HyperSpace: Hypernetworks for spacing-adaptive image segmentation

Medical images are often acquired in different settings, requiring harmonization to adapt to the operating point of algorithms. Specifically, to standardize the physical spacing of imaging voxels in heterogeneous inference settings, images are typically resampled before being processed by deep learning models. However, down-sampling results in loss of information, whereas upsampling introduces redundant information leading to inefficient resource utilization. To overcome these issues, we propose to condition segmentation models on the voxel spacing using hypernetworks. Our approach allows processing images at their native resolutions or at resolutions adjusted to the hardware and time constraints at inference time. Our experiments across multiple datasets demonstrate that our approach achieves competitive performance compared to resolution-specific models, while offering greater flexibility for the end user. This also simplifies model development, deployment and maintenance. Our code is available at https://github.com/ImFusionGmbH/HyperSpace.

Robust vertebra identification using simultaneous node and edge predicting Graph Neural Networks

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.

DISA: DIfferentiable Similarity Approximation for Universal Multimodal Registration

Multimodal image registration is a challenging but essential step for numerous image-guided procedures. Most registration algorithms rely on the computation of complex, frequently non-differentiable similarity metrics to deal with the appearance discrepancy of anatomical structures between imaging modalities. Recent Machine Learning based approaches are limited to specific anatomy-modality combinations and do not generalize to new settings. We propose a generic framework for creating expressive cross-modal descriptors that enable fast deformable global registration. We achieve this by approximating existing metrics with a dot-product in the feature space of a small convolutional neural network (CNN) which is inherently differentiable can be trained without registered data. Our method is several orders of magnitude faster than local patch-based metrics and can be directly applied in clinical settings by replacing the similarity measure with the proposed one. Experiments on three different datasets demonstrate that our approach generalizes well beyond the training data, yielding a broad capture range even on unseen anatomies and modality pairs, without the need for specialized retraining. We make our training code and data publicly available.

Global Multi-modal 2D/3D Registration via Local Descriptors Learning

Multi-modal registration is a required step for many image-guided procedures, especially ultrasound-guided interventions that require anatomical context. While a number of such registration algorithms are already available, they all require a good initialization to succeed due to the challenging appearance of ultrasound images and the arbitrary coordinate system they are acquired in. In this paper, we present a novel approach to solve the problem of registration of an ultrasound sweep to a pre-operative image. We learn dense keypoint descriptors from which we then estimate the registration. We show that our method overcomes the challenges inherent to registration tasks with freehand ultrasound sweeps, namely, the multi-modality and multidimensionality of the data in addition to lack of precise ground truth and low amounts of training examples. We derive a registration method that is fast, generic, fully automatic, does not require any initialization and can naturally generate visualizations aiding interpretability and explainability. Our approach is evaluated on a clinical dataset of paired MR volumes and ultrasound sequences.