Anders Nymark Christensen

Manxi Lin, Zahra Bashir, Martin Grønnebæk Tolsgaard et al.

Curvilinear structure segmentation is important in medical imaging, quantifying structures such as vessels, airways, neurons, or organ boundaries in 2D slices. Segmentation via pixel-wise classification often fails to capture the small and low-contrast curvilinear structures. Prior topological information is typically used to address this problem, often at an expensive computational cost, and sometimes requiring prior knowledge of the expected topology. We present DTU-Net, a data-driven approach to topology-preserving curvilinear structure segmentation. DTU-Net consists of two sequential, lightweight U-Nets, dedicated to texture and topology, respectively. While the texture net makes a coarse prediction using image texture information, the topology net learns topological information from the coarse prediction by employing a triplet loss trained to recognize false and missed splits in the structure. We conduct experiments on a challenging multi-class ultrasound scan segmentation dataset as well as a well-known retinal imaging dataset. Results show that our model outperforms existing approaches in both pixel-wise segmentation accuracy and topological continuity, with no need for prior topological knowledge.

Manxi Lin, Aasa Feragen, Kamil Mikolaj et al.

The quality of fetal ultrasound screening scans directly influences the precision of biometric measurements. However, acquiring high-quality scans is labor-intensive and highly relies on the operator's skills. Considering the low contrastiveness and imaging artifacts that widely exist in ultrasound, even a dedicated deep-learning model can be vulnerable to learning from confounding information in the image. In this paper, we propose a holistic and explainable method for fetal ultrasound quality assessment, where we design a hierarchical concept bottleneck model by introducing human-readable ``concepts" into the task and imitating the sequential expert decision-making process. This hierarchical information flow forces the model to learn concepts from semantically meaningful areas: The model first passes through a layer of visual, segmentation-based concepts, and next a second layer of property concepts directly associated with the decision-making task. We consider the quality assessment to be in a more challenging but more realistic setting, with fine-grained image recognition. Experiments show that our model outperforms equivalent concept-free models on an in-house dataset, and shows better generalizability on two public benchmarks, one from Spain and one from Africa, without any fine-tuning.

Morten Rieger Hannemose, Josefine Vilsbøll Sundgaard, Niels Kvorning Ternov et al.

When doctors are trained to diagnose a specific disease, they learn faster when presented with cases in order of increasing difficulty. This creates the need for automatically estimating how difficult it is for doctors to classify a given case. In this paper, we introduce methods for estimating how hard it is for a doctor to diagnose a case represented by a medical image, both when ground truth difficulties are available for training, and when they are not. Our methods are based on embeddings obtained with deep metric learning. Additionally, we introduce a practical method for obtaining ground truth human difficulty for each image case in a dataset using self-assessed certainty. We apply our methods to two different medical datasets, achieving high Kendall rank correlation coefficients, showing that we outperform existing methods by a large margin on our problem and data.

Chun Kit Wong, Manxi Lin, Alberto Raheli et al.

Examination of the umbilical artery with Doppler ultrasonography is performed to investigate blood supply to the fetus through the umbilical cord, which is vital for the monitoring of fetal health. Such examination involves several steps that must be performed correctly: identifying suitable sites on the umbilical artery for the measurement, acquiring the blood flow curve in the form of a Doppler spectrum, and ensuring compliance to a set of quality standards. These steps rely heavily on the operator's skill, and the shortage of experienced sonographers has thus created a demand for machine assistance. In this work, we propose an automatic system to fill the gap. By using a modified Faster R-CNN network, we obtain an algorithm that can suggest locations suitable for Doppler measurement. Meanwhile, we have also developed a method for assessment of the Doppler spectrum's quality. The proposed system is validated on 657 images from a national ultrasound screening database, with results demonstrating its potential as a guidance system.

Pawel Tomasz Pieta, Anders Bjorholm Dahl, Jeppe Revall Frisvad et al.

The structure tensor method is often used for 2D and 3D analysis of imaged structures, but its results are in many cases very dependent on the user's choice of method parameters. We simplify this parameter choice in first order structure tensor scale-space by directly connecting the width of the derivative filter to the size of image features. By introducing a ring-filter step, we substitute the Gaussian integration/smoothing with a method that more accurately shifts the derivative filter response from feature edges to their center. We further demonstrate how extracted structural measures can be used to correct known inaccuracies in the scale map, resulting in a reliable representation of the feature sizes both in 2D and 3D. Compared to the traditional first order structure tensor, or previous structure tensor scale-space approaches, our solution is much more accurate and can serve as an out-of-the-box method for extracting a wide range of structural parameters with minimal user input.

Manxi Lin, Nina Weng, Kamil Mikolaj et al.

Shortcut learning is a phenomenon where machine learning models prioritize learning simple, potentially misleading cues from data that do not generalize well beyond the training set. While existing research primarily investigates this in the realm of image classification, this study extends the exploration of shortcut learning into medical image segmentation. We demonstrate that clinical annotations such as calipers, and the combination of zero-padded convolutions and center-cropped training sets in the dataset can inadvertently serve as shortcuts, impacting segmentation accuracy. We identify and evaluate the shortcut learning on two different but common medical image segmentation tasks. In addition, we suggest strategies to mitigate the influence of shortcut learning and improve the generalizability of the segmentation models. By uncovering the presence and implications of shortcuts in medical image segmentation, we provide insights and methodologies for evaluating and overcoming this pervasive challenge and call for attention in the community for shortcuts in segmentation. Our code is public at https://github.com/nina-weng/shortcut_skinseg .

Markus Ditlev Sjøgren Olsen, Jakob Ambsdorf, Manxi Lin et al.

Congenital malformations of the brain are among the most common fetal abnormalities that impact fetal development. Previous anomaly detection methods on ultrasound images are based on supervised learning, rely on manual annotations, and risk missing underrepresented categories. In this work, we frame fetal brain anomaly detection as an unsupervised task using diffusion models. To this end, we employ an inpainting-based Noise Agnostic Anomaly Detection approach that identifies the abnormality using diffusion-reconstructed fetal brain images from multiple noise levels. Our approach only requires normal fetal brain ultrasound images for training, addressing the limited availability of abnormal data. Our experiments on a real-world clinical dataset show the potential of using unsupervised methods for fetal brain anomaly detection. Additionally, we comprehensively evaluate how different noise types affect diffusion models in the fetal anomaly detection domain.

Paraskevas Pegios, Manxi Lin, Nina Weng et al.

Obstetric ultrasound image quality is crucial for accurate diagnosis and monitoring of fetal health. However, acquiring high-quality standard planes is difficult, influenced by the sonographer's expertise and factors like the maternal BMI or fetus dynamics. In this work, we explore diffusion-based counterfactual explainable AI to generate realistic, high-quality standard planes from low-quality non-standard ones. Through quantitative and qualitative evaluation, we demonstrate the effectiveness of our approach in generating plausible counterfactuals of increased quality. This shows future promise for enhancing training of clinicians by providing visual feedback and potentially improving standard plane quality and acquisition for downstream diagnosis and monitoring.

Manxi Lin, Jakob Ambsdorf, Emilie Pi Fogtmann Sejer et al.

We introduce the notion of semantic image quality for applications where image quality relies on semantic requirements. Working in fetal ultrasound, where ranking is challenging and annotations are noisy, we design a robust coarse-to-fine model that ranks images based on their semantic image quality and endow our predicted rankings with an uncertainty estimate. To annotate rankings on training data, we design an efficient ranking annotation scheme based on the merge sort algorithm. Finally, we compare our ranking algorithm to a number of state-of-the-art ranking algorithms on a challenging fetal ultrasound quality assessment task, showing the superior performance of our method on the majority of rank correlation metrics.

Jakob Ambsdorf, Asbjørn Munk, Sebastian Llambias et al.

With access to large-scale, unlabeled medical datasets, researchers are confronted with two questions: Should they attempt to pretrain a custom foundation model on this medical data, or use transfer-learning from an existing generalist model? And, if a custom model is pretrained, are novel methods required? In this paper we explore these questions by conducting a case-study, in which we train a foundation model on a large regional fetal ultrasound dataset of 2M images. By selecting the well-established DINOv2 method for pretraining, we achieve state-of-the-art results on three fetal ultrasound datasets, covering data from different countries, classification, segmentation, and few-shot tasks. We compare against a series of models pretrained on natural images, ultrasound images, and supervised baselines. Our results demonstrate two key insights: (i) Pretraining on custom data is worth it, even if smaller models are trained on less data, as scaling in natural image pretraining does not translate to ultrasound performance. (ii) Well-tuned methods from computer vision are making it feasible to train custom foundation models for a given medical domain, requiring no hyperparameter tuning and little methodological adaptation. Given these findings, we argue that a bias towards methodological innovation should be avoided when developing domain specific foundation models under common computational resource constraints.

Changlu Guo, Anders Nymark Christensen, Morten Rieger Hannemose

Text-to-image generative models have achieved remarkable breakthroughs in recent years. However, their application in medical image generation still faces significant challenges, including small dataset sizes, and scarcity of medical textual data. To address these challenges, we propose Med-Art, a framework specifically designed for medical image generation with limited data. Med-Art leverages vision-language models to generate visual descriptions of medical images which overcomes the scarcity of applicable medical textual data. Med-Art adapts a large-scale pre-trained text-to-image model, PixArt-$α$, based on the Diffusion Transformer (DiT), achieving high performance under limited data. Furthermore, we propose an innovative Hybrid-Level Diffusion Fine-tuning (HLDF) method, which enables pixel-level losses, effectively addressing issues such as overly saturated colors. We achieve state-of-the-art performance on two medical image datasets, measured by FID, KID, and downstream classification performance.

Chun Kit Wong, Mary Ngo, Manxi Lin et al.

Despite the rapid development of AI models in medical image analysis, their validation in real-world clinical settings remains limited. To address this, we introduce a generic framework designed for deploying image-based AI models in such settings. Using this framework, we deployed a trained model for fetal ultrasound standard plane detection, and evaluated it in real-time sessions with both novice and expert users. Feedback from these sessions revealed that while the model offers potential benefits to medical practitioners, the need for navigational guidance was identified as a key area for improvement. These findings underscore the importance of early deployment of AI models in real-world settings, leading to insights that can guide the refinement of the model and system based on actual user feedback.

Changlu Guo, Anders Nymark Christensen, Anders Bjorholm Dahl et al.

Visual counterfactual explanations aim to reveal the minimal semantic modifications that can alter a model's prediction, providing causal and interpretable insights into deep neural networks. However, existing diffusion-based counterfactual generation methods are often computationally expensive, slow to sample, and imprecise in localizing the modified regions. To address these limitations, we propose MaskDiME, a simple, fast, and effective diffusion framework that unifies semantic consistency and spatial precision through localized sampling. Our approach adaptively focuses on decision-relevant regions to achieve localized and semantically consistent counterfactual generation while preserving high image fidelity. Our training-free framework, MaskDiME, achieves over 30x faster inference than the baseline method and achieves comparable or state-of-the-art performance across five benchmark datasets spanning diverse visual domains, establishing a practical and generalizable solution for efficient counterfactual explanation.

Chun Kit Wong, Paraskevas Pegios, Nina Weng et al.

Deep learning models in medical imaging are susceptible to shortcut learning, relying on confounding metadata (e.g., scanner model) that is often encoded in image embeddings. The crucial question is whether the model actively utilizes this encoded information for its final prediction. We introduce Weight Space Correlation Analysis, an interpretable methodology that quantifies feature utilization by measuring the alignment between the classification heads of a primary clinical task and auxiliary metadata tasks. We first validate our method by successfully detecting artificially induced shortcut learning. We then apply it to probe the feature utilization of an SA-SonoNet model trained for Spontaneous Preterm Birth (sPTB) prediction. Our analysis confirmed that while the embeddings contain substantial metadata, the sPTB classifier's weight vectors were highly correlated with clinically relevant factors (e.g., birth weight) but decoupled from clinically irrelevant acquisition factors (e.g. scanner). Our methodology provides a tool to verify model trustworthiness, demonstrating that, in the absence of induced bias, the clinical model selectively utilizes features related to the genuine clinical signal.

Changlu Guo, Anders Nymark Christensen, Anders Bjorholm Dahl et al.

Retinal vessel segmentation is essential for early diagnosis of diseases such as diabetic retinopathy, hypertension, and neurodegenerative disorders. Although SA-UNet introduces spatial attention in the bottleneck, it underuses attention in skip connections and does not address the severe foreground-background imbalance. We propose SA-UNetv2, a lightweight model that injects cross-scale spatial attention into all skip connections to strengthen multi-scale feature fusion and adopts a weighted Binary Cross-Entropy (BCE) plus Matthews Correlation Coefficient (MCC) loss to improve robustness to class imbalance. On the public DRIVE and STARE datasets, SA-UNetv2 achieves state-of-the-art performance with only 1.2MB memory and 0.26M parameters (less than 50% of SA-UNet), and 1 second CPU inference on 592 x 592 x 3 images, demonstrating strong efficiency and deployability in resource-constrained, CPU-only settings.

Jakub Maciej Wiśniewski, Anders Nymark Christensen, Mary Le Ngo et al.

Cognitive demands of fetal ultrasound examinations pose unique challenges among clinicians. With the goal of providing an assistive tool, we developed an automated pipeline for predicting fetal orientation from ultrasound videos acquired following a simple blind sweep protocol. Leveraging on a pre-trained head detection and segmentation model, this is achieved by first determining the fetal presentation (cephalic or breech) with a template matching approach, followed by the fetal lie (facing left or right) by analyzing the spatial distribution of segmented brain anatomies. Evaluation on a dataset of third-trimester ultrasound scans demonstrated the promising accuracy of our pipeline. This work distinguishes itself by introducing automated fetal lie prediction and by proposing an assistive paradigm that augments sonographer expertise rather than replacing it. Future research will focus on enhancing acquisition efficiency, and exploring real-time clinical integration to improve workflow and support for obstetric clinicians.

Pawel Tomasz Pieta, Peter Winkel Rasumssen, Anders Bjorholm Dahl et al.

Sphericity and roundness are fundamental measures used for assessing object uniformity in 2D and 3D images. However, using their strict definition makes computation costly. As both 2D and 3D microscopy imaging datasets grow larger, there is an increased demand for efficient algorithms that can quantify multiple objects in large volumes. We propose a novel approach for extracting sphericity and roundness based on the output of a local thickness algorithm. For sphericity, we simplify the surface area computation by modeling objects as spheroids/ellipses of varying lengths and widths of mean local thickness. For roundness, we avoid a complex corner curvature determination process by approximating it with local thickness values on the contour/surface of the object. The resulting methods provide an accurate representation of the exact measures while being significantly faster than their existing implementations.

Pawel Tomasz Pieta, Peter Winkel Rasmussen, Anders Bjorholm Dahl et al.

Influenced by the complexity of volumetric imaging, there is a shortage of established datasets useful for benchmarking volumetric deep-learning models. As a consequence, new and existing models are not easily comparable, limiting the development of architectures optimized specifically for volumetric data. To counteract this trend, we introduce MozzaVID - a large, clean, and versatile volumetric classification dataset. Our dataset contains X-ray computed tomography (CT) images of mozzarella microstructure and enables the classification of 25 cheese types and 149 cheese samples. We provide data in three different resolutions, resulting in three dataset instances containing from 591 to 37,824 images. While being general-purpose, the dataset also facilitates investigating mozzarella structure properties. The structure of food directly affects its functional properties and thus its consumption experience. Understanding food structure helps tune the production and mimicking it enables sustainable alternatives to animal-derived food products. The complex and disordered nature of food structures brings a unique challenge, where a choice of appropriate imaging method, scale, and sample size is not trivial. With this dataset we aim to address these complexities, contributing to more robust structural analysis models. The dataset can be downloaded from: https://archive.compute.dtu.dk/files/public/projects/MozzaVID/.

Josefine Vilsbøll Sundgaard, Morten Rieger Hannemose, Søren Laugesen et al.

We present a deep metric variational autoencoder for multi-modal data generation. The variational autoencoder employs triplet loss in the latent space, which allows for conditional data generation by sampling in the latent space within each class cluster. The approach is evaluated on a multi-modal dataset consisting of otoscopy images of the tympanic membrane with corresponding wideband tympanometry measurements. The modalities in this dataset are correlated, as they represent different aspects of the state of the middle ear, but they do not present a direct pixel-to-pixel correlation. The approach shows promising results for the conditional generation of pairs of images and tympanograms, and will allow for efficient data augmentation of data from multi-modal sources.

Jesper Sören Dramsch, Mikael Lüthje, Anders Nymark Christensen

Deep learning has become an area of interest in most scientific areas, including physical sciences. Modern networks apply real-valued transformations on the data. Particularly, convolutions in convolutional neural networks discard phase information entirely. Many deterministic signals, such as seismic data or electrical signals, contain significant information in the phase of the signal. We explore complex-valued deep convolutional networks to leverage non-linear feature maps. Seismic data commonly has a lowcut filter applied, to attenuate noise from ocean waves and similar long wavelength contributions. Discarding the phase information leads to low-frequency aliasing analogous to the Nyquist-Shannon theorem for high frequencies. In non-stationary data, the phase content can stabilize training and improve the generalizability of neural networks. While it has been shown that phase content can be restored in deep neural networks, we show how including phase information in feature maps improves both training and inference from deterministic physical data. Furthermore, we show that the reduction of parameters in a complex network outperforms larger real-valued networks.