arXiv subjects

Stefanie Schreiber

Publications and source records attributed to Stefanie Schreiber.

4 recordsLinked to original sources

arXiv2026

Synthetic training for long-tail haemorrhagic lesion segmentation in data-scarce settings

Cerebral microbleeds (CMBs) and cortical superficial siderosis (cSS) are imaging markers of cerebral small vessel disease, but their automated segmentation is limited by the scarcity of positive cases and voxel-level annotations. We propose a synthetic training framework for long-tail haemorrhagic lesion segmentation that requires no real lesion annotations for training and leverages radiological description of the lesions. Starting from anatomical brain parcellations, the framework applies spatial augmentation and voxel resampling, procedurally inserts cSS and CMB labels using clinical priors on lesion location and morphology, and synthesises images through randomised intensity assignment, blurring, and Rician noise simulation. Models were trained on dynamically generated image-label pairs and evaluated against manual delineations in 10 cSS cases and 13 CMB cases. The proposed configurations outperformed classical filter baselines. For cSS, the hypointensity constrained model achieved higher AUPRC and AUROC than the Frangi filter (AUPRC: 0.284 vs 0.083; AUROC: 0.907 vs 0.731). For CMBs, explicit synthesis of blood vessels as lesion mimics improved performance over the classical baseline (AUPRC: 0.538 vs 0.004; AUROC: 0.999 vs 0.968). These results support our proposal as a feasible strategy for data-scarce haemorrhagic lesion segmentation.

cs.CV↗

arXiv2026

SMILE-UHURA Challenge -- Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms

The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, making it possible to visualise such vessels in the brain. However, the lack of publicly available annotated datasets has impeded the development of robust, machine learning-driven segmentation algorithms. To address this, the SMILE-UHURA challenge was organised. This challenge, held in conjunction with the ISBI 2023, in Cartagena de Indias, Colombia, aimed to provide a platform for researchers working on related topics. The SMILE-UHURA challenge addresses the gap in publicly available annotated datasets by providing an annotated dataset of Time-of-Flight angiography acquired with 7T MRI. This dataset was created through a combination of automated pre-segmentation and extensive manual refinement. In this manuscript, sixteen submitted methods and two baseline methods are compared both quantitatively and qualitatively on two different datasets: held-out test MRAs from the same dataset as the training data (with labels kept secret) and a separate 7T ToF MRA dataset where both input volumes and labels are kept secret. The results demonstrate that most of the submitted deep learning methods, trained on the provided training dataset, achieved reliable segmentation performance. Dice scores reached up to 0.838 $\pm$ 0.066 and 0.716 $\pm$ 0.125 on the respective datasets, with an average performance of up to 0.804 $\pm$ 0.15.

eess.IV↗

arXiv2023

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

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

cs.CV↗

arXiv2022

Narrative Visualization to Communicate Neurological Diseases

While narrative visualization has been used successfully in various applications to communicate scientific data in the format of a story to a general audience, the same has not been true for medical data. There are only a few exceptions that present tabular medical data to non-experts. However, a key component of medical visualization is the interactive analysis of 3D data, such as 3D models of anatomical structures, which were rarely included in narrative visualizations so far. In this design study, we investigate how neurological disease data can be communicated through narrative visualization techniques to a general audience in an understandable way. We designed a narrative visualization explaining cerebral small vessel disease. Learning about its avoidable risk factors serves to motivate the audience watching the resulting visual data story. Using this example, we discuss the adaption of basic narrative components. This includes the conflict and characters of a story, as well as the story's structure and content to address and communicate specific characteristics of medical data. Furthermore, we explore the extent to which complex medical relationships need to be simplified to be understandable to a general audience without distorting the underlying data and evidence. In particular, the data needs to be preprocessed for non-experts and appropriate forms of interaction must be found. We explore approaches to make the data more personally relatable, such as including a fictional patient. We evaluated our approach in a user study with 40 participants in a web-based implementation of the designed story. We found that the combination of a carefully thought-out storyline with a clear key message, appealing visualizations combined with easy-to-use interactions, and credible references are crucial for creating a narrative visualization about a neurological disease that engages an audience.

cs.HC↗