Mattias Heinrich

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al. · utoronto

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al.

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Ron Keuth, Mattias Heinrich, Martin Eichenlaub et al.

Purpose: Navigation guidance is a key requirement for a multitude of lung interventions using video bronchoscopy. State-of-the-art solutions focus on lung biopsies using electromagnetic tracking and intraoperative image registration w.r.t. preoperative CT scans for guidance. The requirement of patient-specific CT scans hampers the utilisation of navigation guidance for other applications such as intensive care units. Methods: This paper addresses navigation guidance solely incorporating bronchosopy video data. In contrast to state-of-the-art approaches we entirely omit the use of electromagnetic tracking and patient-specific CT scans. Guidance is enabled by means of topological bronchoscope localization w.r.t. an interpatient airway model. Particularly, we take maximally advantage of anatomical constraints of airway trees being sequentially traversed. This is realized by incorporating sequences of CNN-based airway likelihoods into a Hidden Markov Model. Results: Our approach is evaluated based on multiple experiments inside a lung phantom model. With the consideration of temporal context and use of anatomical knowledge for regularization, we are able to improve the accuracy up to to 0.98 compared to 0.81 (weighted F1: 0.98 compared to 0.81) for a classification based on individual frames. Conclusion: We combine CNN-based single image classification of airway segments with anatomical constraints and temporal HMM-based inference for the first time. Our approach renders vision-only guidance for bronchoscopy interventions in the absence of electromagnetic tracking and patient-specific CT scans possible.

Ron Keuth, Mattias Heinrich, Martin Eichenlaub et al.

Video bronchoscopy is routinely conducted for biopsies of lung tissue suspected for cancer, monitoring of COPD patients and clarification of acute respiratory problems at intensive care units. The navigation within complex bronchial trees is particularly challenging and physically demanding, requiring long-term experiences of physicians. This paper addresses the automatic segmentation of bronchial orifices in bronchoscopy videos. Deep learning-based approaches to this task are currently hampered due to the lack of readily-available ground truth segmentation data. Thus, we present a data-driven pipeline consisting of a k-means followed by a compact marker-based watershed algorithm which enables to generate airway instance segmentation maps from given depth images. In this way, these traditional algorithms serve as weak supervision for training a shallow CNN directly on RGB images solely based on a phantom dataset. We evaluate generalization capabilities of this model on two in-vivo datasets covering 250 frames on 21 different bronchoscopies. We demonstrate that its performance is comparable to those models being directly trained on in-vivo data, reaching an average error of 11 vs 5 pixels for the detected centers of the airway segmentation by an image resolution of 128x128. Our quantitative and qualitative results indicate that in the context of video bronchoscopy, phantom data and weak supervision using non-learning-based approaches enable to gain a semantic understanding of airway structures.

Abhishek Dinkar Jagtap, Mattias Heinrich, Marian Himstedt

An increasing number of colonoscopic guidance and assistance systems rely on machine learning algorithms which require a large amount of high-quality training data. In order to ensure high performance, the latter has to resemble a substantial portion of possible configurations. This particularly addresses varying anatomy, mucosa appearance and image sensor characteristics which are likely deteriorated by motion blur and inadequate illumination. The limited amount of readily available training data hampers to account for all of these possible configurations which results in reduced generalization capabilities of machine learning models. We propose an exemplary solution for synthesizing colonoscopy videos with substantial appearance and anatomical variations which enables to learn discriminative domain-randomized representations of the interior colon while mimicking real-world settings.

Hanna Siebert, Marian Himstedt, Mattias Heinrich

In order to be able to use artificial intelligence (AI) in medicine without scepticism and to recognise and assess its growing potential, a basic understanding of this topic is necessary among current and future medical staff. Under the premise of "trust through understanding", we developed an innovative online course as a learning opportunity within the framework of the German KI Campus (AI campus) project, which is a self-guided course that teaches the basics of AI for the analysis of medical image data. The main goal is to provide a learning environment for a sufficient understanding of AI in medical image analysis so that further interest in this topic is stimulated and inhibitions towards its use can be overcome by means of positive application experience. The focus was on medical applications and the fundamentals of machine learning. The online course was divided into consecutive lessons, which include theory in the form of explanatory videos, practical exercises in the form of Streamlit and practical exercises and/or quizzes to check learning progress. A survey among the participating medical students in the first run of the course was used to analyse our research hypotheses quantitatively.

Xuan Loc Pham, Gwendolyn Vuurberg, Marjan Doppen et al.

Image registration is a fundamental technique in the analysis of longitudinal and multi-phase CT images within clinical practice. However, most existing methods are tailored for single-organ applications, limiting their generalizability to other anatomical regions. This work presents TotalRegistrator, an image registration framework capable of aligning multiple anatomical regions simultaneously using a standard UNet architecture and a novel field decomposition strategy. The model is lightweight, requiring only 11GB of GPU memory for training. To train and evaluate our method, we constructed a large-scale longitudinal dataset comprising 695 whole-body (thorax-abdomen-pelvic) paired CT scans from individual patients acquired at different time points. We benchmarked TotalRegistrator against a generic classical iterative algorithm and a recent foundation model for image registration. To further assess robustness and generalizability, we evaluated our model on three external datasets: the public thoracic and abdominal datasets from the Learn2Reg challenge, and a private multiphase abdominal dataset from a collaborating hospital. Experimental results on the in-house dataset show that the proposed approach generally surpasses baseline methods in multi-organ abdominal registration, with a slight drop in lung alignment performance. On out-of-distribution datasets, it achieved competitive results compared to leading single-organ models, despite not being fine-tuned for those tasks, demonstrating strong generalizability. The source code will be publicly available at: https://github.com/DIAGNijmegen/oncology_image_registration.git.

Ron Keuth, Lasse Hansen, Maren Balks et al.

Semantic segmentation is a crucial task in medical imaging. Although supervised learning techniques have proven to be effective in performing this task, they heavily depend on large amounts of annotated training data. The recently introduced Segment Anything Model (SAM) enables prompt-based segmentation and offers zero-shot generalization to unfamiliar objects. In our work, we leverage SAM's abstract object understanding for medical image segmentation to provide pseudo labels for semi-supervised learning, thereby mitigating the need for extensive annotated training data. Our approach refines initial segmentations that are derived from a limited amount of annotated data (comprising up to 43 cases) by extracting bounding boxes and seed points as prompts forwarded to SAM. Thus, it enables the generation of dense segmentation masks as pseudo labels for unlabelled data. The results show that training with our pseudo labels yields an improvement in Dice score from $74.29\,\%$ to $84.17\,\%$ and from $66.63\,\%$ to $74.87\,\%$ for the segmentation of bones of the paediatric wrist and teeth in dental radiographs, respectively. As a result, our method outperforms intensity-based post-processing methods, state-of-the-art supervised learning for segmentation (nnU-Net), and the semi-supervised mean teacher approach. Our Code is available on GitHub.

Ron Keuth, Maren Balks, Sebastian Tschauner et al.

Fractures, particularly in the distal forearm, are among the most common injuries in children and adolescents, with approximately 800 000 cases treated annually in Germany. The AO/OTA system provides a structured fracture type classification, which serves as the foundation for treatment decisions. Although accurately classifying fractures can be challenging, current deep learning models have demonstrated performance comparable to that of experienced radiologists. While most existing approaches rely solely on radiographs, the potential impact of incorporating other additional modalities, such as automatic bone segmentation, fracture location, and radiology reports, remains underexplored. In this work, we systematically analyse the contribution of these three additional information types, finding that combining them with radiographs increases the AUROC from 91.71 to 93.25. Our code is available on GitHub.

Ron Keuth, Mattias Heinrich

When solving a segmentation task, shaped-base methods can be beneficial compared to pixelwise classification due to geometric understanding of the target object as shape, preventing the generation of anatomical implausible predictions in particular for corrupted data. In this work, we propose a novel hybrid method that combines a lightweight CNN backbone with a geometric neural network (Point Transformer) for shape regression. Using the same CNN encoder, the Point Transformer reaches segmentation quality on per with current state-of-the-art convolutional decoders ($4\pm1.9$ vs $3.9\pm2.9$ error in mm and $85\pm13$ vs $88\pm10$ Dice), but crucially, is more stable w.r.t image distortion, starting to outperform them at a corruption level of 30%. Furthermore, we include the nnU-Net as an upper baseline, which has $3.7\times$ more trainable parameters than our proposed method.

Lena Harkämper, Leo Lebrat, David Ahmedt-Aristizabal et al.

Chronic wound monitoring and management require accurate and efficient wound measurement methods. This paper presents a fast, non-invasive 3D wound measurement algorithm based on RGB-D imaging. The method combines RGB-D odometry with B-spline surface reconstruction to generate detailed 3D wound meshes, enabling automatic computation of clinically relevant wound measurements such as perimeter, surface area, and dimensions. We evaluated our system on realistic silicone wound phantoms and measured sub-millimetre 3D reconstruction accuracy compared with high-resolution ground-truth scans. The extracted measurements demonstrated low variability across repeated captures and strong agreement with manual assessments. The proposed pipeline also outperformed a state-of-the-art object-centric RGB-D reconstruction method while maintaining runtimes suitable for real-time clinical deployment. Our approach offers a promising tool for automated wound assessment in both clinical and remote healthcare settings.

Ho Hin Lee, Yucheng Tang, Kaiwen Xu et al.

The construction of three-dimensional multi-modal tissue maps provides an opportunity to spur interdisciplinary innovations across temporal and spatial scales through information integration. While the preponderance of effort is allocated to the cellular level and explore the changes in cell interactions and organizations, contextualizing findings within organs and systems is essential to visualize and interpret higher resolution linkage across scales. There is a substantial normal variation of kidney morphometry and appearance across body size, sex, and imaging protocols in abdominal computed tomography (CT). A volumetric atlas framework is needed to integrate and visualize the variability across scales. However, there is no abdominal and retroperitoneal organs atlas framework for multi-contrast CT. Hence, we proposed a high-resolution CT retroperitoneal atlas specifically optimized for the kidney across non-contrast CT and early arterial, late arterial, venous and delayed contrast enhanced CT. Briefly, we introduce a deep learning-based volume of interest extraction method and an automated two-stage hierarchal registration pipeline to register abdominal volumes to a high-resolution CT atlas template. To generate and evaluate the atlas, multi-contrast modality CT scans of 500 subjects (without reported history of renal disease, age: 15-50 years, 250 males & 250 females) were processed. We demonstrate a stable generalizability of the atlas template for integrating the normal kidney variation from small to large, across contrast modalities and populations with great variability of demographics. The linkage of atlas and demographics provided a better understanding of the variation of kidney anatomy across populations.

Alessa Hering, Sven Kuckertz, Stefan Heldmann et al.

While deep learning has achieved significant advances in accuracy for medical image segmentation, its benefits for deformable image registration have so far remained limited to reduced computation times. Previous work has either focused on replacing the iterative optimization of distance and smoothness terms with CNN-layers or using supervised approaches driven by labels. Our method is the first to combine the complementary strengths of global semantic information (represented by segmentation labels) and local distance metrics that help align surrounding structures. We demonstrate significant higher Dice scores (of 86.5\%) for deformable cardiac image registration compared to classic registration (79.0\%) as well as label-driven deep learning frameworks (83.4\%).

Jo Schlemper, Ozan Oktay, Michiel Schaap et al.

We propose a novel attention gate (AG) model for medical image analysis that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules when using convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed AG models are evaluated on a variety of tasks, including medical image classification and segmentation. For classification, we demonstrate the use case of AGs in scan plane detection for fetal ultrasound screening. We show that the proposed attention mechanism can provide efficient object localisation while improving the overall prediction performance by reducing false positives. For segmentation, the proposed architecture is evaluated on two large 3D CT abdominal datasets with manual annotations for multiple organs. Experimental results show that AG models consistently improve the prediction performance of the base architectures across different datasets and training sizes while preserving computational efficiency. Moreover, AGs guide the model activations to be focused around salient regions, which provides better insights into how model predictions are made. The source code for the proposed AG models is publicly available.

Ozan Oktay, Jo Schlemper, Loic Le Folgoc et al.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.

Ozan Oktay, Enzo Ferrante, Konstantinos Kamnitsas et al.

Incorporation of prior knowledge about organ shape and location is key to improve performance of image analysis approaches. In particular, priors can be useful in cases where images are corrupted and contain artefacts due to limitations in image acquisition. The highly constrained nature of anatomical objects can be well captured with learning based techniques. However, in most recent and promising techniques such as CNN based segmentation it is not obvious how to incorporate such prior knowledge. State-of-the-art methods operate as pixel-wise classifiers where the training objectives do not incorporate the structure and inter-dependencies of the output. To overcome this limitation, we propose a generic training strategy that incorporates anatomical prior knowledge into CNNs through a new regularisation model, which is trained end-to-end. The new framework encourages models to follow the global anatomical properties of the underlying anatomy (e.g. shape, label structure) via learned non-linear representations of the shape. We show that the proposed approach can be easily adapted to different analysis tasks (e.g. image enhancement, segmentation) and improve the prediction accuracy of the state-of-the-art models. The applicability of our approach is shown on multi-modal cardiac datasets and public benchmarks. Additionally, we demonstrate how the learned deep models of 3D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies.