground truth (pGT) cortical surfaces for training. Such pGT surfaces are generated by traditional neuroimage processing pipelines, which are time consuming and difficult to generalize well to low-resolution brain MRI, e.g., from fetuses and neonates. In this work, we present CoSeg, a learning-based cortical surface reconstruction framework weakly supervised by brain segmentations without the need for pGT surfaces. CoSeg introduces temporal attention networks to learn time-varying velocity fields from brain MRI for diffeomorphic surface deformations, which fit an initial surface to target cortical surfaces within only 0.11 s for each brain hemisphere. A weakly supervised loss is designed to reconstruct pial surfaces by inflating the white surface along the normal direction towards the boundary of the cortical gray matter segmentation. This alleviates partial volume effects and encourages the pial surface to deform into deep and challenging cortical sulci. We evaluate CoSeg on 1,113 adult brain MRI at 1 mm and 2 mm resolution. CoSeg achieves superior geometric and morphological accuracy compared to existing learning-based approaches. We also verify that CoSeg can extract high-quality cortical surfaces from fetal brain MRI on which traditional pipelines fail to produce acceptable results.

Segmenting teeth in 2D oral CT images is crucial for diagnosing dental conditions. However, many current models for 2D tooth segmentation depend solely on end-to-end segmentation loss during training, which can fail to capture the image's intrinsic features. Additionally, neighboring regions may interfere with tooth segmentation, leading to less-than-optimal results. To address these challenges, we introduce a novel framework named Multi-Path Restorative Pre-training with Localized Adaptive Graph Convolution (MPRP-LAGC) for 2D tooth segmentation. The MPRP utilizes two paths—one for image reconstruction and another for tooth edge reconstruction — as auxiliary tasks for pretraining the segmentation model. This enables the model to better capture both global image characteristics and the specific features of tooth edges. After dividing the feature maps to correspond to the tooth, maxillary, and mandibular regions, dynamic convolution is applied to emphasize the distinctions between the tooth area and surrounding tissues in the feature space. Experiments on one publicly available 2D oral CT dataset show that the proposed method surpasses current state-of-the-art models and accurately segments the boundaries of teeth, particularly where they meet the maxilla and mandible.

Inverse problems describe the process of estimating the causal factors from a set of measurements or data. Mapping of often incomplete or degraded data to parameters is ill-posed, thus data-driven iterative solutions are required, for example when reconstructing clean images from poor signals. Diffusion models have shown promise as potent generative tools for solving inverse problems due to their superior reconstruction quality and their compatibility with iterative solvers. However, most existing approaches are limited to linear inverse problems represented as Stochastic Differential Equations (SDEs). This simplification falls short of addressing the challenging nature of real-world problems, leading to amplified cumulative errors and biases. We provide an explanation for this gap through the lens of measure-preserving dynamics of Random Dynamical Systems (RDS) with which we analyse Temporal Distribution Discrepancy and thus introduce a theoretical framework based on RDS for SDE diffusion models. We uncover several strategies that inherently enhance the stability and generalizability of diffusion models for inverse problems and introduce a novel score-based diffusion framework, the Dynamics-aware SDE Diffusion Generative Model (D^3GM). The Measure-preserving property can return the degraded measurement to the original state despite complex degradation with the RDS concept of stability. Our extensive experimental results corroborate the effectiveness of D^3GM across multiple benchmarks including a prominent application for inverse problems, magnetic resonance imaging.

The Developing Human Connectome Project (dHCP) aims to explore developmental patterns of the human brain during the perinatal period. An automated processing pipeline has been developed to extract high-quality cortical surfaces from structural brain magnetic resonance (MR) images for the dHCP neonatal dataset. However, the current implementation of the pipeline requires more than 6.5 h to process a single MRI scan, making it expensive for large-scale neuroimaging studies. In this paper, we propose a fast deep learning (DL) based pipeline for dHCP neonatal cortical surface reconstruction, incorporating DL-based brain extraction, cortical surface reconstruction and spherical projection, as well as GPU-accelerated cortical surface inflation and cortical feature estimation. We introduce a multiscale deformation network to learn diffeomorphic cortical surface reconstruction end-to-end from T2-weighted brain MRI. A fast unsupervised spherical mapping approach is integrated to minimize metric distortions between cortical surfaces and projected spheres. The entire workflow of our DL-based dHCP pipeline completes within only 24 s on a modern GPU, which is nearly 1000 times faster than the original dHCP pipeline. The qualitative assessment demonstrates that for 82.5% of the test samples, the cortical surfaces reconstructed by our DL-based pipeline achieve superior (54.2%) or equal (28.3%) surface quality compared to the original dHCP pipeline.

Cortical surface reconstruction plays a fundamental role in modeling the rapid brain development during the perinatal period. In this work, we propose Conditional Temporal Attention Network (CoTAN), a fast end-to-end framework for diffeomorphic neonatal cortical surface reconstruction. CoTAN predicts multi-resolution stationary velocity fields (SVF) from neonatal brain magnetic resonance images (MRI). Instead of integrating multiple SVFs, CoTAN introduces attention mechanisms to learn a conditional time-varying velocity field (CTVF) by computing the weighted sum of all SVFs at each integration step. The importance of each SVF, which is estimated by learned attention maps, is conditioned on the age of the neonates and varies with the time step of integration. The proposed CTVF defines a diffeomorphic surface deformation, which reduces mesh self-intersection errors effectively. It only requires 0.21 seconds to deform an initial template mesh to cortical white matter and pial surfaces for each brain hemisphere. CoTAN is validated on the Developing Human Connectome Project (dHCP) dataset with 877 3D brain MR images acquired from preterm and term born neonates. Compared to state-of-the-art baselines, CoTAN achieves superior performance with only 0.12mm geometric error and 0.07 self-intersecting faces. The visualization of our attention maps illustrates that CoTAN indeed learns coarse-to-fine surface deformations automatically without intermediate supervision.

We present CortexODE, a deep learning framework for cortical surface reconstruction. CortexODE leverages neural ordinary differential equations (ODEs) to deform an input surface into a target shape by learning a diffeomorphic flow. The trajectories of the points on the surface are modeled as ODEs, where the derivatives of their coordinates are parameterized via a learnable Lipschitz-continuous deformation network. This provides theoretical guarantees for the prevention of self-intersections. CortexODE can be integrated to an automatic learning-based pipeline, which reconstructs cortical surfaces efficiently in less than 5 seconds. The pipeline utilizes a 3D U-Net to predict a white matter segmentation from brain Magnetic Resonance Imaging (MRI) scans, and further generates a signed distance function that represents an initial surface. Fast topology correction is introduced to guarantee homeomorphism to a sphere. Following the isosurface extraction step, two CortexODE models are trained to deform the initial surface to white matter and pial surfaces respectively. The proposed pipeline is evaluated on large-scale neuroimage datasets in various age groups including neonates (25-45 weeks), young adults (22-36 years) and elderly subjects (55-90 years). Our experiments demonstrate that the CortexODE-based pipeline can achieve less than 0.2mm average geometric error while being orders of magnitude faster compared to conventional processing pipelines.

Despite recent progress of deep learning-based medical image segmentation techniques, fully automatic results often fail to meet clinically acceptable accuracy, especially when topological constraints should be observed, e.g. , closed surfaces. Although modern image segmentation methods show promising results when evaluated based on conventional metrics such as the Dice score or Intersection-over-Union, these metrics do not reflect the correctness of a segmentation in terms of a required topological genus. Existing approaches estimate and constrain the topological structure via persistent homology (PH). However, these methods are not computationally efficient as calculating PH is not differentiable. To overcome this problem, we propose a novel approach for topological constraints based on the multi-scale Euler Characteristic (EC). To mitigate computational complexity, we propose a fast formulation for the EC that can inform the learning process of arbitrary segmentation networks via topological violation maps. Topological performance is further facilitated through a corrective convolutional network block. Our experiments on two datasets show that our method can significantly improve topological correctness.

The segmentation of the fetal cerebral cortex from magnetic resonance imaging (MRI) is an important tool for neurobiological research about the developing human brain. Manual segmentation is difficult and time-consuming. Limited image resolution and partial volume effects introduce errors and labeling noise when attempting to automate the process through machine learning. The significant morphological changes observed during brain growth pose additional challenges for learning-based image segmentation methods, which may drastically increase the amount of necessary training data. In this paper, we propose a framework to learn from noisy labels by using additional regularization via shape priors for the accurate segmentation of the cortical gray matter (CGM) in 3D. Firstly, we introduce a novel structure consistency loss based on persistent homology analysis of the cortical topology. Secondly, a regularization loss term is proposed by integrating assumptions about the cortical thickness within each sample. Our experiments on the developing human connectome project (dHCP) dataset show that our method can predict accurate CGM segmentation learned from noisy labels.

While medical images such as computed tomography (CT) are stored in DICOM format in hospital PACS, it is still quite routine in many countries to print a film as a transferable medium for the purposes of self-storage and secondary consultation. Also, with the ubiquitousness of mobile phone cameras, it is quite common to take pictures of CT films, which unfortunately suffer from geometric deformation and illumination variation. In this work, we study the problem of recovering a CT film, which marks \textbf{the first attempt} in the literature, to the best of our knowledge. We start with building a large-scale head CT film database CTFilm20K, consisting of approximately 20,000 pictures, using the widely used computer graphics software Blender. We also record all accompanying information related to the geometric deformation (such as 3D coordinate, depth, normal, and UV maps) and illumination variation (such as albedo map). Then we propose a deep framework called \textbf{F}ilm \textbf{I}mage \textbf{Re}covery \textbf{Net}work (\textbf{FIReNet}) to tackle geometric deformation and illumination variation using the multiple maps extracted from the CT films to collaboratively guide the recovery process. Finally, we convert the dewarped images to DICOM files with our cascade model for further analysis such as radiomics feature extraction. Extensive experiments demonstrate the superiority of our approach over the previous approaches. We plan to open source the simulated images and deep models for promoting the research on CT film image analysis.

Fetal Magnetic Resonance Imaging (MRI) is used in prenatal diagnosis and to assess early brain development. Accurate segmentation of the different brain tissues is a vital step in several brain analysis tasks, such as cortical surface reconstruction and tissue thickness measurements. Fetal MRI scans, however, are prone to motion artifacts that can affect the correctness of both manual and automatic segmentation techniques. In this paper, we propose a novel network structure that can simultaneously generate conditional atlases and predict brain tissue segmentation, called CAS-Net. The conditional atlases provide anatomical priors that can constrain the segmentation connectivity, despite the heterogeneity of intensity values caused by motion or partial volume effects. The proposed method is trained and evaluated on 253 subjects from the developing Human Connectome Project (dHCP). The results demonstrate that the proposed method can generate conditional age-specific atlas with sharp boundary and shape variance. It also segment multi-category brain tissues for fetal MRI with a high overall Dice similarity coefficient (DSC) of 85.2% for the selected 9 tissue labels.

Diabetic retinopathy (DR) is a leading cause of permanent blindness among the working-age people. Automatic DR grading can help ophthalmologists make timely treatment for patients. However, the existing grading methods are usually trained with high resolution (HR) fundus images, such that the grading performance decreases a lot given low resolution (LR) images, which are common in clinic. In this paper, we mainly focus on DR grading with LR fundus images. According to our analysis on the DR task, we find that: 1) image super-resolution (ISR) can boost the performance of both DR grading and lesion segmentation; 2) the lesion segmentation regions of fundus images are highly consistent with pathological regions for DR grading. Based on our findings, we propose a convolutional neural network (CNN)-based method for joint learning of multi-level tasks for DR grading, called DeepMT-DR, which can simultaneously handle the low-level task of ISR, the mid-level task of lesion segmentation and the high-level task of disease severity classification on LR fundus images. Moreover, a novel task-aware loss is developed to encourage ISR to focus on the pathological regions for its subsequent tasks: lesion segmentation and DR grading. Extensive experimental results show that our DeepMT-DR method significantly outperforms other state-of-the-art methods for DR grading over three datasets. In addition, our method achieves comparable performance in two auxiliary tasks of ISR and lesion segmentation.

The application of deep learning algorithms for medical diagnosis in the real world faces challenges with transparency and interpretability. The labeling of large-scale samples leads to costly investment in developing deep learning algorithms. The application of human prior knowledge is an effective way to solve these problems. Previously, we developed a deep learning system for glaucoma diagnosis based on a large number of samples that had high sensitivity and specificity. However, it is a black box and the specific analytic methods cannot be elucidated. Here, we establish a hierarchical deep learning system based on a small number of samples that comprehensively simulates the diagnostic thinking of human experts. This system can extract the anatomical characteristics of the fundus images, including the optic disc, optic cup, and appearance of the retinal nerve fiber layer to realize automatic diagnosis of glaucoma. In addition, this system is transparent and interpretable, and the intermediate process of prediction can be visualized. Applying this system to three validation datasets of fundus images, we demonstrate performance comparable to that of human experts in diagnosing glaucoma. Moreover, it markedly improves the diagnostic accuracy of ophthalmologists. This system may expedite the screening and diagnosis of glaucoma, resulting in improved clinical outcomes.

Given the outbreak of COVID-19 pandemic and the shortage of medical resource, extensive deep learning models have been proposed for automatic COVID-19 diagnosis, based on 3D computed tomography (CT) scans.However, the existing models independently process the 3D lesion segmentation and disease classification, ignoring the inherent correlation between these two tasks.In this paper, we propose a joint deep learning model of 3D lesion segmentation and classification for diagnosing COVID-19, called DeepSC-COVID, as the first attempt in this direction.Specifically, we establish a large-scale CT database containing 1,805 3D CT scans with fine-grained lesion annotations, and reveal 4 findings about lesion difference between COVID-19 and community acquired pneumonia (CAP).Inspired by our findings, DeepSC-COVID is designed with 3 subnets: a cross-task feature subnet for feature extraction, a 3D lesion subnet for lesion segmentation, and a classification subnet for disease diagnosis.Besides, the task-aware loss is proposed for learning the task interaction across the 3D lesion and classification subnets.Different from all existing models for COVID-19 diagnosis, our model is interpretable with fine-grained 3D lesion distribution.Finally, extensive experimental results show that the joint learning framework in our model significantly improves the performance of 3D lesion segmentation and disease classification in both efficiency and efficacy.

Recent years have witnessed the growing interest in disease severity grading, especially for ocular diseases based on fundus images. The existing grading methods are usually trained with high resolution (HR) images. However, the grading performance decreases a lot given low resolution (LR) images, which are common in practice. In this paper, we mainly focus on diabetic retinopathy (DR) grading with LR fundus images. According to our analysis on the DR task, we find that: 1) image super-resolution (ISR) can boost the performance of DR grading and lesion segmentation; 2) the lesion segmentation regions of fundus images are highly consistent with pathological regions for DR grading. Thus, we propose a deep multi-task learning based DR grading (DeepMT-DR) method for LR fundus images, which simultaneously handles the auxiliary tasks of ISR and lesion segmentation. Specifically, based on our findings, we propose a hierarchical deep learning structure that simultaneously processes the low-level task of ISR, the mid-level task of lesion segmentation and the high-level task of DR grading. Moreover, a novel task-aware loss is developed to encourage ISR to focus on the pathological regions for its subsequent tasks: lesion segmentation and DR grading. Extensive experimental results show that our DeepMT-DR method significantly outperforms other state-of-the-art methods for DR grading over two public datasets. In addition, our method achieves comparable performance in two auxiliary tasks of ISR and lesion segmentation.

Disease forecast is an effective solution to early treatment and prevention for some irreversible diseases, e.g., glaucoma. Different from existing disease detection methods that predict the current status of a patient, disease forecast aims to predict the future state for early treatment. This paper is a first attempt to address the glaucoma forecast task utilizing the sequential fundus images of a patient. Specifically, we establish a database of sequential fundus images for glaucoma forecast (SIGF), which includes an average of 9 images per eye, corresponding to 3,671 fundus images in total. Besides, a novel deep learning method for glaucoma forecast (DeepGF) is proposed based on our SIGF database, consisting of an attention-polar convolution neural network (AP-CNN) and a variable time interval long short-term memory (VTI-LSTM) network to learn the spatio-temporal transition at different time intervals across sequential medical images of a person. In addition, a novel active convergence (AC) training strategy is proposed to solve the imbalanced sample distribution problem of glaucoma forecast. Finally, the experimental results show the effectiveness of our DeepGF method in glaucoma forecast.