arXiv subjects

Georg Langs

Publications and source records attributed to Georg Langs.

At least 37 records · Page 2Linked to original sources

arXiv2025

CADS: A Comprehensive Anatomical Dataset and Segmentation for Whole-Body Anatomy in Computed Tomography

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

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arXiv2025

Identifying Signatures of Image Phenotypes to Track Treatment Response in Liver Disease

Quantifiable image patterns associated with disease progression and treatment response are critical tools for guiding individual treatment, and for developing novel therapies. Here, we show that unsupervised machine learning can identify a pattern vocabulary of liver tissue in magnetic resonance images that quantifies treatment response in diffuse liver disease. Deep clustering networks simultaneously encode and cluster patches of medical images into a low-dimensional latent space to establish a tissue vocabulary. The resulting tissue types capture differential tissue change and its location in the liver associated with treatment response. We demonstrate the utility of the vocabulary on a randomized controlled trial cohort of non-alcoholic steatohepatitis patients. First, we use the vocabulary to compare longitudinal liver change in a placebo and a treatment cohort. Results show that the method identifies specific liver tissue change pathways associated with treatment, and enables a better separation between treatment groups than established non-imaging measures. Moreover, we show that the vocabulary can predict biopsy derived features from non-invasive imaging data. We validate the method on a separate replication cohort to demonstrate the applicability of the proposed method.

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arXiv2024

Detection of Emerging Infectious Diseases in Lung CT based on Spatial Anomaly Patterns

Fast detection of emerging diseases is important for containing their spread and treating patients effectively. Local anomalies are relevant, but often novel diseases involve familiar disease patterns in new spatial distributions. Therefore, established local anomaly detection approaches may fail to identify them as new. Here, we present a novel approach to detect the emergence of new disease phenotypes exhibiting distinct patterns of the spatial distribution of lesions. We first identify anomalies in lung CT data, and then compare their distribution in a continually acquired new patient cohorts with historic patient population observed over a long prior period. We evaluate how accumulated evidence collected in the stream of patients is able to detect the onset of an emerging disease. In a gram-matrix based representation derived from the intermediate layers of a three-dimensional convolutional neural network, newly emerging clusters indicate emerging diseases.

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arXiv2024

Rigid Single-Slice-in-Volume registration via rotation-equivariant 2D/3D feature matching

2D to 3D registration is essential in tasks such as diagnosis, surgical navigation, environmental understanding, navigation in robotics, autonomous systems, or augmented reality. In medical imaging, the aim is often to place a 2D image in a 3D volumetric observation to w. Current approaches for rigid single slice in volume registration are limited by requirements such as pose initialization, stacks of adjacent slices, or reliable anatomical landmarks. Here, we propose a self-supervised 2D/3D registration approach to match a single 2D slice to the corresponding 3D volume. The method works in data without anatomical priors such as images of tumors. It addresses the dimensionality disparity and establishes correspondences between 2D in-plane and 3D out-of-plane rotation-equivariant features by using group equivariant CNNs. These rotation-equivariant features are extracted from the 2D query slice and aligned with their 3D counterparts. Results demonstrate the robustness of the proposed slice-in-volume registration on the NSCLC-Radiomics CT and KIRBY21 MRI datasets, attaining an absolute median angle error of less than 2 degrees and a mean-matching feature accuracy of 89% at a tolerance of 3 pixels.

cs.CV↗

arXiv2023

Predicting dynamic, motion-related changes in B0 field in the brain at a 7 T MRI using a subject-specific fine-tuned U-net

Subject movement during the magnetic resonance examination is inevitable and causes not only image artefacts but also deteriorates the homogeneity of the main magnetic field (B0), which is a prerequisite for high quality data. Thus, characterization of changes to B0, e.g. induced by patient movement, is important for MR applications that are prone to B0 inhomogeneities. We propose a deep learning based method to predict such changes within the brain from the change of the head position to facilitate retrospective or even real-time correction. A 3D U-net was trained on in vivo brain 7T MRI data. The input consisted of B0 maps and anatomical images at an initial position, and anatomical images at a different head position (obtained by applying a rigid-body transformation on the initial anatomical image). The output consisted of B0 maps at the new head positions. We further fine-tuned the network weights to each subject by measuring a limited number of head positions of the given subject, and trained the U-net with these data. Our approach was compared to established dynamic B0 field mapping via interleaved navigators, which suffer from limited spatial resolution and the need for undesirable sequence modifications. Qualitative and quantitative comparison showed similar performance between an interleaved navigator-equivalent method and proposed method. We therefore conclude that it is feasible to predict B0 maps from rigid subject movement and, when combined with external tracking hardware, this information could be used to improve the quality of magnetic resonance acquisitions without the use of navigators.

cs.CV↗

arXiv2022

Spatio-temporal motion correction and iterative reconstruction of in-utero fetal fMRI

Resting-state functional Magnetic Resonance Imaging (fMRI) is a powerful imaging technique for studying functional development of the brain in utero. However, unpredictable and excessive movement of fetuses have limited its clinical applicability. Previous studies have focused primarily on the accurate estimation of the motion parameters employing a single step 3D interpolation at each individual time frame to recover a motion-free 4D fMRI image. Using only information from a 3D spatial neighborhood neglects the temporal structure of fMRI and useful information from neighboring timepoints. Here, we propose a novel technique based on four dimensional iterative reconstruction of the motion scattered fMRI slices. Quantitative evaluation of the proposed method on a cohort of real clinical fetal fMRI data indicates improvement of reconstruction quality compared to the conventional 3D interpolation approaches.

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arXiv2022

Distributionally Robust Deep Learning using Hardness Weighted Sampling

Limiting failures of machine learning systems is of paramount importance for safety-critical applications. In order to improve the robustness of machine learning systems, Distributionally Robust Optimization (DRO) has been proposed as a generalization of Empirical Risk Minimization (ERM). However, its use in deep learning has been severely restricted due to the relative inefficiency of the optimizers available for DRO in comparison to the wide-spread variants of Stochastic Gradient Descent (SGD) optimizers for ERM. We propose SGD with hardness weighted sampling, a principled and efficient optimization method for DRO in machine learning that is particularly suited in the context of deep learning. Similar to a hard example mining strategy in practice, the proposed algorithm is straightforward to implement and computationally as efficient as SGD-based optimizers used for deep learning, requiring minimal overhead computation. In contrast to typical ad hoc hard mining approaches, we prove the convergence of our DRO algorithm for over-parameterized deep learning networks with ReLU activation and a finite number of layers and parameters. Our experiments on fetal brain 3D MRI segmentation and brain tumor segmentation in MRI demonstrate the feasibility and the usefulness of our approach. Using our hardness weighted sampling for training a state-of-the-art deep learning pipeline leads to improved robustness to anatomical variabilities in automatic fetal brain 3D MRI segmentation using deep learning and to improved robustness to the image protocol variations in brain tumor segmentation. Our code is available at https://github.com/LucasFidon/HardnessWeightedSampler.

cs.LG↗

arXiv2022

Fetal Brain Tissue Annotation and Segmentation Challenge Results

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

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arXiv2022

Continual Active Learning Using Pseudo-Domains for Limited Labelling Resources and Changing Acquisition Characteristics

Machine learning in medical imaging during clinical routine is impaired by changes in scanner protocols, hardware, or policies resulting in a heterogeneous set of acquisition settings. When training a deep learning model on an initial static training set, model performance and reliability suffer from changes of acquisition characteristics as data and targets may become inconsistent. Continual learning can help to adapt models to the changing environment by training on a continuous data stream. However, continual manual expert labelling of medical imaging requires substantial effort. Thus, ways to use labelling resources efficiently on a well chosen sub-set of new examples is necessary to render this strategy feasible. Here, we propose a method for continual active learning operating on a stream of medical images in a multi-scanner setting. The approach automatically recognizes shifts in image acquisition characteristics - new domains -, selects optimal examples for labelling and adapts training accordingly. Labelling is subject to a limited budget, resembling typical real world scenarios. To demonstrate generalizability, we evaluate the effectiveness of our method on three tasks: cardiac segmentation, lung nodule detection and brain age estimation. Results show that the proposed approach outperforms other active learning methods, while effectively counteracting catastrophic forgetting.

cs.CV↗

arXiv2022

Motion Correction and Volumetric Reconstruction for Fetal Functional Magnetic Resonance Imaging Data

Motion correction is an essential preprocessing step in functional Magnetic Resonance Imaging (fMRI) of the fetal brain with the aim to remove artifacts caused by fetal movement and maternal breathing and consequently to suppress erroneous signal correlations. Current motion correction approaches for fetal fMRI choose a single 3D volume from a specific acquisition timepoint with least motion artefacts as reference volume, and perform interpolation for the reconstruction of the motion corrected time series. The results can suffer, if no low-motion frame is available, and if reconstruction does not exploit any assumptions about the continuity of the fMRI signal. Here, we propose a novel framework, which estimates a high-resolution reference volume by using outlier-robust motion correction, and by utilizing Huber L2 regularization for intra-stack volumetric reconstruction of the motion-corrected fetal brain fMRI. We performed an extensive parameter study to investigate the effectiveness of motion estimation and present in this work benchmark metrics to quantify the effect of motion correction and regularised volumetric reconstruction approaches on functional connectivity computations. We demonstrate the proposed framework's ability to improve functional connectivity estimates, reproducibility and signal interpretability, which is clinically highly desirable for the establishment of prognostic noninvasive imaging biomarkers. The motion correction and volumetric reconstruction framework is made available as an open-source package of NiftyMIC.

cs.CV↗

arXiv2021

4D iterative reconstruction of brain fMRI in the moving fetus

Resting-state functional Magnetic Resonance Imaging (fMRI) is a powerful imaging technique for studying functional development of the brain in utero. However, unpredictable and excessive movement of fetuses has limited clinical application since it causes substantial signal fluctuations which can systematically alter observed patterns of functional connectivity. Previous studies have focused on the accurate estimation of the motion parameters in case of large fetal head movement and used a 3D single step interpolation approach at each timepoint to recover motion-free fMRI images. This does not guarantee that the reconstructed image corresponds to the minimum error representation of fMRI time series given the acquired data. Here, we propose a novel technique based on four dimensional iterative reconstruction of the scattered slices acquired during fetal fMRI. The accuracy of the proposed method was quantitatively evaluated on a group of real clinical fMRI fetuses. The results indicate improvements of reconstruction quality compared to the conventional 3D interpolation approach.

eess.IV↗

arXiv2021

Pseudo-domains in imaging data improve prediction of future disease status in multi-center studies

In multi-center randomized clinical trials imaging data can be diverse due to acquisition technology or scanning protocols. Models predicting future outcome of patients are impaired by this data heterogeneity. Here, we propose a prediction method that can cope with a high number of different scanning sites and a low number of samples per site. We cluster sites into pseudo-domains based on visual appearance of scans, and train pseudo-domain specific models. Results show that they improve the prediction accuracy for steatosis after 48 weeks from imaging data acquired at an initial visit and 12-weeks follow-up in liver disease

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arXiv2021

Distributionally Robust Segmentation of Abnormal Fetal Brain 3D MRI

The performance of deep neural networks typically increases with the number of training images. However, not all images have the same importance towards improved performance and robustness. In fetal brain MRI, abnormalities exacerbate the variability of the developing brain anatomy compared to non-pathological cases. A small number of abnormal cases, as is typically available in clinical datasets used for training, are unlikely to fairly represent the rich variability of abnormal developing brains. This leads machine learning systems trained by maximizing the average performance to be biased toward non-pathological cases. This problem was recently referred to as hidden stratification. To be suited for clinical use, automatic segmentation methods need to reliably achieve high-quality segmentation outcomes also for pathological cases. In this paper, we show that the state-of-the-art deep learning pipeline nnU-Net has difficulties to generalize to unseen abnormal cases. To mitigate this problem, we propose to train a deep neural network to minimize a percentile of the distribution of per-volume loss over the dataset. We show that this can be achieved by using Distributionally Robust Optimization (DRO). DRO automatically reweights the training samples with lower performance, encouraging nnU-Net to perform more consistently on all cases. We validated our approach using a dataset of 368 fetal brain T2w MRIs, including 124 MRIs of open spina bifida cases and 51 MRIs of cases with other severe abnormalities of brain development.

cs.CV↗

arXiv2021

Continual Active Learning for Efficient Adaptation of Machine Learning Models to Changing Image Acquisition

Imaging in clinical routine is subject to changing scanner protocols, hardware, or policies in a typically heterogeneous set of acquisition hardware. Accuracy and reliability of deep learning models suffer from those changes as data and targets become inconsistent with their initial static training set. Continual learning can adapt to a continuous data stream of a changing imaging environment. Here, we propose a method for continual active learning on a data stream of medical images. It recognizes shifts or additions of new imaging sources - domains -, adapts training accordingly, and selects optimal examples for labelling. Model training has to cope with a limited labelling budget, resembling typical real world scenarios. We demonstrate our method on T1-weighted magnetic resonance images from three different scanners with the task of brain age estimation. Results demonstrate that the proposed method outperforms naive active learning while requiring less manual labelling.

cs.LG↗

arXiv2020

The Effects of Skin Lesion Segmentation on the Performance of Dermatoscopic Image Classification

Malignant melanoma (MM) is one of the deadliest types of skin cancer. Analysing dermatoscopic images plays an important role in the early detection of MM and other pigmented skin lesions. Among different computer-based methods, deep learning-based approaches and in particular convolutional neural networks have shown excellent classification and segmentation performances for dermatoscopic skin lesion images. These models can be trained end-to-end without requiring any hand-crafted features. However, the effect of using lesion segmentation information on classification performance has remained an open question. In this study, we explicitly investigated the impact of using skin lesion segmentation masks on the performance of dermatoscopic image classification. To do this, first, we developed a baseline classifier as the reference model without using any segmentation masks. Then, we used either manually or automatically created segmentation masks in both training and test phases in different scenarios and investigated the classification performances. Evaluated on the ISIC 2017 challenge dataset which contained two binary classification tasks (i.e. MM vs. all and seborrheic keratosis (SK) vs. all) and based on the derived area under the receiver operating characteristic curve scores, we observed four main outcomes. Our results show that 1) using segmentation masks did not significantly improve the MM classification performance in any scenario, 2) in one of the scenarios (using segmentation masks for dilated cropping), SK classification performance was significantly improved, 3) removing all background information by the segmentation masks significantly degraded the overall classification performance, and 4) in case of using the appropriate scenario (using segmentation for dilated cropping), there is no significant difference of using manually or automatically created segmentation masks.

cs.CV↗

arXiv2020

Automatic lung segmentation in routine imaging is primarily a data diversity problem, not a methodology problem

Automated segmentation of anatomical structures is a crucial step in image analysis. For lung segmentation in computed tomography, a variety of approaches exist, involving sophisticated pipelines trained and validated on different datasets. However, the clinical applicability of these approaches across diseases remains limited. We compared four generic deep learning approaches trained on various datasets and two readily available lung segmentation algorithms. We performed evaluation on routine imaging data with more than six different disease patterns and three published data sets. Using different deep learning approaches, mean Dice similarity coefficients (DSCs) on test datasets varied not over 0.02. When trained on a diverse routine dataset (n = 36) a standard approach (U-net) yields a higher DSC (0.97 $\pm$ 0.05) compared to training on public datasets such as Lung Tissue Research Consortium (0.94 $\pm$ 0.13, p = 0.024) or Anatomy 3 (0.92 $\pm$ 0.15, p = 0.001). Trained on routine data (n = 231) covering multiple diseases, U-net compared to reference methods yields a DSC of 0.98 $\pm$ 0.03 versus 0.94 $\pm$ 0.12 (p = 0.024).

eess.IV↗

arXiv2020

Dynamic memory to alleviate catastrophic forgetting in continuous learning settings

In medical imaging, technical progress or changes in diagnostic procedures lead to a continuous change in image appearance. Scanner manufacturer, reconstruction kernel, dose, other protocol specific settings or administering of contrast agents are examples that influence image content independent of the scanned biology. Such domain and task shifts limit the applicability of machine learning algorithms in the clinical routine by rendering models obsolete over time. Here, we address the problem of data shifts in a continuous learning scenario by adapting a model to unseen variations in the source domain while counteracting catastrophic forgetting effects. Our method uses a dynamic memory to facilitate rehearsal of a diverse training data subset to mitigate forgetting. We evaluated our approach on routine clinical CT data obtained with two different scanner protocols and synthetic classification tasks. Experiments show that dynamic memory counters catastrophic forgetting in a setting with multiple data shifts without the necessity for explicit knowledge about when these shifts occur.

cs.LG↗

arXiv2020

Separation of target anatomical structure and occlusions in chest radiographs

Chest radiographs are commonly performed low-cost exams for screening and diagnosis. However, radiographs are 2D representations of 3D structures causing considerable clutter impeding visual inspection and automated image analysis. Here, we propose a Fully Convolutional Network to suppress, for a specific task, undesired visual structure from radiographs while retaining the relevant image information such as lung-parenchyma. The proposed algorithm creates reconstructed radiographs and ground-truth data from high resolution CT-scans. Results show that removing visual variation that is irrelevant for a classification task improves the performance of a classifier when only limited training data are available. This is particularly relevant because a low number of ground-truth cases is common in medical imaging.

physics.med-ph↗