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Item type:Publication, Access status: with files , Robust motion tracking and classification of zebrafish with deep learning(IEEE, 2026-09-01); ; ; ; Zebrafish serve as a key pre-clinical model for disease research. Studying disease progression requires long-term tracking of fish motion, particularly when considering the function of the musculoskeletal apparatus. While vision-based tracking has been studied, current approaches typically require substantial fine tuning and often lack robustness, especially when multiple fish need to be tracked and motion occurs along all three spatial dimensions. We propose a simplified setup and a 3D tracking method using only two cameras and two convolutional neural networks (CNN) to localize and track multiple fish robustly. We separate the localization of fish and their classification as an individual. This allows for simple training data acquisition by placing fish into the basin individually, without the need for manual annotation. We evaluate the approach on sets of two, five, and ten fish resulting in multiple object tracking accuracies (MOTA) of 0.997, 0.994, and 0.966, respectively. The mean MOTA over all scenarios is 0.99 compared to a mean MOTA of 0.89 for a state-of-the-art tracking algorithm (idtracker.ai). Finally, we present comprehensive data on the motion activity of individual fish in a 30-minute video sequence, demonstrating robust tracking and unique activity profiles of each fish.Publicationtype: Journal Article20 8 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , A review of deep learning-based unsupervised anomaly detection in brain MRI(Elsevier, 2026-07-01); ; ; ; The manual assessment of brain Magnetic Resonance Imaging (MRI) scans can be labor-intensive and time-consuming for radiologists. Deep Learning methods have demonstrated the potential to aid this process. However, their effectiveness relies on the availability of large, annotated data sets. Unsupervised Anomaly Detection (UAD) presents a promising alternative, offering the potential to identify and localize anomalies without per-pixel annotations. Instead, a normative distribution is learned using healthy data, enabling the identification of abnormalities as deviations. This allows UAD methods to detect abnormalities that were unseen during training. This appealing feature has led to numerous studies proposing innovations and novel approaches. In this work, we provide a review of the literature and systematically collect and compare the proposed approaches. We observe that UAD has made significant advancements in brain MRI analysis. However, individual approaches are often evaluated in different contexts, i.e., changes in acquisition parameters, pre- and post-processing, and anomaly scoring. This variability makes it challenging to assess which models perform best, underscoring the need for comprehensive comparative studies concerning the specific context of MRI scans. Our collection, featuring public data sets, research studies, and open implementations, is available at our GitHub repository https://github.com/FinnBehrendt/Unsupervised-Anomaly-Detection-in-Brain-MRI .Publicationtype: Review Article11 25 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Guided reconstruction with conditioned diffusion models for unsupervised anomaly detection in brain MRIs(2025-01-22); ; ; ; The application of supervised models to clinical screening tasks is challenging due to the need for annotated data for each considered pathology. Unsupervised Anomaly Detection (UAD) is an alternative approach that aims to identify any anomaly as an outlier from a healthy training distribution. A prevalent strategy for UAD in brain MRI involves using generative models to learn the reconstruction of healthy brain anatomy for a given input image. As these models should fail to reconstruct unhealthy structures, the reconstruction errors indicate anomalies. However, a significant challenge is to balance the accurate reconstruction of healthy anatomy and the undesired replication of abnormal structures. While diffusion models have shown promising results with detailed and accurate reconstructions, they face challenges in preserving intensity characteristics, resulting in false positives. We propose conditioning the denoising process of diffusion models with additional information derived from a latent representation of the input image. We demonstrate that this conditioning allows for accurate and local adaptation to the general input intensity distribution while avoiding the replication of unhealthy structures. We compare the novel approach to different state-of-the-art methods and for different data sets. Our results show substantial improvements in the segmentation performance, with the Dice score improved by 11.9%, 20.0%, and 44.6%, for the BraTS, ATLAS and MSLUB data sets, respectively, while maintaining competitive performance on the WMH data set. Furthermore, our results indicate effective domain adaptation across different MRI acquisitions and simulated contrasts, an important attribute for general anomaly detection methods. The code for our work is available at https://github.com/FinnBehrendt/Conditioned-Diffusion-Models-UAD.Publicationtype: Journal Article39 40 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Deep learning for paranasal anomaly classificationThe susceptibility of the paranasal sinuses to allergic and non-allergic infections complicates diagnosis as symptoms vary from mucosal thickening to polypoid masses. Previous manual analysis is resource intensive and leads to clinician fatigue. Computer-aided diagnosis (CAD) can optimize this process. While deep learning has made great strides in medical image analysis, the study of paranasal abnormalities has remained limited. This work proposes different deep learning approaches to classify maxillary sinus opacities, including unsupervised learning, self-supervised learning, and hybrid architectures of CNNs and transformers.Publicationtype: Doctoral Thesis45 84 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Automatic Segmentation of Vestibular Schwannoma From MRI Using Two Cascaded Deep Learning Networks(Wiley, 2025); ; ; Objective: Automatic segmentation and detection of vestibular schwannoma (VS) in MRI by deep learning is an upcoming topic. However, deep learning faces generalization challenges due to tumor variability even though measurements and segmentation of VS are essential for growth monitoring and treatment planning. Therefore, we introduce a novel model combining two Convolutional Neural Network (CNN) models for the detection of VS by deep learning aiming to improve performance of automatic segmentation. Methods: Deep learning techniques have been employed for automatic VS tumor segmentation, including 2D, 2.5D, and 3D UNet-like architectures, which is a specific CNN designed to improve automatic segmentation for medical imaging. Specifically, we introduce a sequential connection where the first UNet's predicted segmentation map is passed to a second complementary network for refinement. Additionally, spatial attention mechanisms are utilized to further guide refinement in the second network. Results: We conducted experiments on both public and private datasets containing contrast-enhanced T1 and high-resolution T2-weighted magnetic resonance imaging (MRI). Across the public dataset, we observed consistent improvements in Dice scores for all variants of 2D, 2.5D, and 3D CNN methods, with a notable enhancement of 8.86% for the 2D UNet variant on T1. In our private dataset, a 3.75% improvement was reported for 2D T1. Moreover, we found that T1 images generally outperformed T2 in VS segmentation. Conclusion: We demonstrate that sequential connection of UNets combined with spatial attention mechanisms enhances VS segmentation performance across state-of-the-art 2D, 2.5D, and 3D deep learning methods. Level of Evidence: 3 Laryngoscope, 2024.Publicationtype: Journal Article16 43 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Validating polyp and instrument segmentation methods in colonoscopy through Medico 2020 and MedAI 2021 Challenges(Elsevier, 2025-01); ; ; ; Roy, KaushikiAutomatic analysis of colonoscopy images has been an active field of research motivated by the importance of early detection of precancerous polyps. However, detecting polyps during the live examination can be challenging due to various factors such as variation of skills and experience among the endoscopists, lack of attentiveness, and fatigue leading to a high polyp miss-rate. Therefore, there is a need for an automated system that can flag missed polyps during the examination and improve patient care. Deep learning has emerged as a promising solution to this challenge as it can assist endoscopists in detecting and classifying overlooked polyps and abnormalities in real time, improving the accuracy of diagnosis and enhancing treatment. In addition to the algorithm's accuracy, transparency and interpretability are crucial to explaining the whys and hows of the algorithm's prediction. Further, conclusions based on incorrect decisions may be fatal, especially in medicine. Despite these pitfalls, most algorithms are developed in private data, closed source, or proprietary software, and methods lack reproducibility. Therefore, to promote the development of efficient and transparent methods, we have organized the “Medico automatic polyp segmentation (Medico 2020)” and “MedAI: Transparency in Medical Image Segmentation (MedAI 2021)” competitions. The Medico 2020 challenge received submissions from 17 teams, while the MedAI 2021 challenge also gathered submissions from another 17 distinct teams in the following year. We present a comprehensive summary and analyze each contribution, highlight the strength of the best-performing methods, and discuss the possibility of clinical translations of such methods into the clinic. Our analysis revealed that the participants improved dice coefficient metrics from 0.8607 in 2020 to 0.8993 in 2021 despite adding diverse and challenging frames (containing irregular, smaller, sessile, or flat polyps), which are frequently missed during a routine clinical examination. For the instrument segmentation task, the best team obtained a mean Intersection over union metric of 0.9364. For the transparency task, a multi-disciplinary team, including expert gastroenterologists, accessed each submission and evaluated the team based on open-source practices, failure case analysis, ablation studies, usability and understandability of evaluations to gain a deeper understanding of the models’ credibility for clinical deployment. The best team obtained a final transparency score of 21 out of 25. Through the comprehensive analysis of the challenge, we not only highlight the advancements in polyp and surgical instrument segmentation but also encourage subjective evaluation for building more transparent and understandable AI-based colonoscopy systems. Moreover, we discuss the need for multi-center and out-of-distribution testing to address the current limitations of the methods to reduce the cancer burden and improve patient care.Publicationtype: Journal Article20 21 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Computer-aided diagnosis of maxillary sinus anomalies : validation and clinical correlation(Wiley, 2024-09); ; ; ; Objective: Computer aided diagnostics (CAD) systems can automate the differentiation of maxillary sinus (MS) with and without opacification, simplifying the typically laborious process and aiding in clinical insight discovery within large cohorts. Methods: This study uses Hamburg City Health Study (HCHS) a large, prospective, long-term, population-based cohort study of participants between 45 and 74 years of age. We develop a CAD system using an ensemble of 3D Convolutional Neural Network (CNN) to analyze cranial MRIs, distinguishing MS with opacifications (polyps, cysts, mucosal thickening) from MS without opacifications. The system is used to find correlations of participants with and without MS opacifications with clinical data (smoking, alcohol, BMI, asthma, bronchitis, sex, age, leukocyte count, C-reactive protein, allergies). Results: The evaluation metrics of CAD system (Area Under Receiver Operator Characteristic: 0.95, sensitivity: 0.85, specificity: 0.90) demonstrated the effectiveness of our approach. MS with opacification group exhibited higher alcohol consumption, higher BMI, higher incidence of intrinsic asthma and extrinsic asthma. Male sex had higher prevalence of MS opacifications. Participants with MS opacifications had higher incidence of hay fever and house dust allergy but lower incidence of bee/wasp venom allergy. Conclusion: The study demonstrates a 3D CNN's ability to distinguish MS with and without opacifications, improving automated diagnosis and aiding in correlating clinical data in population studies. Level of Evidence: 3 Laryngoscope, 134:3927–3934, 2024.Publicationtype: Journal Article20 63 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , PolypNextLSTM: a lightweight and fast polyp video segmentation network using ConvNext and ConvLSTM(Springer, 2024-08-08); ; ; ; Purpose: Commonly employed in polyp segmentation, single-image UNet architectures lack the temporal insight clinicians gain from video data in diagnosing polyps. To mirror clinical practices more faithfully, our proposed solution, PolypNextLSTM, leverages video-based deep learning, harnessing temporal information for superior segmentation performance with least parameter overhead, making it possibly suitable for edge devices. Methods: PolypNextLSTM employs a UNet-like structure with ConvNext-Tiny as its backbone, strategically omitting the last two layers to reduce parameter overhead. Our temporal fusion module, a Convolutional Long Short Term Memory (ConvLSTM), effectively exploits temporal features. Our primary novelty lies in PolypNextLSTM, which stands out as the leanest in parameters and the fastest model, surpassing the performance of five state-of-the-art image and video-based deep learning models. The evaluation of the SUN-SEG dataset spans easy-to-detect and hard-to-detect polyp scenarios, along with videos containing challenging artefacts like fast motion and occlusion. Results: Comparison against 5 image-based and 5 video-based models demonstrates PolypNextLSTM’s superiority, achieving a Dice score of 0.7898 on the hard-to-detect polyp test set, surpassing image-based PraNet (0.7519) and video-based PNS+ (0.7486). Notably, our model excels in videos featuring complex artefacts such as ghosting and occlusion. Conclusion: PolypNextLSTM, integrating pruned ConvNext-Tiny with ConvLSTM for temporal fusion, not only exhibits superior segmentation performance but also maintains the highest frames per speed among evaluated models. Code can be found here: https://github.com/mtec-tuhh/PolypNextLSTM.Publicationtype: Journal Article19 21 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , TransRUPNet for Improved Polyp Segmentation(IEEE, 2024-07); ; 6 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Combining Reconstruction-based Unsupervised Anomaly Detection with Supervised Segmentation for Brain MRIsIn contrast to supervised deep learning approaches, unsupervised anomaly detection (UAD) methods can be trained with healthy data only and do not require pixel-level annotations, enabling the identification of unseen pathologies. While this is promising for clinical screening tasks, reconstruction-based UAD methods fall short in segmentation accuracy compared to supervised models. Therefore, self-supervised UAD approaches have been proposed to improve segmentation accuracy. Typically, synthetic anomalies are used to train a segmentation network in a supervised fashion. However, this approach does not effectively generalize to real pathologies. We propose a framework combining reconstruction-based and self-supervised UAD methods to improve both segmentation performance for known anomalies and generalization to unknown pathologies. The framework includes an unsupervised diffusion model trained on healthy data to produce pseudo-healthy reconstructions and a supervised Unet trained to delineate anomalies from deviations between input- reconstruction pairs. Besides the effective use of synthetic training data, this framework allows for weakly-supervised training with small annotated data sets, generalizing to unseen pathologies. Our results show that with our approach, utilizing annotated data sets during training can substantially improve the segmentation performance for in-domain data while maintaining the generalizability of reconstruction-based approaches to pathologies unseen during trainingPublicationtype: Conference Paper30 26