Michael Baumgartner

Lena Maier-Hein, Annika Reinke, Patrick Godau et al. · utoronto

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.

Saikat Roy, Gregor Koehler, Constantin Ulrich et al.

There has been exploding interest in embracing Transformer-based architectures for medical image segmentation. However, the lack of large-scale annotated medical datasets make achieving performances equivalent to those in natural images challenging. Convolutional networks, in contrast, have higher inductive biases and consequently, are easily trainable to high performance. Recently, the ConvNeXt architecture attempted to modernize the standard ConvNet by mirroring Transformer blocks. In this work, we improve upon this to design a modernized and scalable convolutional architecture customized to challenges of data-scarce medical settings. We introduce MedNeXt, a Transformer-inspired large kernel segmentation network which introduces - 1) A fully ConvNeXt 3D Encoder-Decoder Network for medical image segmentation, 2) Residual ConvNeXt up and downsampling blocks to preserve semantic richness across scales, 3) A novel technique to iteratively increase kernel sizes by upsampling small kernel networks, to prevent performance saturation on limited medical data, 4) Compound scaling at multiple levels (depth, width, kernel size) of MedNeXt. This leads to state-of-the-art performance on 4 tasks on CT and MRI modalities and varying dataset sizes, representing a modernized deep architecture for medical image segmentation. Our code is made publicly available at: https://github.com/MIC-DKFZ/MedNeXt.

M. Jorge Cardoso, Wenqi Li, Richard Brown et al.

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare.

Annika Reinke, Minu D. Tizabi, Michael Baumgartner et al.

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

Arunkumar Kannan, Yanbo Zhang, Han Liu et al.

While automated diagnosis systems have achieved remarkable success in computed tomography (CT)-based lung cancer screening, their development remains limited by the scarcity of diverse, annotated pulmonary nodule datasets. Diffusion-based generative models offer a promising strategy for data synthesis; however, many existing conditional approaches primarily optimize spatial reconstruction losses, which encourage voxel-wise similarity but may inadequately constrain lesion-level intensity distributions. As a result, these methods may produce over-smoothed texture profiles and underrepresent the distinct attenuation characteristics of different nodule subtypes, including solid, part-solid, and ground-glass nodules. To address this challenge, we propose a controllable latent diffusion model that synthesizes pulmonary nodules within full 3D CT volumes while accurately modeling nodule-specific intensity distributions. Specifically, rather than relying solely on spatial losses, we introduce a histogram-based regularization term that constrains voxel intensity distributions during the generative process. The model combines subtype, spatial mask, and Hounsfield unit (HU) histogram conditioning with the differentiable feature-space histogram regularization term to better align lesion-level intensity distributions, improving the visual plausibility and subtype consistency of synthesized nodules. Extensive experiments on lung CT data demonstrate that our framework achieves strong visual realism, validated through both quantitative metrics and a visual Turing test. Furthermore, when used for data augmentation, the generated nodules improve performance in downstream clinical tasks, particularly for underrepresented nodule subtypes, and show a potential benefit for subtype-informed malignancy classification.

Constantin Ulrich, Fabian Isensee, Tassilo Wald et al.

The medical imaging community generates a wealth of datasets, many of which are openly accessible and annotated for specific diseases and tasks such as multi-organ or lesion segmentation. Current practices continue to limit model training and supervised pre-training to one or a few similar datasets, neglecting the synergistic potential of other available annotated data. We propose MultiTalent, a method that leverages multiple CT datasets with diverse and conflicting class definitions to train a single model for a comprehensive structure segmentation. Our results demonstrate improved segmentation performance compared to previous related approaches, systematically, also compared to single dataset training using state-of-the-art methods, especially for lesion segmentation and other challenging structures. We show that MultiTalent also represents a powerful foundation model that offers a superior pre-training for various segmentation tasks compared to commonly used supervised or unsupervised pre-training baselines. Our findings offer a new direction for the medical imaging community to effectively utilize the wealth of available data for improved segmentation performance. The code and model weights will be published here: [tba]

Balint Kovacs, Nils Netzer, Michael Baumgartner et al.

Data augmentation (DA) is a key factor in medical image analysis, such as in prostate cancer (PCa) detection on magnetic resonance images. State-of-the-art computer-aided diagnosis systems still rely on simplistic spatial transformations to preserve the pathological label post transformation. However, such augmentations do not substantially increase the organ as well as tumor shape variability in the training set, limiting the model's ability to generalize to unseen cases with more diverse localized soft-tissue deformations. We propose a new anatomy-informed transformation that leverages information from adjacent organs to simulate typical physiological deformations of the prostate and generates unique lesion shapes without altering their label. Due to its lightweight computational requirements, it can be easily integrated into common DA frameworks. We demonstrate the effectiveness of our augmentation on a dataset of 774 biopsy-confirmed examinations, by evaluating a state-of-the-art method for PCa detection with different augmentation settings.

Jeremias Traub, Till J. Bungert, Carsten T. Lüth et al.

Selective Classification, wherein models can reject low-confidence predictions, promises reliable translation of machine-learning based classification systems to real-world scenarios such as clinical diagnostics. While current evaluation of these systems typically assumes fixed working points based on pre-defined rejection thresholds, methodological progress requires benchmarking the general performance of systems akin to the $\mathrm{AUROC}$ in standard classification. In this work, we define 5 requirements for multi-threshold metrics in selective classification regarding task alignment, interpretability, and flexibility, and show how current approaches fail to meet them. We propose the Area under the Generalized Risk Coverage curve ($\mathrm{AUGRC}$), which meets all requirements and can be directly interpreted as the average risk of undetected failures. We empirically demonstrate the relevance of $\mathrm{AUGRC}$ on a comprehensive benchmark spanning 6 data sets and 13 confidence scoring functions. We find that the proposed metric substantially changes metric rankings on 5 out of the 6 data sets.

Marc K. Ickler, Michael Baumgartner, Saikat Roy et al.

The accurate detection of suspicious regions in medical images is an error-prone and time-consuming process required by many routinely performed diagnostic procedures. To support clinicians during this difficult task, several automated solutions were proposed relying on complex methods with many hyperparameters. In this study, we investigate the feasibility of DEtection TRansformer (DETR) models for volumetric medical object detection. In contrast to previous works, these models directly predict a set of objects without relying on the design of anchors or manual heuristics such as non-maximum-suppression to detect objects. We show by conducting extensive experiments with three models, namely DETR, Conditional DETR, and DINO DETR on four data sets (CADA, RibFrac, KiTS19, and LIDC) that these set prediction models can perform on par with or even better than currently existing methods. DINO DETR, the best-performing model in our experiments demonstrates this by outperforming a strong anchor-based one-stage detector, Retina U-Net, on three out of four data sets.

Saikat Roy, Gregor Koehler, Michael Baumgartner et al.

Owing to success in the data-rich domain of natural images, Transformers have recently become popular in medical image segmentation. However, the pairing of Transformers with convolutional blocks in varying architectural permutations leaves their relative effectiveness to open interpretation. We introduce Transformer Ablations that replace the Transformer blocks with plain linear operators to quantify this effectiveness. With experiments on 8 models on 2 medical image segmentation tasks, we explore -- 1) the replaceable nature of Transformer-learnt representations, 2) Transformer capacity alone cannot prevent representational replaceability and works in tandem with effective design, 3) The mere existence of explicit feature hierarchies in transformer blocks is more beneficial than accompanying self-attention modules, 4) Major spatial downsampling before Transformer modules should be used with caution.

Tassilo Wald, Constantin Ulrich, Fabian Isensee et al.

Independently trained machine learning models tend to learn similar features. Given an ensemble of independently trained models, this results in correlated predictions and common failure modes. Previous attempts focusing on decorrelation of output predictions or logits yielded mixed results, particularly due to their reduction in model accuracy caused by conflicting optimization objectives. In this paper, we propose the novel idea of utilizing methods of the representational similarity field to promote dissimilarity during training instead of measuring similarity of trained models. To this end, we promote intermediate representations to be dissimilar at different depths between architectures, with the goal of learning robust ensembles with disjoint failure modes. We show that highly dissimilar intermediate representations result in less correlated output predictions and slightly lower error consistency, resulting in higher ensemble accuracy. With this, we shine first light on the connection between intermediate representations and their impact on the output predictions.

Francesca Venturini, Silvan Fluri, Manas Mejari et al.

This work systematically investigates the oxidation of extra virgin olive oil (EVOO) under accelerated storage conditions with UV absorption and total fluorescence spectroscopy. With the large amount of data collected, it proposes a method to monitor the oil's quality based on machine learning applied to highly-aggregated data. EVOO is a high-quality vegetable oil that has earned worldwide reputation for its numerous health benefits and excellent taste. Despite its outstanding quality, EVOO degrades over time owing to oxidation, which can affect both its health qualities and flavour. Therefore, it is highly relevant to quantify the effects of oxidation on EVOO and develop methods to assess it that can be easily implemented under field conditions, rather than in specialized laboratories. The following study demonstrates that fluorescence spectroscopy has the capability to monitor the effect of oxidation and assess the quality of EVOO, even when the data are highly aggregated. It shows that complex laboratory equipment is not necessary to exploit fluorescence spectroscopy using the proposed method and that cost-effective solutions, which can be used in-field by non-scientists, could provide an easily-accessible assessment of the quality of EVOO.

Michael Baumgartner, Peter M. Full, Klaus H. Maier-Hein

The accurate detection of mediastinal lesions is one of the rarely explored medical object detection problems. In this work, we applied a modified version of the self-configuring method nnDetection to the Mediastinal Lesion Analysis (MELA) Challenge 2022. By incorporating automatically generated pseudo masks, training high capacity models with large patch sizes in a multi GPU setup and an adapted augmentation scheme to reduce localization errors caused by rotations, our method achieved an excellent FROC score of 0.9922 at IoU 0.10 and 0.9880 at IoU 0.3 in our cross-validation experiments. The submitted ensemble ranked third in the competition with a FROC score of 0.9897 on the MELA challenge leaderboard.

Han Liu, Bogdan Georgescu, Yanbo Zhang et al.

3D medical image classification is essential for modern clinical workflows. Medical foundation models (FMs) have emerged as a promising approach for scaling to new tasks, yet current research suffers from three critical pitfalls: data-regime bias, suboptimal adaptation, and insufficient task coverage. In this paper, we address these pitfalls and introduce AnyMC3D, a scalable 3D classifier adapted from 2D FMs. Our method scales efficiently to new tasks by adding only lightweight plugins (about 1M parameters per task) on top of a single frozen backbone. This versatile framework also supports multi-view inputs, auxiliary pixel-level supervision, and interpretable heatmap generation. We establish a comprehensive benchmark of 12 tasks covering diverse pathologies, anatomies, and modalities, and systematically analyze state-of-the-art 3D classification techniques. Our analysis reveals key insights: (1) effective adaptation is essential to unlock FM potential, (2) general-purpose FMs can match medical-specific FMs if properly adapted, and (3) 2D-based methods surpass 3D architectures for 3D classification. For the first time, we demonstrate the feasibility of achieving state-of-the-art performance across diverse applications using a single scalable framework (including 1st place in the VLM3D challenge), eliminating the need for separate task-specific models.

Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.

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.

Nicolas Baumann, Michael Baumgartner, Edoardo Ghignone et al.

To enable self-driving vehicles accurate detection and tracking of surrounding objects is essential. While Light Detection and Ranging (LiDAR) sensors have set the benchmark for high-performance systems, the appeal of camera-only solutions lies in their cost-effectiveness. Notably, despite the prevalent use of Radio Detection and Ranging (RADAR) sensors in automotive systems, their potential in 3D detection and tracking has been largely disregarded due to data sparsity and measurement noise. As a recent development, the combination of RADARs and cameras is emerging as a promising solution. This paper presents Camera-RADAR 3D Detection and Tracking (CR3DT), a camera-RADAR fusion model for 3D object detection, and Multi-Object Tracking (MOT). Building upon the foundations of the State-of-the-Art (SotA) camera-only BEVDet architecture, CR3DT demonstrates substantial improvements in both detection and tracking capabilities, by incorporating the spatial and velocity information of the RADAR sensor. Experimental results demonstrate an absolute improvement in detection performance of 5.3% in mean Average Precision (mAP) and a 14.9% increase in Average Multi-Object Tracking Accuracy (AMOTA) on the nuScenes dataset when leveraging both modalities. CR3DT bridges the gap between high-performance and cost-effective perception systems in autonomous driving, by capitalizing on the ubiquitous presence of RADAR in automotive applications. The code is available at: https://github.com/ETH-PBL/CR3DT.

Muhammad Imran, Jonathan R. Krebs, Vishal Balaji Sivaraman et al.

Multi-class segmentation of the aorta in computed tomography angiography (CTA) scans is essential for diagnosing and planning complex endovascular treatments for patients with aortic dissections. However, existing methods reduce aortic segmentation to a binary problem, limiting their ability to measure diameters across different branches and zones. Furthermore, no open-source dataset is currently available to support the development of multi-class aortic segmentation methods. To address this gap, we organized the AortaSeg24 MICCAI Challenge, introducing the first dataset of 100 CTA volumes annotated for 23 clinically relevant aortic branches and zones. This dataset was designed to facilitate both model development and validation. The challenge attracted 121 teams worldwide, with participants leveraging state-of-the-art frameworks such as nnU-Net and exploring novel techniques, including cascaded models, data augmentation strategies, and custom loss functions. We evaluated the submitted algorithms using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD), highlighting the approaches adopted by the top five performing teams. This paper presents the challenge design, dataset details, evaluation metrics, and an in-depth analysis of the top-performing algorithms. The annotated dataset, evaluation code, and implementations of the leading methods are publicly available to support further research. All resources can be accessed at https://aortaseg24.grand-challenge.org.

Michael Baumgartner, David Müller, Agon Serifi et al.

Robust state estimation for highly dynamic motion of legged robots remains challenging, especially in dynamic, contact-rich scenarios. Traditional approaches often rely on binary contact states that fail to capture the nuances of partial contact or directional slippage. This paper presents CoCo-InEKF, a differentiable invariant extended Kalman filter that utilizes continuous contact velocity covariances instead of binary contact states. These learned covariances allow the method to dynamically modulate contact confidence, accounting for more nuanced conditions ranging from firm contact to directional slippage or no contact. To predict these covariances for a set of predefined contact candidate points, we employ a lightweight neural network trained end-to-end using a state-error loss. This approach eliminates the need for heuristic ground-truth contact labels. In addition, we propose an automated contact candidate selection procedure and demonstrate that our method is insensitive to their exact placement. Experiments on a bipedal robot demonstrate a superior accuracy-efficiency tradeoff for linear velocity estimation, as well as improved filter consistency compared to baseline methods. This enables the robust execution of challenging motions, including dancing and complex ground interactions -- both in simulation and in the real world.

Fabian Isensee, Tassilo Wald, Constantin Ulrich et al.

The release of nnU-Net marked a paradigm shift in 3D medical image segmentation, demonstrating that a properly configured U-Net architecture could still achieve state-of-the-art results. Despite this, the pursuit of novel architectures, and the respective claims of superior performance over the U-Net baseline, continued. In this study, we demonstrate that many of these recent claims fail to hold up when scrutinized for common validation shortcomings, such as the use of inadequate baselines, insufficient datasets, and neglected computational resources. By meticulously avoiding these pitfalls, we conduct a thorough and comprehensive benchmarking of current segmentation methods including CNN-based, Transformer-based, and Mamba-based approaches. In contrast to current beliefs, we find that the recipe for state-of-the-art performance is 1) employing CNN-based U-Net models, including ResNet and ConvNeXt variants, 2) using the nnU-Net framework, and 3) scaling models to modern hardware resources. These results indicate an ongoing innovation bias towards novel architectures in the field and underscore the need for more stringent validation standards in the quest for scientific progress.

Katharina Eckstein, Constantin Ulrich, Michael Baumgartner et al.

Large-scale pre-training holds the promise to advance 3D medical object detection, a crucial component of accurate computer-aided diagnosis. Yet, it remains underexplored compared to segmentation, where pre-training has already demonstrated significant benefits. Existing pre-training approaches for 3D object detection rely on 2D medical data or natural image pre-training, failing to fully leverage 3D volumetric information. In this work, we present the first systematic study of how existing pre-training methods can be integrated into state-of-the-art detection architectures, covering both CNNs and Transformers. Our results show that pre-training consistently improves detection performance across various tasks and datasets. Notably, reconstruction-based self-supervised pre-training outperforms supervised pre-training, while contrastive pre-training provides no clear benefit for 3D medical object detection. Our code is publicly available at: https://github.com/MIC-DKFZ/nnDetection-finetuning.

Michael Baumgartner, Paul F. Jaeger, Fabian Isensee et al.

Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of high clinical relevance because diagnostic decisions often depend on rating of objects rather than e.g. pixels. For this task, the cumbersome and iterative process of method configuration constitutes a major research bottleneck. Recently, nnU-Net has tackled this challenge for the task of image segmentation with great success. Following nnU-Net's agenda, in this work we systematize and automate the configuration process for medical object detection. The resulting self-configuring method, nnDetection, adapts itself without any manual intervention to arbitrary medical detection problems while achieving results en par with or superior to the state-of-the-art. We demonstrate the effectiveness of nnDetection on two public benchmarks, ADAM and LUNA16, and propose 11 further medical object detection tasks on public data sets for comprehensive method evaluation. Code is at https://github.com/MIC-DKFZ/nnDetection .

Gongning Luo, Mingwang Xu, Hongyu Chen et al.

Breast cancer is one of the most common causes of death among women worldwide. Early detection helps in reducing the number of deaths. Automated 3D Breast Ultrasound (ABUS) is a newer approach for breast screening, which has many advantages over handheld mammography such as safety, speed, and higher detection rate of breast cancer. Tumor detection, segmentation, and classification are key components in the analysis of medical images, especially challenging in the context of 3D ABUS due to the significant variability in tumor size and shape, unclear tumor boundaries, and a low signal-to-noise ratio. The lack of publicly accessible, well-labeled ABUS datasets further hinders the advancement of systems for breast tumor analysis. Addressing this gap, we have organized the inaugural Tumor Detection, Segmentation, and Classification Challenge on Automated 3D Breast Ultrasound 2023 (TDSC-ABUS2023). This initiative aims to spearhead research in this field and create a definitive benchmark for tasks associated with 3D ABUS image analysis. In this paper, we summarize the top-performing algorithms from the challenge and provide critical analysis for ABUS image examination. We offer the TDSC-ABUS challenge as an open-access platform at https://tdsc-abus2023.grand-challenge.org/ to benchmark and inspire future developments in algorithmic research.

Tassilo Wald, Saikat Roy, Fabian Isensee et al.

Transformers have achieved remarkable success across multiple fields, yet their impact on 3D medical image segmentation remains limited with convolutional networks still dominating major benchmarks. In this work, we a) analyze current Transformer-based segmentation models and identify critical shortcomings, particularly their over-reliance on convolutional blocks. Further, we demonstrate that in some architectures, performance is unaffected by the absence of the Transformer, thereby demonstrating their limited effectiveness. To address these challenges, we move away from hybrid architectures and b) introduce a fully Transformer-based segmentation architecture, termed Primus. Primus leverages high-resolution tokens, combined with advances in positional embeddings and block design, to maximally leverage its Transformer blocks. Through these adaptations Primus surpasses current Transformer-based methods and competes with state-of-the-art convolutional models on multiple public datasets. By doing so, we create the first pure Transformer architecture and take a significant step towards making Transformers state-of-the-art for 3D medical image segmentation.

Vladyslav Zalevskyi, Thomas Sanchez, Misha Kaandorp et al.

Accurate fetal brain tissue segmentation and biometric analysis are essential for studying brain development in utero. The FeTA Challenge 2024 advanced automated fetal brain MRI analysis by introducing biometry prediction as a new task alongside tissue segmentation. For the first time, our diverse multi-centric test set included data from a new low-field (0.55T) MRI dataset. Evaluation metrics were also expanded to include the topology-specific Euler characteristic difference (ED). Sixteen teams submitted segmentation methods, most of which performed consistently across both high- and low-field scans. However, longitudinal trends indicate that segmentation accuracy may be reaching a plateau, with results now approaching inter-rater variability. The ED metric uncovered topological differences that were missed by conventional metrics, while the low-field dataset achieved the highest segmentation scores, highlighting the potential of affordable imaging systems when paired with high-quality reconstruction. Seven teams participated in the biometry task, but most methods failed to outperform a simple baseline that predicted measurements based solely on gestational age, underscoring the challenge of extracting reliable biometric estimates from image data alone. Domain shift analysis identified image quality as the most significant factor affecting model generalization, with super-resolution pipelines also playing a substantial role. Other factors, such as gestational age, pathology, and acquisition site, had smaller, though still measurable, effects. Overall, FeTA 2024 offers a comprehensive benchmark for multi-class segmentation and biometry estimation in fetal brain MRI, underscoring the need for data-centric approaches, improved topological evaluation, and greater dataset diversity to enable clinically robust and generalizable AI tools.

Maximilian Fischer, Peter Neher, Peter Schüffler et al.

Digital pathology offers a groundbreaking opportunity to transform clinical practice in histopathological image analysis, yet faces a significant hurdle: the substantial file sizes of pathological Whole Slide Images (WSI). While current digital pathology solutions rely on lossy JPEG compression to address this issue, lossy compression can introduce color and texture disparities, potentially impacting clinical decision-making. While prior research addresses perceptual image quality and downstream performance independently of each other, we jointly evaluate compression schemes for perceptual and downstream task quality on four different datasets. In addition, we collect an initially uncompressed dataset for an unbiased perceptual evaluation of compression schemes. Our results show that deep learning models fine-tuned for perceptual quality outperform conventional compression schemes like JPEG-XL or WebP for further compression of WSI. However, they exhibit a significant bias towards the compression artifacts present in the training data and struggle to generalize across various compression schemes. We introduce a novel evaluation metric based on feature similarity between original files and compressed files that aligns very well with the actual downstream performance on the compressed WSI. Our metric allows for a general and standardized evaluation of lossy compression schemes and mitigates the requirement to independently assess different downstream tasks. Our study provides novel insights for the assessment of lossy compression schemes for WSI and encourages a unified evaluation of lossy compression schemes to accelerate the clinical uptake of digital pathology.

Tassilo Wald, Constantin Ulrich, Gregor Köhler et al.

What representation do deep neural networks learn? How similar are images to each other for neural networks? Despite the overwhelming success of deep learning methods key questions about their internal workings still remain largely unanswered, due to their internal high dimensionality and complexity. To address this, one approach is to measure the similarity of activation responses to various inputs. Representational Similarity Matrices (RSMs) distill this similarity into scalar values for each input pair. These matrices encapsulate the entire similarity structure of a system, indicating which input leads to similar responses. While the similarity between images is ambiguous, we argue that the spatial location of semantic objects does neither influence human perception nor deep learning classifiers. Thus this should be reflected in the definition of similarity between image responses for computer vision systems. Revisiting the established similarity calculations for RSMs we expose their sensitivity to spatial alignment. In this paper, we propose to solve this through semantic RSMs, which are invariant to spatial permutation. We measure semantic similarity between input responses by formulating it as a set-matching problem. Further, we quantify the superiority of semantic RSMs over spatio-semantic RSMs through image retrieval and by comparing the similarity between representations to the similarity between predicted class probabilities.

Constantin Ulrich, Catherine Knobloch, Julius C. Holzschuh et al.

Despite considerable strides in developing deep learning models for 3D medical image segmentation, the challenge of effectively generalizing across diverse image distributions persists. While domain generalization is acknowledged as vital for robust application in clinical settings, the challenges stemming from training with a limited Field of View (FOV) remain unaddressed. This limitation leads to false predictions when applied to body regions beyond the FOV of the training data. In response to this problem, we propose a novel loss function that penalizes predictions in implausible body regions, applicable in both single-dataset and multi-dataset training schemes. It is realized with a Body Part Regression model that generates axial slice positional scores. Through comprehensive evaluation using a test set featuring varying FOVs, our approach demonstrates remarkable improvements in generalization capabilities. It effectively mitigates false positive tumor predictions up to 85% and significantly enhances overall segmentation performance.

Annika Reinke, Minu D. Tizabi, Carole H. Sudre et al.

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.

Francesca Venturini, Michela Sperti, Umberto Michelucci et al.

Extra virgin olive oil (EVOO) is the highest quality of olive oil and is characterized by highly beneficial nutritional properties. The large increase in both consumption and fraud, for example through adulteration, creates new challenges and an increasing demand for developing new quality assessment methodologies that are easier and cheaper to perform. As of today, the determination of olive oil quality is performed by producers through chemical analysis and organoleptic evaluation. The chemical analysis requires the advanced equipment and chemical knowledge of certified laboratories, and has therefore a limited accessibility. In this work a minimalist, portable and low-cost sensor is presented, which can perform olive oil quality assessment using fluorescence spectroscopy. The potential of the proposed technology is explored by analyzing several olive oils of different quality levels, EVOO, virgin olive oil (VOO), and lampante olive oil (LOO). The spectral data were analyzed using a large number of machine learning methods, including artificial neural networks. The analysis performed in this work demonstrates the possibility of performing classification of olive oil in the three mentioned classes with an accuracy of 100$\%$. These results confirm that this minimalist low-cost sensor has the potential of substituting expensive and complex chemical analysis.

Umberto Michelucci, Michael Baumgartner, Francesca Venturini

Luminescence-based sensors for measuring oxygen concentration are widely used both in industry and research due to the practical advantages and sensitivity of this type of sensing. The measuring principle is the luminescence quenching by oxygen molecules, which results in a change of the luminescence decay time and intensity. In the classical approach, this change is related to an oxygen concentration using the Stern-Volmer equation. This equation, which in most of the cases is non-linear, is parametrized through device-specific constants. Therefore, to determine these parameters every sensor needs to be precisely calibrated at one or more known concentrations. This work explores an entirely new artificial intelligence approach and demonstrates the feasibility of oxygen sensing through machine learning. The specifically developed neural network learns very efficiently to relate the input quantities to the oxygen concentration. The results show a mean deviation of the predicted from the measured concentration of 0.5 percent air, comparable to many commercial and low-cost sensors. Since the network was trained using synthetically generated data, the accuracy of the model predictions is limited by the ability of the generated data to describe the measured data, opening up future possibilities for significant improvement by using a large number of experimental measurements for training. The approach described in this work demonstrates the applicability of artificial intelligence to sensing of sensors.

Christoph Haarburger, Michael Baumgartner, Daniel Truhn et al.

Classification of malignancy for breast cancer and other cancer types is usually tackled as an object detection problem: Individual lesions are first localized and then classified with respect to malignancy. However, the drawback of this approach is that abstract features incorporating several lesions and areas that are not labelled as a lesion but contain global medically relevant information are thus disregarded: especially for dynamic contrast-enhanced breast MRI, criteria such as background parenchymal enhancement and location within the breast are important for diagnosis and cannot be captured by object detection approaches properly. In this work, we propose a 3D CNN and a multi scale curriculum learning strategy to classify malignancy globally based on an MRI of the whole breast. Thus, the global context of the whole breast rather than individual lesions is taken into account. Our proposed approach does not rely on lesion segmentations, which renders the annotation of training data much more effective than in current object detection approaches. Achieving an AUROC of 0.89, we compare the performance of our approach to Mask R-CNN and Retina U-Net as well as a radiologist. Our performance is on par with approaches that, in contrast to our method, rely on pixelwise segmentations of lesions.