StrokeTimer: Robust Representation Learning for Ischemic Stroke Onset-Time Estimation from Non-contrast CT

Ischemic stroke is a major global disease. Treatment decisions are highly time-sensitive, as eligibility for reperfusion therapies relies on the interval between stroke onset and intervention. However, the true onset time is often uncertain in clinical practice, necessitating imaging-based assessment of tissue age as a surrogate marker. Early ischemic changes on routinely acquired non-contrast CT (NCCT) are often subtle, and real-world clinical datasets exhibit pronounced onset-time class imbalance and center-scanner-related heterogeneity. In this work, we propose StrokeTimer, a fully automated framework for onset-time estimation in acute ischemic stroke. StrokeTimer integrates self-supervised disentanglement learning with energy-guided contrastive learning to capture subtle ischemic patterns while addressing long-tailed data distributions under acquisition variability. Onset time is categorized into three clinically relevant windows: <4.5 h, 4.5-6 h, and >6 h. Experimental results on a large multi-center NCCT dataset from two national cohorts, MR CLEAN Registry and MR CLEAN LATE, show that StrokeTimer achieves a macro AUC of 0.69 and a macro F1-score of 0.57, improving the strongest baseline by nearly 50% (p < 0.005). In this realistic, challenging setting, representative baseline approaches exhibit near-chance macro performance. Model explanations further highlight subtle gray-white matter blurring and hypodense regions consistent with established radiological biomarkers. These findings demonstrate the potential of StrokeTimer to support treatment decision-making in acute ischemic stroke. Code is available at https://github.com/BrainVas/StrokeTimer.

PyPeT: A Python Perfusion Tool for Automated Quantitative Brain CT and MR Perfusion Analysis

Computed tomography perfusion (CTP) and magnetic resonance perfusion (MRP) are widely used in acute ischemic stroke assessment and other cerebrovascular conditions to generate quantitative maps of cerebral hemodynamics. While commercial perfusion analysis software exists, it is often costly, closed source, and lacks customizability. This work introduces PyPeT, an openly available Python Perfusion Tool for head CTP and MRP processing. PyPeT is capable of producing cerebral blood flow (CBF), cerebral blood volume (CBV), mean transit time (MTT), time-to-peak (TTP), and time-to-maximum (Tmax) maps from raw four-dimensional perfusion data. PyPeT aims to make perfusion research as accessible and customizable as possible. This is achieved through a unified framework in which both CTP and MRP data can be processed, with a strong focus on modularity, low computational burden, and significant inline documentation. PyPeT's outputs can be validated through an extensive debug mode in which every step of the process is visualized. Additional validation was performed via visual and quantitative comparison with reference perfusion maps generated by three FDA-approved commercial perfusion tools and a research tool. These comparisons show a mean SSIM around 0.8 for all comparisons, indicating a good and stable correlation with FDA-approved tools. The code for PyPeT is openly available at our GitHub https://github.com/Marijn311/CT-and-MR-Perfusion-Tool

OccluNet: Spatio-Temporal Deep Learning for Occlusion Detection on DSA

Accurate detection of vascular occlusions during endovascular thrombectomy (EVT) is critical in acute ischemic stroke (AIS). Interpretation of digital subtraction angiography (DSA) sequences poses challenges due to anatomical complexity and time constraints. This work proposes OccluNet, a spatio-temporal deep learning model that integrates YOLOX, a single-stage object detector, with transformer-based temporal attention mechanisms to automate occlusion detection in DSA sequences. We compared OccluNet with a YOLOv11 baseline trained on either individual DSA frames or minimum intensity projections. Two spatio-temporal variants were explored for OccluNet: pure temporal attention and divided space-time attention. Evaluation on DSA images from the MR CLEAN Registry revealed the model's capability to capture temporally consistent features, achieving precision and recall of 89.02% and 74.87%, respectively. OccluNet significantly outperformed the baseline models, and both attention variants attained similar performance. Source code is available at https://github.com/anushka-kore/OccluNet.git

PathoPainter: Augmenting Histopathology Segmentation via Tumor-aware Inpainting

Tumor segmentation plays a critical role in histopathology, but it requires costly, fine-grained image-mask pairs annotated by pathologists. Thus, synthesizing histopathology data to expand the dataset is highly desirable. Previous works suffer from inaccuracies and limited diversity in image-mask pairs, both of which affect training segmentation, particularly in small-scale datasets and the inherently complex nature of histopathology images. To address this challenge, we propose PathoPainter, which reformulates image-mask pair generation as a tumor inpainting task. Specifically, our approach preserves the background while inpainting the tumor region, ensuring precise alignment between the generated image and its corresponding mask. To enhance dataset diversity while maintaining biological plausibility, we incorporate a sampling mechanism that conditions tumor inpainting on regional embeddings from a different image. Additionally, we introduce a filtering strategy to exclude uncertain synthetic regions, further improving the quality of the generated data. Our comprehensive evaluation spans multiple datasets featuring diverse tumor types and various training data scales. As a result, segmentation improved significantly with our synthetic data, surpassing existing segmentation data synthesis approaches, e.g., 75.69% -> 77.69% on CAMELYON16. The code is available at https://github.com/HongLiuuuuu/PathoPainter.

ISLES 2024: The first longitudinal multimodal multi-center real-world dataset in (sub-)acute stroke

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

ISLES'24: Improving final infarct prediction in ischemic stroke using multimodal imaging and clinical data

Accurate estimation of core (irreversibly damaged tissue) and penumbra (salvageable tissue) volumes is essential for ischemic stroke treatment decisions. Perfusion CT, the clinical standard, estimates these volumes but is affected by variations in deconvolution algorithms, implementations, and thresholds. Core tissue expands over time, with growth rates influenced by thrombus location, collateral circulation, and inherent patient-specific factors. Understanding this tissue growth is crucial for determining the need to transfer patients to comprehensive stroke centers, predicting the benefits of additional reperfusion attempts during mechanical thrombectomy, and forecasting final clinical outcomes. This work presents the ISLES'24 challenge, which addresses final post-treatment stroke infarct prediction from pre-interventional acute stroke imaging and clinical data. ISLES'24 establishes a unique 360-degree setting where all feasibly accessible clinical data are available for participants, including full CT acute stroke imaging, sub-acute follow-up MRI, and clinical tabular data. The contributions of this work are two-fold: first, we introduce a standardized benchmarking of final stroke infarct segmentation algorithms through the ISLES'24 challenge; second, we provide insights into infarct segmentation using multimodal imaging and clinical data strategies by identifying outperforming methods on a finely curated dataset. The outputs of this challenge are anticipated to enhance clinical decision-making and improve patient outcome predictions. All ISLES'24 materials, including data, performance evaluation scripts, and leading algorithmic strategies, are available to the research community following \url{https://isles-24.grand-challenge.org/}.

DSCA: A Digital Subtraction Angiography Sequence Dataset and Spatio-Temporal Model for Cerebral Artery Segmentation

Cerebrovascular diseases (CVDs) remain a leading cause of global disability and mortality. Digital Subtraction Angiography (DSA) sequences, recognized as the golden standard for diagnosing CVDs, can clearly visualize the dynamic flow and reveal pathological conditions within the cerebrovasculature. Therefore, precise segmentation of cerebral arteries (CAs) and classification between their main trunks and branches are crucial for physicians to accurately quantify diseases. However, achieving accurate CA segmentation in DSA sequences remains a challenging task due to small vessels with low contrast, and ambiguity between vessels and residual skull structures. Moreover, the lack of publicly available datasets limits exploration in the field. In this paper, we introduce a DSA Sequence-based Cerebral Artery segmentation dataset (DSCA), the first publicly accessible dataset designed specifically for pixel-level semantic segmentation of CAs. Additionally, we propose DSANet, a spatio-temporal network for CA segmentation in DSA sequences. Unlike existing DSA segmentation methods that focus only on a single frame, the proposed DSANet introduces a separate temporal encoding branch to capture dynamic vessel details across multiple frames. To enhance small vessel segmentation and improve vessel connectivity, we design a novel TemporalFormer module to capture global context and correlations among sequential frames. Furthermore, we develop a Spatio-Temporal Fusion (STF) module to effectively integrate spatial and temporal features from the encoder. Extensive experiments demonstrate that DSANet outperforms other state-of-the-art methods in CA segmentation, achieving a Dice of 0.9033.

UDCR: Unsupervised Aortic DSA/CTA Rigid Registration Using Deep Reinforcement Learning and Overlap Degree Calculation

The rigid registration of aortic Digital Subtraction Angiography (DSA) and Computed Tomography Angiography (CTA) can provide 3D anatomical details of the vasculature for the interventional surgical treatment of conditions such as aortic dissection and aortic aneurysms, holding significant value for clinical research. However, the current methods for 2D/3D image registration are dependent on manual annotations or synthetic data, as well as the extraction of landmarks, which is not suitable for cross-modal registration of aortic DSA/CTA. In this paper, we propose an unsupervised method, UDCR, for aortic DSA/CTA rigid registration based on deep reinforcement learning. Leveraging the imaging principles and characteristics of DSA and CTA, we have constructed a cross-dimensional registration environment based on spatial transformations. Specifically, we propose an overlap degree calculation reward function that measures the intensity difference between the foreground and background, aimed at assessing the accuracy of registration between segmentation maps and DSA images. This method is highly flexible, allowing for the loading of pre-trained models to perform registration directly or to seek the optimal spatial transformation parameters through online learning. We manually annotated 61 pairs of aortic DSA/CTA for algorithm evaluation. The results indicate that the proposed UDCR achieved a Mean Absolute Error (MAE) of 2.85 mm in translation and 4.35{\deg} in rotation, showing significant potential for clinical applications.

Image-Guided Autonomous Guidewire Navigation in Robot-Assisted Endovascular Interventions using Reinforcement Learning

Autonomous robots in endovascular interventions possess the potential to navigate guidewires with safety and reliability, while reducing human error and shortening surgical time. However, current methods of guidewire navigation based on Reinforcement Learning (RL) depend on manual demonstration data or magnetic guidance. In this work, we propose an Image-guided Autonomous Guidewire Navigation (IAGN) method. Specifically, we introduce BDA-star, a path planning algorithm with boundary distance constraints, for the trajectory planning of guidewire navigation. We established an IAGN-RL environment where the observations are real-time guidewire feeding images highlighting the position of the guidewire tip and the planned path. We proposed a reward function based on the distances from both the guidewire tip to the planned path and the target to evaluate the agent's actions. Furthermore, in policy network, we employ a pre-trained convolutional neural network to extract features, mitigating stability issues and slow convergence rates associated with direct learning from raw pixels. Experiments conducted on the aortic simulation IAGN platform demonstrated that the proposed method, targeting the left subclavian artery and the brachiocephalic artery, achieved a 100% guidewire navigation success rate, along with reduced movement and retraction distances and trajectories tend to the center of the vessels.

An automated framework for brain vessel centerline extraction from CTA images

Accurate automated extraction of brain vessel centerlines from CTA images plays an important role in diagnosis and therapy of cerebrovascular diseases, such as stroke. However, this task remains challenging due to the complex cerebrovascular structure, the varying imaging quality, and vessel pathology effects. In this paper, we consider automatic lumen segmentation generation without additional annotation effort by physicians and more effective use of the generated lumen segmentation for improved centerline extraction performance. We propose an automated framework for brain vessel centerline extraction from CTA images. The framework consists of four major components: (1) pre-processing approaches that register CTA images with a CT atlas and divide these images into input patches, (2) lumen segmentation generation from annotated vessel centerlines using graph cuts and robust kernel regression, (3) a dual-branch topology-aware UNet (DTUNet) that can effectively utilize the annotated vessel centerlines and the generated lumen segmentation through a topology-aware loss (TAL) and its dual-branch design, and (4) post-processing approaches that skeletonize the predicted lumen segmentation. Extensive experiments on a multi-center dataset demonstrate that the proposed framework outperforms state-of-the-art methods in terms of average symmetric centerline distance (ASCD) and overlap (OV). Subgroup analyses further suggest that the proposed framework holds promise in clinical applications for stroke treatment. Code is publicly available at https://github.com/Liusj-gh/DTUNet.