Karol Gotkowski

Karol Gotkowski, Shuvam Gupta, Jose R. A. Godinho et al.

Minerals, metals, and plastics are indispensable for a functioning modern society. Yet, their supply is limited causing a need for optimizing ore extraction and recuperation from recyclable materials.Typically, those processes must be meticulously adapted to the precise properties of the processed materials. Advancing our understanding of these materials is thus vital and can be achieved by crushing them into particles of micrometer size followed by their characterization. Current imaging approaches perform this analysis based on segmentation and characterization of particles imaged with computed tomography (CT), and rely on rudimentary postprocessing techniques to separate touching particles. However, their inability to reliably perform this separation as well as the need to retrain methods for each new image, these approaches leave untapped potential to be leveraged. Here, we propose ParticleSeg3D, an instance segmentation method able to extract individual particles from large CT images of particle samples containing different materials. Our approach is based on the powerful nnU-Net framework, introduces a particle size normalization, uses a border-core representation to enable instance segmentation, and is trained with a large dataset containing particles of numerous different sizes, shapes, and compositions of various materials. We demonstrate that ParticleSeg3D can be applied out-of-the-box to a large variety of particle types, including materials and appearances that have not been part of the training set. Thus, no further manual annotations and retraining are required when applying the method to new particle samples, enabling substantially higher scalability of experiments than existing methods. Our code and dataset are made publicly available.

Yudi Sang, Yanzhen Liu, Sutuke Yibulayimu et al.

The segmentation of pelvic fracture fragments in CT and X-ray images is crucial for trauma diagnosis, surgical planning, and intraoperative guidance. However, accurately and efficiently delineating the bone fragments remains a significant challenge due to complex anatomy and imaging limitations. The PENGWIN challenge, organized as a MICCAI 2024 satellite event, aimed to advance automated fracture segmentation by benchmarking state-of-the-art algorithms on these complex tasks. A diverse dataset of 150 CT scans was collected from multiple clinical centers, and a large set of simulated X-ray images was generated using the DeepDRR method. Final submissions from 16 teams worldwide were evaluated under a rigorous multi-metric testing scheme. The top-performing CT algorithm achieved an average fragment-wise intersection over union (IoU) of 0.930, demonstrating satisfactory accuracy. However, in the X-ray task, the best algorithm attained an IoU of 0.774, highlighting the greater challenges posed by overlapping anatomical structures. Beyond the quantitative evaluation, the challenge revealed methodological diversity in algorithm design. Variations in instance representation, such as primary-secondary classification versus boundary-core separation, led to differing segmentation strategies. Despite promising results, the challenge also exposed inherent uncertainties in fragment definition, particularly in cases of incomplete fractures. These findings suggest that interactive segmentation approaches, integrating human decision-making with task-relevant information, may be essential for improving model reliability and clinical applicability.

Karol Gotkowski, Klaus H. Maier-Hein, Fabian Isensee

Scribble supervision has emerged as a promising approach for reducing annotation costs in medical 3D segmentation by leveraging sparse annotations instead of voxel-wise labels. While existing methods report strong performance, a closer analysis reveals that the majority of research is confined to the cardiac domain, predominantly using ACDC and MSCMR datasets. This over-specialization has resulted in severe overfitting, misleading claims of performance improvements, and a lack of generalization across broader segmentation tasks. In this work, we formulate a set of key requirements for practical scribble supervision and introduce ScribbleBench, a comprehensive benchmark spanning over seven diverse medical imaging datasets, to systematically evaluate the fulfillment of these requirements. Consequently, we uncover a general failure of methods to generalize across tasks and that many widely used novelties degrade performance outside of the cardiac domain, whereas simpler overlooked approaches achieve superior generalization. Finally, we raise awareness for a strong yet overlooked baseline, nnU-Net coupled with a partial loss, which consistently outperforms specialized methods across a diverse range of tasks. By identifying fundamental limitations in existing research and establishing a new benchmark-driven evaluation standard, this work aims to steer scribble supervision toward more practical, robust, and generalizable methodologies for medical image segmentation.

Camila Gonzalez, Karol Gotkowski, Moritz Fuchs et al.

Automatic segmentation of ground glass opacities and consolidations in chest computer tomography (CT) scans can potentially ease the burden of radiologists during times of high resource utilisation. However, deep learning models are not trusted in the clinical routine due to failing silently on out-of-distribution (OOD) data. We propose a lightweight OOD detection method that leverages the Mahalanobis distance in the feature space and seamlessly integrates into state-of-the-art segmentation pipelines. The simple approach can even augment pre-trained models with clinically relevant uncertainty quantification. We validate our method across four chest CT distribution shifts and two magnetic resonance imaging applications, namely segmentation of the hippocampus and the prostate. Our results show that the proposed method effectively detects far- and near-OOD samples across all explored scenarios.

Camila Gonzalez, Karol Gotkowski, Andreas Bucher et al.

Automatic segmentation of lung lesions in computer tomography has the potential to ease the burden of clinicians during the Covid-19 pandemic. Yet predictive deep learning models are not trusted in the clinical routine due to failing silently in out-of-distribution (OOD) data. We propose a lightweight OOD detection method that exploits the Mahalanobis distance in the feature space. The proposed approach can be seamlessly integrated into state-of-the-art segmentation pipelines without requiring changes in model architecture or training procedure, and can therefore be used to assess the suitability of pre-trained models to new data. We validate our method with a patch-based nnU-Net architecture trained with a multi-institutional dataset and find that it effectively detects samples that the model segments incorrectly.

Sarthak Pati, Siddhesh P. Thakur, İbrahim Ethem Hamamcı et al.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Karol Gotkowski, Camila Gonzalez, Andreas Bucher et al.

M3d-CAM is an easy to use library for generating attention maps of CNN-based PyTorch models improving the interpretability of model predictions for humans. The attention maps can be generated with multiple methods like Guided Backpropagation, Grad-CAM, Guided Grad-CAM and Grad-CAM++. These attention maps visualize the regions in the input data that influenced the model prediction the most at a certain layer. Furthermore, M3d-CAM supports 2D and 3D data for the task of classification as well as for segmentation. A key feature is also that in most cases only a single line of code is required for generating attention maps for a model making M3d-CAM basically plug and play.