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.

Why does my medical AI look at pictures of birds? Exploring the efficacy of transfer learning across domain boundaries

It is an open secret that ImageNet is treated as the panacea of pretraining. Particularly in medical machine learning, models not trained from scratch are often finetuned based on ImageNet-pretrained models. We posit that pretraining on data from the domain of the downstream task should almost always be preferred instead. We leverage RadNet-12M, a dataset containing more than 12 million computed tomography (CT) image slices, to explore the efficacy of self-supervised pretraining on medical and natural images. Our experiments cover intra- and cross-domain transfer scenarios, varying data scales, finetuning vs. linear evaluation, and feature space analysis. We observe that intra-domain transfer compares favorably to cross-domain transfer, achieving comparable or improved performance (0.44% - 2.07% performance increase using RadNet pretraining, depending on the experiment) and demonstrate the existence of a domain boundary-related generalization gap and domain-specific learned features.

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications. However, it is a challenging task due to nuclei variances in staining and size, overlapping boundaries, and nuclei clustering. While convolutional neural networks have been extensively used for this task, we explore the potential of Transformer-based networks in this domain. Therefore, we introduce a new method for automated instance segmentation of cell nuclei in digitized tissue samples using a deep learning architecture based on Vision Transformer called CellViT. CellViT is trained and evaluated on the PanNuke dataset, which is one of the most challenging nuclei instance segmentation datasets, consisting of nearly 200,000 annotated Nuclei into 5 clinically important classes in 19 tissue types. We demonstrate the superiority of large-scale in-domain and out-of-domain pre-trained Vision Transformers by leveraging the recently published Segment Anything Model and a ViT-encoder pre-trained on 104 million histological image patches - achieving state-of-the-art nuclei detection and instance segmentation performance on the PanNuke dataset with a mean panoptic quality of 0.51 and an F1-detection score of 0.83. The code is publicly available at https://github.com/TIO-IKIM/CellViT

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.

Multimodal Interactive Lung Lesion Segmentation: A Framework for Annotating PET/CT Images based on Physiological and Anatomical Cues

Recently, deep learning enabled the accurate segmentation of various diseases in medical imaging. These performances, however, typically demand large amounts of manual voxel annotations. This tedious process for volumetric data becomes more complex when not all required information is available in a single imaging domain as is the case for PET/CT data. We propose a multimodal interactive segmentation framework that mitigates these issues by combining anatomical and physiological cues from PET/CT data. Our framework utilizes the geodesic distance transform to represent the user annotations and we implement a novel ellipsoid-based user simulation scheme during training. We further propose two annotation interfaces and conduct a user study to estimate their usability. We evaluated our model on the in-domain validation dataset and an unseen PET/CT dataset. We make our code publicly available: https://github.com/verena-hallitschke/pet-ct-annotate.

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Breaking with Fixed Set Pathology Recognition through Report-Guided Contrastive Training

When reading images, radiologists generate text reports describing the findings therein. Current state-of-the-art computer-aided diagnosis tools utilize a fixed set of predefined categories automatically extracted from these medical reports for training. This form of supervision limits the potential usage of models as they are unable to pick up on anomalies outside of their predefined set, thus, making it a necessity to retrain the classifier with additional data when faced with novel classes. In contrast, we investigate direct text supervision to break away from this closed set assumption. By doing so, we avoid noisy label extraction via text classifiers and incorporate more contextual information. We employ a contrastive global-local dual-encoder architecture to learn concepts directly from unstructured medical reports while maintaining its ability to perform free form classification. We investigate relevant properties of open set recognition for radiological data and propose a method to employ currently weakly annotated data into training. We evaluate our approach on the large-scale chest X-Ray datasets MIMIC-CXR, CheXpert, and ChestX-Ray14 for disease classification. We show that despite using unstructured medical report supervision, we perform on par with direct label supervision through a sophisticated inference setting.

Towards Automatic Parsing of Structured Visual Content through the Use of Synthetic Data

Structured Visual Content (SVC) such as graphs, flow charts, or the like are used by authors to illustrate various concepts. While such depictions allow the average reader to better understand the contents, images containing SVCs are typically not machine-readable. This, in turn, not only hinders automated knowledge aggregation, but also the perception of displayed in-formation for visually impaired people. In this work, we propose a synthetic dataset, containing SVCs in the form of images as well as ground truths. We show the usage of this dataset by an application that automatically extracts a graph representation from an SVC image. This is done by training a model via common supervised learning methods. As there currently exist no large-scale public datasets for the detailed analysis of SVC, we propose the Synthetic SVC (SSVC) dataset comprising 12,000 images with respective bounding box annotations and detailed graph representations. Our dataset enables the development of strong models for the interpretation of SVCs while skipping the time-consuming dense data annotation. We evaluate our model on both synthetic and manually annotated data and show the transferability of synthetic to real via various metrics, given the presented application. Here, we evaluate that this proof of concept is possible to some extend and lay down a solid baseline for this task. We discuss the limitations of our approach for further improvements. Our utilized metrics can be used as a tool for future comparisons in this domain. To enable further research on this task, the dataset is publicly available at https://bit.ly/3jN1pJJ