arXiv subjects

Tanmay Mukherjee

Publications and source records attributed to Tanmay Mukherjee.

4 recordsLinked to original sources

arXiv2026

AI-enabled cardiac shape reconstruction from routine magnetic resonance imaging

Computational models of cardiac structure and function are increasingly central to the development of subject-specific cardiac digital twins, enabling improved characterization of contractile dysfunction, pathological remodeling, and electrical abnormalities. A critical prerequisite for these models is the accurate reconstruction of three-dimensional (3D) cardiac anatomy from medical imaging. Multi-planar magnetic resonance imaging, particularly when combined with artificial intelligence, offers a clinically feasible alternative to conventional reconstruction techniques. In this study, we present a neural field-based reconstruction framework that recovers 3D cardiac geometries from sparse planar contour data by learning continuous shape representations. Reconstruction performance was evaluated using complementary in-silico and in vivo datasets spanning variations in sampling density and geometric complexity. Across both datasets, reconstructed meshes closely matched reference geometries, demonstrating that the neural field approach faithfully captures cardiac planar contours. Compared with traditional local interpolation methods, the proposed framework exhibited improved geometric fidelity in anatomically challenging regions, including the left ventricular apex and basal segments, particularly under sparse sampling conditions. Collectively, these findings demonstrate that neural field-based reconstruction provides a robust and efficient pathway for multi-planar cardiac shape recovery, with particular relevance for AI-driven modeling pipelines and data-limited settings such as small-animal and time-resolved cardiac imaging.

physics.med-ph↗

arXiv2025

An in-silico lung phantom to assess the performance of pulmonary artery segmentation using angiogram

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 can allow for successful segmentation of the pulmonary vasculature. We expect this method to assist with developing and training ML-based segmentation frameworks and aid in their validation, thereby improving the capability to segment and reconstruct pulmonary vasculature without using contrast-enhanced imaging.

physics.bio-ph↗

arXiv2024

Synthetic ultrasound images to benchmark echocardiography-based biomechanics

Brightness mode (B-mode) ultrasound is a common imaging modality in the clinical assessment of several cardiovascular diseases. The utility of ultrasound-based functional indices such as the ejection fraction (EF) and stroke volume (SV) is widely described in diagnosing advanced-stage cardiovascular diseases. Additionally, structural indices obtained through the analysis of cardiac motion have been found to be important in the early-stage assessment of structural heart diseases, such as hypertrophic cardiomyopathy and myocardial infarction. Estimating heterogeneous variations in cardiac motion through B-mode ultrasound imaging is a crucial component of patient care. Despite the benefits of such imaging techniques, motion estimation algorithms are susceptible to variability between vendors due to the lack of benchmark motion quantities. In contrast, finite element (FE) simulations of cardiac biomechanics leverage well-established constitutive models of the myocardium to ensure reproducibility. In this study, we developed a methodology to create synthetic B-mode ultrasound images from FE simulations. The proposed methodology provides a detailed representation of displacements and strains under complex mouse-specific loading protocols of the LV. A comparison between the synthetic images and FE simulations revealed qualitative similarity in displacement patterns, thereby yielding benchmark quantities to improve the reproducibility of motion estimation algorithms. Thus, the study provides a methodology to create an extensive repository of images describing complex motion patterns to facilitate the enhanced reproducibility of cardiac motion analysis.

physics.med-ph↗

arXiv2024

Physics-informed motion registration of lung parenchyma across static CT images

Lung injuries, such as ventilator-induced lung injury and radiation-induced lung injury, can lead to heterogeneous alterations in the biomechanical behavior of the lungs. While imaging methods, e.g., X-ray and static computed tomography (CT), can point to regional alterations in lung structure between healthy and diseased tissue, they fall short of delineating timewise kinematic variations between the former and the latter. Image registration has gained recent interest as a tool to estimate the displacement experienced by the lungs during respiration via regional deformation metrics such as volumetric expansion and distortion. However, successful image registration commonly relies on a temporal series of image stacks with small displacements in the lungs across succeeding image stacks, which remains limited in static imaging. In this study, we have presented a finite element (FE) method to estimate strains from static images acquired at the end-expiration (EE) and end-inspiration (EI) timepoints, i.e., images with a large deformation between the two distant timepoints. Physiologically realistic loads were applied to the geometry obtained at EE to deform this geometry to match the geometry obtained at EI. The results indicated that the simulation could minimize the error between the two geometries. Using four-dimensional (4D) dynamic CT in a rat, the strain at an isolated transverse plane estimated by our method showed sufficient agreement with that estimated through non-rigid image registration that used all the timepoints. Through the proposed method, we can estimate the lung deformation at any timepoint between EE and EI. The proposed method offers a tool to estimate timewise regional deformation in the lungs using only static images acquired at EE and EI.

physics.med-ph↗