Anatomy-guided Pathology Segmentation

Pathological structures in medical images are typically deviations from the expected anatomy of a patient. While clinicians consider this interplay between anatomy and pathology, recent deep learning algorithms specialize in recognizing either one of the two, rarely considering the patient's body from such a joint perspective. In this paper, we develop a generalist segmentation model that combines anatomical and pathological information, aiming to enhance the segmentation accuracy of pathological features. Our Anatomy-Pathology Exchange (APEx) training utilizes a query-based segmentation transformer which decodes a joint feature space into query-representations for human anatomy and interleaves them via a mixing strategy into the pathology-decoder for anatomy-informed pathology predictions. In doing so, we are able to report the best results across the board on FDG-PET-CT and Chest X-Ray pathology segmentation tasks with a margin of up to 3.3% as compared to strong baseline methods. Code and models will be publicly available at github.com/alexanderjaus/APEx.

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

We present MedShapeNet, a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D surgical instrument models. Prior to the deep learning era, the broad application of statistical shape models (SSMs) in medical image analysis is evidence that shapes have been commonly used to describe medical data. Nowadays, however, state-of-the-art (SOTA) deep learning algorithms in medical imaging are predominantly voxel-based. In computer vision, on the contrary, shapes (including, voxel occupancy grids, meshes, point clouds and implicit surface models) are preferred data representations in 3D, as seen from the numerous shape-related publications in premier vision conferences, such as the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), as well as the increasing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models) in computer vision research. MedShapeNet is created as an alternative to these commonly used shape benchmarks to facilitate the translation of data-driven vision algorithms to medical applications, and it extends the opportunities to adapt SOTA vision algorithms to solve critical medical problems. Besides, the majority of the medical shapes in MedShapeNet are modeled directly on the imaging data of real patients, and therefore it complements well existing shape benchmarks comprising of computer-aided design (CAD) models. MedShapeNet currently includes more than 100,000 medical shapes, and provides annotations in the form of paired data. It is therefore also a freely available repository of 3D models for extended reality (virtual reality - VR, augmented reality - AR, mixed reality - MR) and medical 3D printing. This white paper describes in detail the motivations behind MedShapeNet, the shape acquisition procedures, the use cases, as well as the usage of the online shape search portal: https://medshapenet.ikim.nrw/

Towards Unifying Anatomy Segmentation: Automated Generation of a Full-body CT Dataset via Knowledge Aggregation and Anatomical Guidelines

In this study, we present a method for generating automated anatomy segmentation datasets using a sequential process that involves nnU-Net-based pseudo-labeling and anatomy-guided pseudo-label refinement. By combining various fragmented knowledge bases, we generate a dataset of whole-body CT scans with $142$ voxel-level labels for 533 volumes providing comprehensive anatomical coverage which experts have approved. Our proposed procedure does not rely on manual annotation during the label aggregation stage. We examine its plausibility and usefulness using three complementary checks: Human expert evaluation which approved the dataset, a Deep Learning usefulness benchmark on the BTCV dataset in which we achieve 85% dice score without using its training dataset, and medical validity checks. This evaluation procedure combines scalable automated checks with labor-intensive high-quality expert checks. Besides the dataset, we release our trained unified anatomical segmentation model capable of predicting $142$ anatomical structures on CT data.

Accurate Fine-Grained Segmentation of Human Anatomy in Radiographs via Volumetric Pseudo-Labeling

Purpose: Interpreting chest radiographs (CXR) remains challenging due to the ambiguity of overlapping structures such as the lungs, heart, and bones. To address this issue, we propose a novel method for extracting fine-grained anatomical structures in CXR using pseudo-labeling of three-dimensional computed tomography (CT) scans. Methods: We created a large-scale dataset of 10,021 thoracic CTs with 157 labels and applied an ensemble of 3D anatomy segmentation models to extract anatomical pseudo-labels. These labels were projected onto a two-dimensional plane, similar to the CXR, allowing the training of detailed semantic segmentation models for CXR without any manual annotation effort. Results: Our resulting segmentation models demonstrated remarkable performance on CXR, with a high average model-annotator agreement between two radiologists with mIoU scores of 0.93 and 0.85 for frontal and lateral anatomy, while inter-annotator agreement remained at 0.95 and 0.83 mIoU. Our anatomical segmentations allowed for the accurate extraction of relevant explainable medical features such as the cardio-thoracic-ratio. Conclusion: Our method of volumetric pseudo-labeling paired with CT projection offers a promising approach for detailed anatomical segmentation of CXR with a high agreement with human annotators. This technique may have important clinical implications, particularly in the analysis of various thoracic pathologies.

Panoramic Panoptic Segmentation: Insights Into Surrounding Parsing for Mobile Agents via Unsupervised Contrastive Learning

In this work, we introduce panoramic panoptic segmentation, as the most holistic scene understanding, both in terms of Field of View (FoV) and image-level understanding for standard camera-based input. A complete surrounding understanding provides a maximum of information to a mobile agent, which is essential for any intelligent vehicle in order to make informed decisions in a safety-critical dynamic environment such as real-world traffic. In order to overcome the lack of annotated panoramic images, we propose a framework which allows model training on standard pinhole images and transfers the learned features to a different domain in a cost-minimizing way. Using our proposed method with dense contrastive learning, we manage to achieve significant improvements over a non-adapted approach. Depending on the efficient panoptic segmentation architecture, we can improve 3.5-6.5% measured in Panoptic Quality (PQ) over non-adapted models on our established Wild Panoramic Panoptic Segmentation (WildPPS) dataset. Furthermore, our efficient framework does not need access to the images of the target domain, making it a feasible domain generalization approach suitable for a limited hardware setting. As additional contributions, we publish WildPPS: The first panoramic panoptic image dataset to foster progress in surrounding perception and explore a novel training procedure combining supervised and contrastive training.

Panoramic Panoptic Segmentation: Towards Complete Surrounding Understanding via Unsupervised Contrastive Learning

In this work, we introduce panoramic panoptic segmentation as the most holistic scene understanding both in terms of field of view and image level understanding. A complete surrounding understanding provides a maximum of information to the agent, which is essential for any intelligent vehicle in order to make informed decisions in a safety-critical dynamic environment such as real-world traffic. In order to overcome the lack of annotated panoramic images, we propose a framework which allows model training on standard pinhole images and transfers the learned features to a different domain. Using our proposed method, we manage to achieve significant improvements of over 5\% measured in PQ over non-adapted models on our Wild Panoramic Panoptic Segmentation (WildPPS) dataset. We show that our proposed Panoramic Robust Feature (PRF) framework is not only suitable to improve performance on panoramic images but can be beneficial whenever model training and deployment are executed on data taken from different distributions. As an additional contribution, we publish WildPPS: The first panoramic panoptic image dataset to foster progress in surrounding perception.