Marijn Stollenga

Vincent Bürgin, Raphael Prevost, Marijn F. Stollenga

Automatic vertebra localization and identification in CT scans is important for numerous clinical applications. Much progress has been made on this topic, but it mostly targets positional localization of vertebrae, ignoring their orientation. Additionally, most methods employ heuristics in their pipeline that can be sensitive in real clinical images which tend to contain abnormalities. We introduce a simple pipeline that employs a standard prediction with a U-Net, followed by a single graph neural network to associate and classify vertebrae with full orientation. To test our method, we introduce a new vertebra dataset that also contains pedicle detections that are associated with vertebra bodies, creating a more challenging landmark prediction, association and classification task. Our method is able to accurately associate the correct body and pedicle landmarks, ignore false positives and classify vertebrae in a simple, fully trainable pipeline avoiding application-specific heuristics. We show our method outperforms traditional approaches such as Hungarian Matching and Hidden Markov Models. We also show competitive performance on the standard VerSe challenge body identification task.

Samuel Joutard, Marijn Stollenga, Marc Balle Sanchez et al.

Medical imaging datasets often contain heterogeneous biases ranging from erroneous labels to inconsistent labeling styles. Such biases can negatively impact deep segmentation networks performance. Yet, the identification and characterization of such biases is a particularly tedious and challenging task. In this paper, we introduce HyperSORT, a framework using a hyper-network predicting UNets' parameters from latent vectors representing both the image and annotation variability. The hyper-network parameters and the latent vector collection corresponding to each data sample from the training set are jointly learned. Hence, instead of optimizing a single neural network to fit a dataset, HyperSORT learns a complex distribution of UNet parameters where low density areas can capture noise-specific patterns while larger modes robustly segment organs in differentiated but meaningful manners. We validate our method on two 3D abdominal CT public datasets: first a synthetically perturbed version of the AMOS dataset, and TotalSegmentator, a large scale dataset containing real unknown biases and errors. Our experiments show that HyperSORT creates a structured mapping of the dataset allowing the identification of relevant systematic biases and erroneous samples. Latent space clusters yield UNet parameters performing the segmentation task in accordance with the underlying learned systematic bias. The code and our analysis of the TotalSegmentator dataset are made available: https://github.com/ImFusionGmbH/HyperSORT

Mert Asim Karaoglu, Nikolas Brasch, Marijn Stollenga et al.

Depth estimation from monocular images is an important task in localization and 3D reconstruction pipelines for bronchoscopic navigation. Various supervised and self-supervised deep learning-based approaches have proven themselves on this task for natural images. However, the lack of labeled data and the bronchial tissue's feature-scarce texture make the utilization of these methods ineffective on bronchoscopic scenes. In this work, we propose an alternative domain-adaptive approach. Our novel two-step structure first trains a depth estimation network with labeled synthetic images in a supervised manner; then adopts an unsupervised adversarial domain feature adaptation scheme to improve the performance on real images. The results of our experiments show that the proposed method improves the network's performance on real images by a considerable margin and can be employed in 3D reconstruction pipelines.

Marijn F. Stollenga, Wonmin Byeon, Marcus Liwicki et al.

Convolutional Neural Networks (CNNs) can be shifted across 2D images or 3D videos to segment them. They have a fixed input size and typically perceive only small local contexts of the pixels to be classified as foreground or background. In contrast, Multi-Dimensional Recurrent NNs (MD-RNNs) can perceive the entire spatio-temporal context of each pixel in a few sweeps through all pixels, especially when the RNN is a Long Short-Term Memory (LSTM). Despite these theoretical advantages, however, unlike CNNs, previous MD-LSTM variants were hard to parallelize on GPUs. Here we re-arrange the traditional cuboid order of computations in MD-LSTM in pyramidal fashion. The resulting PyraMiD-LSTM is easy to parallelize, especially for 3D data such as stacks of brain slice images. PyraMiD-LSTM achieved best known pixel-wise brain image segmentation results on MRBrainS13 (and competitive results on EM-ISBI12).

Marijn Stollenga, Jonathan Masci, Faustino Gomez et al.

Traditional convolutional neural networks (CNN) are stationary and feedforward. They neither change their parameters during evaluation nor use feedback from higher to lower layers. Real brains, however, do. So does our Deep Attention Selective Network (dasNet) architecture. DasNets feedback structure can dynamically alter its convolutional filter sensitivities during classification. It harnesses the power of sequential processing to improve classification performance, by allowing the network to iteratively focus its internal attention on some of its convolutional filters. Feedback is trained through direct policy search in a huge million-dimensional parameter space, through scalable natural evolution strategies (SNES). On the CIFAR-10 and CIFAR-100 datasets, dasNet outperforms the previous state-of-the-art model.