Jürgen Hesser

Sara Monji-Azad, Marvin Kinz, Claudia Scherl et al.

Non-rigid point cloud registration is a crucial task in computer vision. Evaluating a non-rigid point cloud registration method requires a dataset with challenges such as large deformation levels, noise, outliers, and incompleteness. Despite the existence of several datasets for deformable point cloud registration, the absence of a comprehensive benchmark with all challenges makes it difficult to achieve fair evaluations among different methods. This paper introduces SynBench, a new non-rigid point cloud registration dataset created using SimTool, a toolset for soft body simulation in Flex and Unreal Engine. SynBench provides the ground truth of corresponding points between two point sets and encompasses key registration challenges, including varying levels of deformation, noise, outliers, and incompleteness. To the best of the authors' knowledge, compared to existing datasets, SynBench possesses three particular characteristics: (1) it is the first benchmark that provides various challenges for non-rigid point cloud registration, (2) SynBench encompasses challenges of varying difficulty levels, and (3) it includes ground truth corresponding points both before and after deformation. The authors believe that SynBench enables future non-rigid point cloud registration methods to present a fair comparison of their achievements. SynBench is publicly available at: https://doi.org/10.11588/data/R9IKCF.

Sara Monji-Azad, Marvin Kinz, Jürgen Hesser

Point cloud registration is a fundamental problem in computer vision that aims to estimate the transformation between corresponding sets of points. Non-rigid registration, in particular, involves addressing challenges including various levels of deformation, noise, outliers, and data incompleteness. This paper introduces Robust-DefReg, a robust non-rigid point cloud registration method based on graph convolutional networks (GCNNs). Robust-DefReg is a coarse-to-fine registration approach within an end-to-end pipeline, leveraging the advantages of both coarse and fine methods. The method learns global features to find correspondences between source and target point clouds, to enable appropriate initial alignment, and subsequently fine registration. The simultaneous achievement of high accuracy and robustness across all challenges is reported less frequently in existing studies, making it a key objective of the Robust-DefReg method. The proposed method achieves high accuracy in large deformations while maintaining computational efficiency. This method possesses three primary attributes: high accuracy, robustness to different challenges, and computational efficiency. The experimental results show that the proposed Robust-DefReg holds significant potential as a foundational architecture for future investigations in non-rigid point cloud registration. The source code of Robust-DefReg is available.

Wenzhao Zhao, Steffen Albert, Barbara D. Wichtmann et al.

Filter-decomposition-based group equivariant convolutional neural networks (CNNs) have shown promising stability and data efficiency for 3D image feature extraction. However, these networks, which rely on parameter sharing and discrete transformation groups, often underperform in modern deep neural network architectures for processing volumetric images, such as the common 3D medical images. To address these limitations, this paper presents an efficient non-parameter-sharing continuous 3D affine group equivariant neural network for volumetric images. This network uses an adaptive aggregation of Monte Carlo augmented spherical Fourier-Bessel filter bases to improve the efficiency and flexibility of 3D group equivariant CNNs for volumetric data. Unlike existing methods that focus only on angular orthogonality in filter bases, the introduced spherical Bessel Fourier filter base incorporates both angular and radial orthogonality to improve feature extraction. Experiments on four medical image segmentation datasets show that the proposed methods achieve better affine group equivariance and superior segmentation accuracy than existing 3D group equivariant convolutional neural network layers, significantly improving the training stability and data efficiency of conventional CNN layers (at 0.05 significance level). The code is available at https://github.com/ZhaoWenzhao/WMCSFB.

Wenzhao Zhao, Barbara D. Wichtmann, Steffen Albert et al.

Group-equivariant convolutional neural networks (G-CNN) heavily rely on parameter sharing to increase CNN's data efficiency and performance. However, the parameter-sharing strategy greatly increases the computational burden for each added parameter, which hampers its application to deep neural network models. In this paper, we address these problems by proposing a non-parameter-sharing approach for group equivariant neural networks. The proposed methods adaptively aggregate a diverse range of filters by a weighted sum of stochastically augmented decomposed filters. We give theoretical proof about how the group equivariance can be achieved by our methods. Our method applies to both continuous and discrete groups, where the augmentation is implemented using Monte Carlo sampling and bootstrap resampling, respectively. Our methods also serve as an efficient extension of standard CNN. The experiments show that our method outperforms parameter-sharing group equivariant networks and enhances the performance of standard CNNs in image classification and denoising tasks, by using suitable filter bases to build efficient lightweight networks. The code will be available at https://github.com/ZhaoWenzhao/MCG_CNN.

Tomasz Konopczyński, Jitendra Rathore, Thorben Kröger et al.

Comparing different algorithms for segmenting glass fibers in industrial computed tomography (CT) scans is difficult due to the absence of a standard reference dataset. In this work, we introduce a set of annotated scans of short-fiber reinforced polymers (SFRP) as well as synthetically created CT volume data together with the evaluation metrics. We suggest both the metrics and this data set as a reference for studying the performance of different algorithms. The real scans were acquired by a Nikon MCT225 X-ray CT system. The simulated scans were created by the use of an in-house computational model and third-party commercial software. For both types of data, corresponding ground truth annotations have been prepared, including hand annotations for the real scans and STL models for the synthetic scans. Additionally, a Hessian-based Frangi vesselness filter for fiber segmentation has been implemented and open-sourced to serve as a reference for comparisons.

Binwu Wang, Isaac Rodriguez, Leon Breitinger et al.

The objective of this paper is to provide a baseline for performing multi-modal data classification on a novel open multimodal dataset of hepatocellular carcinoma (HCC), which includes both image data (contrast-enhanced CT and MRI images) and tabular data (the clinical laboratory test data as well as case report forms). TNM staging is the classification task. Features from the vectorized preprocessed tabular data and radiomics features from contrast-enhanced CT and MRI images are collected. Feature selection is performed based on mutual information. An XGBoost classifier predicts the TNM staging and it shows a prediction accuracy of $0.89 \pm 0.05$ and an AUC of $0.93 \pm 0.03$. The classifier shows that this high level of prediction accuracy can only be obtained by combining image and clinical laboratory data and therefore is a good example case where multi-model classification is mandatory to achieve accurate results.

Pascal Memmesheimer, Vincent Heuveline, Jürgen Hesser

Treatment effect estimation is essential for informed decision-making in many fields such as healthcare, economics, and public policy. While flexible machine learning models have been widely applied for estimating heterogeneous treatment effects, quantifying the inherent uncertainty of their point predictions remains an issue. Recent advancements in conformal prediction address this limitation by allowing for inexpensive computation, as well as distribution shifts, while still providing frequentist, finite-sample coverage guarantees under minimal assumptions for any point-predictor model. This advancement holds significant potential for improving decision-making in especially high-stakes environments. In this work, we perform a systematic review regarding conformal prediction methods for treatment effect estimation and provide for both the necessary theoretical background. Through a systematic filtering process, we select and analyze eleven key papers, identifying and describing current state-of-the-art methods in this area. Based on our findings, we propose directions for future research.

Karsten Roth, Jürgen Hesser, Tomasz Konopczyński

We propose a novel procedure to improve liver and lesion segmentation from CT scans for U-Net based models. Our method extends standard segmentation pipelines to focus on higher target recall or reduction of noisy false-positive predictions, boosting overall segmentation performance. To achieve this, we include segmentation errors into a new learning process appended to the main training setup, allowing the model to find features which explain away previous errors. We evaluate this on semantically distinct architectures: cascaded two- and three-dimensional as well as combined learning setups for multitask segmentation. Liver and lesion segmentation data are provided by the Liver Tumor Segmentation challenge (LiTS), with an increase in dice score of up to 2 points.

Karsten Roth, Tomasz Konopczyński, Jürgen Hesser

At present, lesion segmentation is still performed manually (or semi-automatically) by medical experts. To facilitate this process, we contribute a fully-automatic lesion segmentation pipeline. This work proposes a method as a part of the LiTS (Liver Tumor Segmentation Challenge) competition for ISBI 17 and MICCAI 17 comparing methods for automatics egmentation of liver lesions in CT scans. By utilizing cascaded, densely connected 2D U-Nets and a Tversky-coefficient based loss function, our framework achieves very good shape extractions with high detection sensitivity, with competitive scores at time of publication. In addition, adjusting hyperparameters in our Tversky-loss allows to tune the network towards higher sensitivity or robustness.

Patrick Bilic, Patrick Christ, Hongwei Bran Li et al.

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

Tomasz Konopczyński, Thorben Kröger, Lei Zheng et al.

We address the vessel segmentation problem by building upon the multiscale feature learning method of Kiros et al., which achieves the current top score in the VESSEL12 MICCAI challenge. Following their idea of feature learning instead of hand-crafted filters, we have extended the method to learn 3D features. The features are learned in an unsupervised manner in a multi-scale scheme using dictionary learning via least angle regression. The 3D feature kernels are further convolved with the input volumes in order to create feature maps. Those maps are used to train a supervised classifier with the annotated voxels. In order to process the 3D data with a large number of filters a parallel implementation has been developed. The algorithm has been applied on the example scans and annotations provided by the VESSEL12 challenge. We have compared our setup with Kiros et al. by running their implementation. Our current results show an improvement in accuracy over the slice wise method from 96.66$\pm$1.10% to 97.24$\pm$0.90%.

Tomasz Konopczyński, Danish Rathore, Jitendra Rathore et al.

We present the first attempt to perform short glass fiber semantic segmentation from X-ray computed tomography volumetric datasets at medium (3.9 μm isotropic) and low (8.3 μm isotropic) resolution using deep learning architectures. We performed experiments on both synthetic and real CT scans and evaluated deep fully convolutional architectures with both 2D and 3D kernels. Our artificial neural networks outperform existing methods at both medium and low resolution scans.

Tomasz Konopczyński, Thorben Kröger, Lei Zheng et al.

We propose a novel approach for automatic extraction (instance segmentation) of fibers from low resolution 3D X-ray computed tomography scans of short glass fiber reinforced polymers. We have designed a 3D instance segmentation architecture built upon a deep fully convolutional network for semantic segmentation with an extra output for embedding learning. We show that the embedding learning is capable of learning a mapping of voxels to an embedded space in which a standard clustering algorithm can be used to distinguish between different instances of an object in a volume. In addition, we discuss a merging post-processing method which makes it possible to process volumes of any size. The proposed 3D instance segmentation network together with our merging algorithm is the first known to authors knowledge procedure that produces results good enough, that they can be used for further analysis of low resolution fiber composites CT scans.

Stanislav Pyatykh, Jürgen Hesser

Poisson noise suppression is an important preprocessing step in several applications, such as medical imaging, microscopy, and astronomical imaging. In this work, we propose a novel patch-wise Poisson noise removal strategy, in which the MMSE estimator is utilized in order to produce the denoising result for each image patch. Fast and accurate computation of the MMSE estimator is carried out using k-d tree search followed by search in the K-nearest neighbor graph. Our experiments show that the proposed method is the preferable choice for low signal-to-noise ratios.