This study performs parameter inference in a partial differential equations system of pulmonary circulation. We use a fluid dynamics network model that takes selected parameter values and mimics the behaviour of the pulmonary haemodynamics under normal physiological and pathological conditions. This is of medical interest as it enables tracking the progression of pulmonary hypertension. We show how we make the fluids model tractable by reducing the parameter dimension from a 55D to a 5D problem. The Delayed Rejection Adaptive Metropolis (DRAM) algorithm, coupled with constraint nonlinear optimization is successfully used to learn the parameter values and quantify the uncertainty in the parameter estimates. To accommodate for different magnitudes of the parameter values, we introduce an improved parameter scaling technique in the DRAM algorithm. Formal convergence diagnostics are employed to check for convergence of the Markov chains. Additionally, we perform model selection using different information criteria, including Watanabe Akaike Information Criteria.
Coupling hemodynamics with vessel wall growth and remodeling (G&R) is crucial for understanding pathology at distal vasculature to study progression of incurable vascular diseases, such as pulmonary arterial hypertension. The present study is the first modeling attempt that focuses on defining homeostatic baseline values in distal pulmonary vascular bed via, a so-called, homeostatic optimization. To define the vascular homeostasis and total hemodynamics in the vascular tree, we consider two time-scales: a cardiac cycle and a longer period of vascular adaptations. An iterative homeostatic optimization is performed at the slow-time scale and incorporates: an extended Murray's law, wall metabolic cost function, stress equilibrium, and hemodynamics. The pulmonary arterial network of small vessels is represented by a fractal bifurcating tree. The pulsatile blood flow is described by a Womersley's deformable wall analytical solution. A vessel wall mechanical response is described by the constrained mixture theory for an orthotropic membrane and then linearized around mean pressure. Wall material parameters are characterized by using available porcine pulmonary artery experiments and
Pulmonary embolism is a life-threatening disease, early detection and treatment can significantly reduce mortality. In recent years, many studies have been using deep learning in the diagnosis of pulmonary embolism with contrast medium computed tomography pulmonary angiography, but the contrast medium is likely to cause acute kidney injury in patients with pulmonary embolism and chronic kidney disease, and the contrast medium takes time to work, patients with acute pulmonary embolism may miss the golden treatment time. This study aims to use deep learning techniques to automatically classify pulmonary embolism in CT images without contrast medium by using a 3D convolutional neural network model. The deep learning model used in this study had a significant impact on the pulmonary embolism classification of computed tomography images without contrast with 85\% accuracy and 0.84 AUC, which confirms the feasibility of the model in the diagnosis of pulmonary embolism.
Pulmonary hypertension (PH) can lead to significant vascular remodeling, resulting in altered pulmonary blood flow. Estimating the patient-specific contributions of each remodeling event is necessary to optimize and individualize clinical intervention strategies. In-silico modeling has emerged as a powerful tool to simulate pulmonary hemodynamics, and one of the primary requirements for robust in-silico modeling is an accurate representation of the pulmonary vasculature structure. Computed tomography (CT) imaging can be used to segment and reconstruct the proximal vasculature. However, contrast-enhanced imaging, such as CT pulmonary angiography, is required to obtain a comprehensive and high-fidelity view of the pulmonary vasculature. The clinical use of CT pulmonary angiography is limited by the complications associated with the injection of contrast agents. Machine learning (ML) approaches have emerged to effectively segment and reconstruct the pulmonary vasculature without the need for contrast-enhanced imaging. We have developed a method to create in-silico pulmonary angiogram phantoms with varying simulated contrast levels. The results indicated that adding simulated contrast
Pulmonary embolism, the obstruction of a pulmonary artery by a blood clot, is one of the leading causes of acute cardiovascular syndrome. In clinical practice, therapeutic decisions after diagnosis via computed tomography pulmonary angiography rely on risk stratification, which categorizes 30-day mortality risk into three categories. This stratification depends on the right-to-left ventricular diameter ratio and blood levels of two cardiac enzymes. However, blood biomarkers are not always available in emergency settings, and manual calculation of established severity scores - such as Qanadli and Mastora - is time-consuming and rarely performed in clinical routine practice. This study introduces an automated pipeline that models a directed graph representation of the pulmonary arterial tree, labeling its hierarchical structure and characterizing pulmonary embolism. The pipeline derives image-based biomarkers, including local artery-level features (morphological information, hierarchical position, clot volume, and resulting obstruction) and global patient-level biomarkers such as automatically calculated severity scores (Qanadli and Mastora) and the total embolic volume distribution
Pulmonary segment segmentation is crucial for cancer localization and surgical planning. However, the pixel-wise annotation of pulmonary segments is laborious, as the boundaries between segments are indistinguishable in medical images. To this end, we propose a weakly supervised learning (WSL) method, termed Anatomy-Hierarchy Supervised Learning (AHSL), which consults the precise clinical anatomical definition of pulmonary segments to perform pulmonary segment segmentation. Since pulmonary segments reside within the lobes and are determined by the bronchovascular tree, i.e., artery, airway and vein, the design of the loss function is founded on two principles. First, segment-level labels are utilized to directly supervise the output of the pulmonary segments, ensuring that they accurately encompass the appropriate bronchovascular tree. Second, lobe-level supervision indirectly oversees the pulmonary segment, ensuring their inclusion within the corresponding lobe. Besides, we introduce a two-stage segmentation strategy that incorporates bronchovascular priori information. Furthermore, a consistency loss is proposed to enhance the smoothness of segment boundaries, along with an evalu
Echocardiographers can detect pulmonary hypertension using Doppler echocardiography; however, accurately assessing its progression often proves challenging. Right heart catheterization (RHC), the gold standard for precise evaluation, is invasive and unsuitable for routine use, limiting its practicality for timely diagnosis and monitoring of pulmonary hypertension progression. Here, we propose MePH, a multi-view, multi-modal vision-language model to accurately assess pulmonary hypertension progression using non-invasive echocardiography. We constructed a large dataset comprising paired standardized echocardiogram videos, spectral images and RHC data, covering 1,237 patient cases from 12 medical centers. For the first time, MePH precisely models the correlation between non-invasive multi-view, multi-modal echocardiography and the pressure and resistance obtained via RHC. We show that MePH significantly outperforms echocardiographers' assessments using echocardiography, reducing the mean absolute error in estimating mean pulmonary arterial pressure (mPAP) and pulmonary vascular resistance (PVR) by 49.73% and 43.81%, respectively. In eight independent external hospitals, MePH achieved
Background: It is fundamental for accurate segmentation and quantification of the pulmonary vessel, particularly smaller vessels, from computed tomography (CT) images in chronic obstructive pulmonary disease (COPD) patients. Objective: The aim of this study was to segment the pulmonary vasculature using a semi-supervised method. Methods: In this study, a self-training framework is proposed by leveraging a teacher-student model for the segmentation of pulmonary vessels. First, the high-quality annotations are acquired in the in-house data by an interactive way. Then, the model is trained in the semi-supervised way. A fully supervised model is trained on a small set of labeled CT images, yielding the teacher model. Following this, the teacher model is used to generate pseudo-labels for the unlabeled CT images, from which reliable ones are selected based on a certain strategy. The training of the student model involves these reliable pseudo-labels. This training process is iteratively repeated until an optimal performance is achieved. Results: Extensive experiments are performed on non-enhanced CT scans of 125 COPD patients. Quantitative and qualitative analyses demonstrate that the p
Computed Tomography Pulmonary Angiography (CTPA) is the reference standard for diagnosing pulmonary vascular diseases such as Pulmonary Embolism (PE) and Chronic Thromboembolic Pulmonary Hypertension (CTEPH). However, its reliance on iodinated contrast agents poses risks including nephrotoxicity and allergic reactions, particularly in high-risk patients. This study proposes a method to generate Digital Contrast CTPA (DCCTPA) from Non-Contrast CT (NCCT) scans using a cascaded synthesizer based on Cycle-Consistent Generative Adversarial Networks (CycleGAN). Totally retrospective 410 paired CTPA and NCCT scans were obtained from three centers. The model was trained and validated internally on 249 paired images. Extra dataset that comprising 161 paired images was as test set for model generalization evaluation and downstream clinical tasks validation. Compared with state-of-the-art (SOTA) methods, the proposed method achieved the best comprehensive performance by evaluating quantitative metrics (For validation, MAE: 156.28, PSNR: 20.71 and SSIM: 0.98; For test, MAE: 165.12, PSNR: 20.27 and SSIM: 0.98) and qualitative visualization, demonstrating valid vessel enhancement, superior image
High-quality 3D reconstruction of pulmonary segments plays a crucial role in segmentectomy and surgical planning for the treatment of lung cancer. Due to the resolution requirement of the target reconstruction, conventional deep learning-based methods often suffer from computational resource constraints or limited granularity. Conversely, implicit modeling is favored due to its computational efficiency and continuous representation at any resolution. We propose a neural implicit function-based method to learn a 3D surface to achieve anatomy-aware, precise pulmonary segment reconstruction, represented as a shape by deforming a learnable template. Additionally, we introduce two clinically relevant evaluation metrics to comprehensively assess the quality of the reconstruction. Furthermore, to address the lack of publicly available shape datasets for benchmarking reconstruction algorithms, we developed a shape dataset named Lung3D, which includes the 3D models of 800 labeled pulmonary segments and their corresponding airways, arteries, veins, and intersegmental veins. We demonstrate that the proposed approach outperforms existing methods, providing a new perspective for pulmonary segme
Pulmonary arterial hypertension (PAH) is a progressive cardiopulmonary disease that leads to increased pulmonary pressures, vascular remodeling, and eventual right ventricular (RV) failure. Pediatric PAH remains understudied due to limited data and the lack of targeted diagnostic and therapeutic strategies. In this study, we developed and calibrated multi-scale, patient-specific cardiovascular models for four pediatric PAH patients using longitudinal MRI and catheterization data collected approximately two years apart. Using the CRIMSON simulation framework, we coupled three-dimensional fluid-structure interaction (FSI) models of the pulmonary arteries with zero-dimensional (0D) lumped-parameter heart and Windkessel models to simulate patient hemodynamics. An automated Python-based optimizer was developed to calibrate boundary conditions by minimizing discrepancies between simulated and clinical metrics, reducing calibration time from weeks to days. Model-derived metrics such as arterial stiffness, pulse wave velocity, resistance, and compliance were found to align with clinical indicators of disease severity and progression. Our findings demonstrate that computational modeling can
3D reconstruction of pulmonary segments plays an important role in surgical treatment planning of lung cancer, which facilitates preservation of pulmonary function and helps ensure low recurrence rates. However, automatic reconstruction of pulmonary segments remains unexplored in the era of deep learning. In this paper, we investigate what makes for automatic reconstruction of pulmonary segments. First and foremost, we formulate, clinically and geometrically, the anatomical definitions of pulmonary segments, and propose evaluation metrics adhering to these definitions. Second, we propose ImPulSe (Implicit Pulmonary Segment), a deep implicit surface model designed for pulmonary segment reconstruction. The automatic reconstruction of pulmonary segments by ImPulSe is accurate in metrics and visually appealing. Compared with canonical segmentation methods, ImPulSe outputs continuous predictions of arbitrary resolutions with higher training efficiency and fewer parameters. Lastly, we experiment with different network inputs to analyze what matters in the task of pulmonary segment reconstruction. Our code is available at https://github.com/M3DV/ImPulSe.
Detection of pulmonary nodules by CT is used for screening lung cancer in early stages.omputer aided diagnosis (CAD) based on deep-learning method can identify the suspected areas of pulmonary nodules in CT images, thus improving the accuracy and efficiency of CT diagnosis. The accuracy and robustness of deep learning models. Method:In this paper, we explore (1) the data augmentation method based on the generation model and (2) the model structure improvement method based on the embedding mechanism. Two strategies have been introduced in this study: a new data augmentation method and a embedding mechanism. In the augmentation method, a 3D pixel-level statistics algorithm is proposed to generate pulmonary nodule and by combing the faked pulmonary nodule and healthy lung, we generate new pulmonary nodule samples. The embedding mechanism are designed to better understand the meaning of pixels of the pulmonary nodule samples by introducing hidden variables. Result: The result of the 3DVNET model with the augmentation method for pulmonary nodule detection shows that the proposed data augmentation method outperforms the method based on generative adversarial network (GAN) framework, trai
Accurate segmentation of pulmonary airways and vessels is crucial for the diagnosis and treatment of pulmonary diseases. However, current deep learning approaches suffer from disconnectivity issues that hinder their clinical usefulness. To address this challenge, we propose a post-processing approach that leverages a data-driven method to repair the topology of disconnected pulmonary tubular structures. Our approach formulates the problem as a keypoint detection task, where a neural network is trained to predict keypoints that can bridge disconnected components. We use a training data synthesis pipeline that generates disconnected data from complete pulmonary structures. Moreover, the new Pulmonary Tree Repairing (PTR) dataset is publicly available, which comprises 800 complete 3D models of pulmonary airways, arteries, and veins, as well as the synthetic disconnected data. Our code and data are available at https://github.com/M3DV/pulmonary-tree-repairing.
Accurate anatomical labeling and analysis of the pulmonary structure and its surrounding anatomy from thoracic CT is getting increasingly important for understanding the etilogy of abnormalities or supporting targetted therapy and early interventions. Whilst lung and airway cell atlases have been attempted, there is a lack of fine-grained morphological atlases that are clinically deployable. In this work, we introduce AirMorph, a robust, end-to-end deep learning pipeline enabling fully automatic and comprehensive airway anatomical labeling at lobar, segmental, and subsegmental resolutions that can be used to create digital atlases of the lung. Evaluated across large-scale multi-center datasets comprising diverse pulmonary conditions, the AirMorph consistently outperformed existing segmentation and labeling methods in terms of accuracy, topological consistency, and completeness. To simplify clinical interpretation, we further introduce a compact anatomical signature quantifying critical morphological airway features, including stenosis, ectasia, tortuosity, divergence, length, and complexity. When applied to various pulmonary diseases such as pulmonary fibrosis, emphysema, atelectas
This study presents an unsupervised, motion-resolved reconstruction framework for high-resolution, free-breathing pulmonary magnetic resonance imaging (MRI), utilizing a three-dimensional Gaussian representation (3DGS). The proposed method leverages 3DGS to address the challenges of motion-resolved 3D isotropic pulmonary MRI reconstruction by enabling data smoothing between voxels for continuous spatial representation. Pulmonary MRI data acquisition is performed using a golden-angle radial sampling trajectory, with respiratory motion signals extracted from the center of k-space in each radial spoke. Based on the estimated motion signal, the k-space data is sorted into multiple respiratory phases. A 3DGS framework is then applied to reconstruct a reference image volume from the first motion state. Subsequently, a patient-specific convolutional neural network is trained to estimate the deformation vector fields (DVFs), which are used to generate the remaining motion states through spatial transformation of the reference volume. The proposed reconstruction pipeline is evaluated on six datasets from six subjects and bench-marked against three state-of-the-art reconstruction methods. Th
Lung cancer is the leading cause of cancer death worldwide. The best solution for lung cancer is to diagnose the pulmonary nodules in the early stage, which is usually accomplished with the aid of thoracic computed tomography (CT). As deep learning thrives, convolutional neural networks (CNNs) have been introduced into pulmonary nodule detection to help doctors in this labor-intensive task and demonstrated to be very effective. However, the current pulmonary nodule detection methods are usually domain-specific, and cannot satisfy the requirement of working in diverse real-world scenarios. To address this issue, we propose a slice grouped domain attention (SGDA) module to enhance the generalization capability of the pulmonary nodule detection networks. This attention module works in the axial, coronal, and sagittal directions. In each direction, we divide the input feature into groups, and for each group, we utilize a universal adapter bank to capture the feature subspaces of the domains spanned by all pulmonary nodule datasets. Then the bank outputs are combined from the perspective of domain to modulate the input group. Extensive experiments demonstrate that SGDA enables substanti
Computational hemodynamics models are becoming increasingly useful in the management and prognosis of complex, multiscale pathologies, including those attributed to the development of pulmonary vascular disease. However, diseases like pulmonary hypertension are heterogeneous, and affect both the proximal arteries and veins as well as the microcirculation. Simulation tools and the data used for model calibration are also inherently uncertain, requiring a full analysis of the sensitivity and uncertainty attributed to model inputs and outputs. Thus, this study quantifies model sensitivity and output uncertainty in a multiscale, pulse-wave propagation model of pulmonary hemodynamics. Our pulmonary circuit model consists of fifteen proximal arteries and twelve proximal veins, connected by a two-sided, structured tree model of the distal vasculature. We use polynomial chaos expansions to expedite the sensitivity and uncertainty quantification analyses and provide results for both the proximal and distal vasculature. Our analyses provide uncertainty in blood pressure, flow, and wave propagation phenomenon, as well as wall shear stress and cyclic stretch, both of which are important stimul
Priori knowledge of pulmonary anatomy plays a vital role in diagnosis of lung diseases. In CT images, pulmonary fissure segmentation is a formidable mission due to various of factors. To address the challenge, an useful approach based on ODoS filter and shape features is presented for pulmonary fissure segmentation. Here, we adopt an ODoS filter by merging the orientation information and magnitude information to highlight structure features for fissure enhancement, which can effectively distinguish between pulmonary fissures and clutters. Motivated by the fact that pulmonary fissures appear as linear structures in 2D space and planar structures in 3D space in orientation field, an orientation curvature criterion and an orientation partition scheme are fused to separate fissure patches and other structures in different orientation partition, which can suppress parts of clutters. Considering the shape difference between pulmonary fissures and tubular structures in magnitude field, a shape measure approach and a 3D skeletonization model are combined to segment pulmonary fissures for clutters removal. When applying our scheme to 55 chest CT scans which acquired from a publicly availabl
Pulmonary hypertension (PH) is a condition of high blood pressure that affects the arteries in the lungs and the right side of the heart (Mayo Clinic, 2017). A mean pulmonary artery pressure greater than 25 mmHg is defined as Pulmonary hypertension. The estimated 5-year survival rate from the time of diagnosis of pulmonary hypertension is only 57% without therapy and patients with right heart failure only survive for approximately 1 year without treatment (Benza et al., 2012). Given the indolent nature of the disease, early detection of PH remains a challenge leading to delays in therapy. Echocardiography is currently used as a screening tool for diagnosing PH. However, electrocardiography (ECG), a more accessible, simple to use, and cost-effective tool compared to echocardiography, is less studied and explored for screening at-risk patients for PH. The goal of this project is to create a neural network model which can process an ECG signal and detect the presence of PH with a confidence probability. I created a dense neural network (DNN) model that has an accuracy of 98% over the available training sample. For future steps, the current model will be updated with a model suited for