arXiv subjects

Jens Petersen

Publications and source records attributed to Jens Petersen.

At least 19 recordsLinked to original sources

arXiv2025

rNCA: Self-Repairing Segmentation Masks

Accurately predicting topologically correct masks remains a difficult task for general segmentation models, which often produce fragmented or disconnected outputs. Fixing these artifacts typically requires hand-crafted refinement rules or architectures specialized to a particular task. Here, we show that Neural Cellular Automata (NCA) can be directly re-purposed as an effective refinement mechanism, using local, iterative updates guided by image context to repair segmentation masks. By training on imperfect masks and ground truths, the automaton learns the structural properties of the target shape while relying solely on local information. When applied to coarse, globally predicted masks, the learned dynamics progressively reconnect broken regions, prune loose fragments and converge towards stable, topologically consistent results. We show how refinement NCA (rNCA) can be easily applied to repair common topological errors produced by different base segmentation models and tasks: for fragmented retinal vessels, it yields 2-3% gains in Dice/clDice and improves Betti errors, reducing $β_0$ errors by 60% and $β_1$ by 20%; for myocardium, it repairs 61.5% of broken cases in a zero-shot setting while lowering ASSD and HD by 19% and 16%, respectively. This showcases NCA as effective and broadly applicable refiners.

cs.CV↗

arXiv2025

Hybrid Gaussian Splatting for Novel Urban View Synthesis

This paper describes the Qualcomm AI Research solution to the RealADSim-NVS challenge, hosted at the RealADSim Workshop at ICCV 2025. The challenge concerns novel view synthesis in street scenes, and participants are required to generate, starting from car-centric frames captured during some training traversals, renders of the same urban environment as viewed from a different traversal (e.g. different street lane or car direction). Our solution is inspired by hybrid methods in scene generation and generative simulators merging gaussian splatting and diffusion models, and it is composed of two stages: First, we fit a 3D reconstruction of the scene and render novel views as seen from the target cameras. Then, we enhance the resulting frames with a dedicated single-step diffusion model. We discuss specific choices made in the initialization of gaussian primitives as well as the finetuning of the enhancer model and its training data curation. We report the performance of our model design and we ablate its components in terms of novel view quality as measured by PSNR, SSIM and LPIPS. On the public leaderboard reporting test results, our proposal reaches an aggregated score of 0.432, achieving the second place overall.

cs.CV↗

arXiv2025

Comparative Analysis of GAN and Diffusion for MRI-to-CT translation

Computed tomography (CT) is essential for treatment and diagnostics; In case CT are missing or otherwise difficult to obtain, methods for generating synthetic CT (sCT) images from magnetic resonance imaging (MRI) images are sought after. Therefore, it is valuable to establish a reference for what strategies are most effective for MRI-to-CT translation. In this paper, we compare the performance of two frequently used architectures for MRI-to-CT translation: a conditional generative adversarial network (cGAN) and a conditional denoising diffusion probabilistic model (cDDPM). We chose well-established implementations to represent each architecture: Pix2Pix for cGAN, and Palette for cDDPM. We separate the classical 3D translation problem into a sequence of 2D translations on the transverse plane, to investigate the viability of a strategy that reduces the computational cost. We also investigate the impact of conditioning the generative process on a single MRI image/slice and on multiple MRI slices. The performance is assessed using a thorough evaluation protocol, including a novel slice-wise metric Similarity Of Slices (SIMOS), which measures the continuity between transverse slices when compiling the sCTs into 3D format. Our comparative analysis revealed that MRI-to-CT generative models benefit from multi-channel conditional input and using cDDPM as an architecture.

eess.IV↗

arXiv2025

Interpretable Artificial Intelligence for Detecting Acute Heart Failure on Acute Chest CT Scans

Introduction: Chest CT scans are increasingly used in dyspneic patients where acute heart failure (AHF) is a key differential diagnosis. Interpretation remains challenging and radiology reports are frequently delayed due to a radiologist shortage, although flagging such information for emergency physicians would have therapeutic implication. Artificial intelligence (AI) can be a complementary tool to enhance the diagnostic precision. We aim to develop an explainable AI model to detect radiological signs of AHF in chest CT with an accuracy comparable to thoracic radiologists. Methods: A single-center, retrospective study during 2016-2021 at Copenhagen University Hospital - Bispebjerg and Frederiksberg, Denmark. A Boosted Trees model was trained to predict AHF based on measurements of segmented cardiac and pulmonary structures from acute thoracic CT scans. Diagnostic labels for training and testing were extracted from radiology reports. Structures were segmented with TotalSegmentator. Shapley Additive explanations values were used to explain the impact of each measurement on the final prediction. Results: Of the 4,672 subjects, 49% were female. The final model incorporated twelve key features of AHF and achieved an area under the ROC of 0.87 on the independent test set. Expert radiologist review of model misclassifications found that 24 out of 64 (38%) false positives and 24 out of 61 (39%) false negatives were actually correct model predictions, with the errors originating from inaccuracies in the initial radiology reports. Conclusion: We developed an explainable AI model with strong discriminatory performance, comparable to thoracic radiologists. The AI model's stepwise, transparent predictions may support decision-making.

eess.IV↗

arXiv2025

Controllable 3D Placement of Objects with Scene-Aware Diffusion Models

Image editing approaches have become more powerful and flexible with the advent of powerful text-conditioned generative models. However, placing objects in an environment with a precise location and orientation still remains a challenge, as this typically requires carefully crafted inpainting masks or prompts. In this work, we show that a carefully designed visual map, combined with coarse object masks, is sufficient for high quality object placement. We design a conditioning signal that resolves ambiguities, while being flexible enough to allow for changing of shapes or object orientations. By building on an inpainting model, we leave the background intact by design, in contrast to methods that model objects and background jointly. We demonstrate the effectiveness of our method in the automotive setting, where we compare different conditioning signals in novel object placement tasks. These tasks are designed to measure edit quality not only in terms of appearance, but also in terms of pose and location accuracy, including cases that require non-trivial shape changes. Lastly, we show that fine location control can be combined with appearance control to place existing objects in precise locations in a scene.

cs.CV↗

arXiv2025

Gaussian Splatting is an Effective Data Generator for 3D Object Detection

We investigate data augmentation for 3D object detection in autonomous driving. We utilize recent advancements in 3D reconstruction based on Gaussian Splatting for 3D object placement in driving scenes. Unlike existing diffusion-based methods that synthesize images conditioned on BEV layouts, our approach places 3D objects directly in the reconstructed 3D space with explicitly imposed geometric transformations. This ensures both the physical plausibility of object placement and highly accurate 3D pose and position annotations. Our experiments demonstrate that even by integrating a limited number of external 3D objects into real scenes, the augmented data significantly enhances 3D object detection performance and outperforms existing diffusion-based 3D augmentation for object detection. Extensive testing on the nuScenes dataset reveals that imposing high geometric diversity in object placement has a greater impact compared to the appearance diversity of objects. Additionally, we show that generating hard examples, either by maximizing detection loss or imposing high visual occlusion in camera images, does not lead to more efficient 3D data augmentation for camera-based 3D object detection in autonomous driving.

cs.CV↗

arXiv2025

Scene-Aware Location Modeling for Data Augmentation in Automotive Object Detection

Generative image models are increasingly being used for training data augmentation in vision tasks. In the context of automotive object detection, methods usually focus on producing augmented frames that look as realistic as possible, for example by replacing real objects with generated ones. Others try to maximize the diversity of augmented frames, for example by pasting lots of generated objects onto existing backgrounds. Both perspectives pay little attention to the locations of objects in the scene. Frame layouts are either reused with little or no modification, or they are random and disregard realism entirely. In this work, we argue that optimal data augmentation should also include realistic augmentation of layouts. We introduce a scene-aware probabilistic location model that predicts where new objects can realistically be placed in an existing scene. By then inpainting objects in these locations with a generative model, we obtain much stronger augmentation performance than existing approaches. We set a new state of the art for generative data augmentation on two automotive object detection tasks, achieving up to $2.8\times$ higher gains than the best competing approach ($+1.4$ vs. $+0.5$ mAP boost). We also demonstrate significant improvements for instance segmentation.

cs.CV↗

arXiv2025

HQColon: A Hybrid Interactive Machine Learning Pipeline for High Quality Colon Labeling and Segmentation

High-resolution colon segmentation is crucial for clinical and research applications, such as digital twins and personalized medicine. However, the leading open-source abdominal segmentation tool, TotalSegmentator, struggles with accuracy for the colon, which has a complex and variable shape, requiring time-intensive labeling. Here, we present the first fully automatic high-resolution colon segmentation method. To develop it, we first created a high resolution colon dataset using a pipeline that combines region growing with interactive machine learning to efficiently and accurately label the colon on CT colonography (CTC) images. Based on the generated dataset consisting of 435 labeled CTC images we trained an nnU-Net model for fully automatic colon segmentation. Our fully automatic model achieved an average symmetric surface distance of 0.2 mm (vs. 4.0 mm from TotalSegmentator) and a 95th percentile Hausdorff distance of 1.0 mm (vs. 18 mm from TotalSegmentator). Our segmentation accuracy substantially surpasses TotalSegmentator. We share our trained model and pipeline code, providing the first and only open-source tool for high-resolution colon segmentation. Additionally, we created a large-scale dataset of publicly available high-resolution colon labels.

cs.CV↗

arXiv2024

Enhancing predictive imaging biomarker discovery through treatment effect analysis

Identifying predictive covariates, which forecast individual treatment effectiveness, is crucial for decision-making across different disciplines such as personalized medicine. These covariates, referred to as biomarkers, are extracted from pre-treatment data, often within randomized controlled trials, and should be distinguished from prognostic biomarkers, which are independent of treatment assignment. Our study focuses on discovering predictive imaging biomarkers, specific image features, by leveraging pre-treatment images to uncover new causal relationships. Unlike labor-intensive approaches relying on handcrafted features prone to bias, we present a novel task of directly learning predictive features from images. We propose an evaluation protocol to assess a model's ability to identify predictive imaging biomarkers and differentiate them from purely prognostic ones by employing statistical testing and a comprehensive analysis of image feature attribution. We explore the suitability of deep learning models originally developed for estimating the conditional average treatment effect (CATE) for this task, which have been assessed primarily for their precision of CATE estimation while overlooking the evaluation of imaging biomarker discovery. Our proof-of-concept analysis demonstrates the feasibility and potential of our approach in discovering and validating predictive imaging biomarkers from synthetic outcomes and real-world image datasets. Our code is available at \url{https://github.com/MIC-DKFZ/predictive_image_biomarker_analysis}.

eess.IV↗

arXiv2024

MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation

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.

eess.IV↗

arXiv2024

Understanding metric-related pitfalls in image analysis validation

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.

cs.CV↗

arXiv2024

Metrics reloaded: Recommendations for image analysis validation

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.

cs.CV↗

arXiv2024

Clockwork Diffusion: Efficient Generation With Model-Step Distillation

This work aims to improve the efficiency of text-to-image diffusion models. While diffusion models use computationally expensive UNet-based denoising operations in every generation step, we identify that not all operations are equally relevant for the final output quality. In particular, we observe that UNet layers operating on high-res feature maps are relatively sensitive to small perturbations. In contrast, low-res feature maps influence the semantic layout of the final image and can often be perturbed with no noticeable change in the output. Based on this observation, we propose Clockwork Diffusion, a method that periodically reuses computation from preceding denoising steps to approximate low-res feature maps at one or more subsequent steps. For multiple baselines, and for both text-to-image generation and image editing, we demonstrate that Clockwork leads to comparable or improved perceptual scores with drastically reduced computational complexity. As an example, for Stable Diffusion v1.5 with 8 DPM++ steps we save 32% of FLOPs with negligible FID and CLIP change.

cs.CV↗

arXiv2023

Common Limitations of Image Processing Metrics: A Picture Story

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.

eess.IV↗

arXiv2023

Prediction of post-radiotherapy recurrence volumes in head and neck squamous cell carcinoma using 3D U-Net segmentation

Locoregional recurrences (LRR) are still a frequent site of treatment failure for head and neck squamous cell carcinoma (HNSCC) patients. Identification of high risk subvolumes based on pretreatment imaging is key to biologically targeted radiation therapy. We investigated the extent to which a Convolutional neural network (CNN) is able to predict LRR volumes based on pre-treatment 18F-fluorodeoxyglucose positron emission tomography (FDG-PET)/computed tomography (CT) scans in HNSCC patients and thus the potential to identify biological high risk volumes using CNNs. For 37 patients who had undergone primary radiotherapy for oropharyngeal squamous cell carcinoma, five oncologists contoured the relapse volumes on recurrence CT scans. Datasets of pre-treatment FDG-PET/CT, gross tumour volume (GTV) and contoured relapse for each of the patients were randomly divided into training (n=23), validation (n=7) and test (n=7) datasets. We compared a CNN trained from scratch, a pre-trained CNN, a SUVmax threshold approach, and using the GTV directly. The SUVmax threshold method included 5 out of the 7 relapse origin points within a volume of median 4.6 cubic centimetres (cc). Both the GTV contour and best CNN segmentations included the relapse origin 6 out of 7 times with median volumes of 28 and 18 cc respectively. The CNN included the same or greater number of relapse volume POs, with significantly smaller relapse volumes. Our novel findings indicate that CNNs may predict LRR, yet further work on dataset development is required to attain clinically useful prediction accuracy.

eess.IV↗

arXiv2023

HORTENSIA, a program package for the simulation of nonadiabatic autoionization dynamics in molecules

We present a program package for the simulation of ultrafast vibration-induced autoionization dynamics in molecular anions in the manifold of the adiabatic anionic states and the discretized ionization continuum. This program, called HORTENSIA ($\underline{Ho}$pping $\underline{r}$eal-time $\underline{t}$rajectories for $\underline{e}$lectron-ejection by $\underline{n}$onadiabatic $\underline{s}$elf-$\underline{i}$onization in $\underline{a}$nions), is based on the nonadiabatic surface-hopping methodology, wherein nuclei are propagated as an ensemble along classical trajectories in the quantum-mechanical potential created by the electronic density of the molecular system. The electronic Schrödinger equation is numerically integrated along the trajectory, providing the time evolution of electronic state coefficients, from which switching probabilities into discrete electronic states are determined. In the case of a discretized continuum state, this hopping event is interpreted as the ejection on an electron. The derived diabatic and nonadiabatic couplings in the time-dependent electronic Schrödinger equation are calculated from anionic and neutral wavefunctions obtained from quantum chemical calculations with commercially available program packages interfaced with our program. Based on this methodology, we demonstrate the simulation of autoionization electron kinetic energy spectra that are both time- and angle-resolved. In addition, the program yields data that can be interpreted easily with respect to geometric characteristics such as bonding distances and angles, which facilitates the detection of molecular configurations important for the autoionization process. Moreover, useful extensions are included, namely generation tools for initial conditions and input files as well as for the evaluation of output files both through console commands and a graphical user interface.

physics.chem-ph↗

arXiv2023

Localise to segment: crop to improve organ at risk segmentation accuracy

Increased organ at risk segmentation accuracy is required to reduce cost and complications for patients receiving radiotherapy treatment. Some deep learning methods for the segmentation of organs at risk use a two stage process where a localisation network first crops an image to the relevant region and then a locally specialised network segments the cropped organ of interest. We investigate the accuracy improvements brought about by such a localisation stage by comparing to a single-stage baseline network trained on full resolution images. We find that localisation approaches can improve both training time and stability and a two stage process involving both a localisation and organ segmentation network provides a significant increase in segmentation accuracy for the spleen, pancreas and heart from the Medical Segmentation Decathlon dataset. We also observe increased benefits of localisation for smaller organs. Source code that recreates the main results is available at \href{https://github.com/Abe404/localise_to_segment}{this https URL}.

eess.IV↗

arXiv2023

Transformer Utilization in Medical Image Segmentation Networks

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.

cs.CV↗