arXiv subjects

Annette Birkhold

Publications and source records attributed to Annette Birkhold.

14 recordsLinked to original sources

arXiv2024

ProPLIKS: Probablistic 3D human body pose estimation

We present a novel approach for 3D human pose estimation by employing probabilistic modeling. This approach leverages the advantages of normalizing flows in non-Euclidean geometries to address uncertain poses. Specifically, our method employs normalizing flow tailored to the SO(3) rotational group, incorporating a coupling mechanism based on the M\"obius transformation. This enables the framework to accurately represent any distribution on SO(3), effectively addressing issues related to discontinuities. Additionally, we reinterpret the challenge of reconstructing 3D human figures from 2D pixel-aligned inputs as the task of mapping these inputs to a range of probable poses. This perspective acknowledges the intrinsic ambiguity of the task and facilitates a straightforward integration method for multi-view scenarios. The combination of these strategies showcases the effectiveness of probabilistic models in complex scenarios for human pose estimation techniques. Our approach notably surpasses existing methods in the field of pose estimation. We also validate our methodology on human pose estimation from RGB images as well as medical X-Ray datasets.

cs.CV↗

arXiv2024

Physics-Informed Learning for Time-Resolved Angiographic Contrast Agent Concentration Reconstruction

Three-dimensional Digital Subtraction Angiography (3D-DSA) is a well-established X-ray-based technique for visualizing vascular anatomy. Recently, four-dimensional DSA (4D-DSA) reconstruction algorithms have been developed to enable the visualization of volumetric contrast flow dynamics through time-series of volumes. . This reconstruction problem is ill-posed mainly due to vessel overlap in the projection direction and geometric vessel foreshortening, which leads to information loss in the recorded projection images. However, knowledge about the underlying fluid dynamics can be leveraged to constrain the solution space. In our work, we implicitly include this information in a neural network-based model that is trained on a dataset of image-based blood flow simulations. The model predicts the spatially averaged contrast agent concentration for each centerline point of the vasculature over time, lowering the overall computational demand. The trained network enables the reconstruction of relative contrast agent concentrations with a mean absolute error of 0.02 $\pm$ 0.02 and a mean absolute percentage error of 5.31 % $\pm$ 9.25 %. Moreover, the network is robust to varying degrees of vessel overlap and vessel foreshortening. Our approach demonstrates the potential of the integration of machine learning and blood flow simulations in time-resolved angiographic flow reconstruction.

cs.CV↗

arXiv2023

PLIKS: A Pseudo-Linear Inverse Kinematic Solver for 3D Human Body Estimation

We introduce PLIKS (Pseudo-Linear Inverse Kinematic Solver) for reconstruction of a 3D mesh of the human body from a single 2D image. Current techniques directly regress the shape, pose, and translation of a parametric model from an input image through a non-linear mapping with minimal flexibility to any external influences. We approach the task as a model-in-the-loop optimization problem. PLIKS is built on a linearized formulation of the parametric SMPL model. Using PLIKS, we can analytically reconstruct the human model via 2D pixel-aligned vertices. This enables us with the flexibility to use accurate camera calibration information when available. PLIKS offers an easy way to introduce additional constraints such as shape and translation. We present quantitative evaluations which confirm that PLIKS achieves more accurate reconstruction with greater than 10% improvement compared to other state-of-the-art methods with respect to the standard 3D human pose and shape benchmarks while also obtaining a reconstruction error improvement of 12.9 mm on the newer AGORA dataset.

cs.CV↗

arXiv2023

BOSS: Bones, Organs and Skin Shape Model

Objective: A digital twin of a patient can be a valuable tool for enhancing clinical tasks such as workflow automation, patient-specific X-ray dose optimization, markerless tracking, positioning, and navigation assistance in image-guided interventions. However, it is crucial that the patient's surface and internal organs are of high quality for any pose and shape estimates. At present, the majority of statistical shape models (SSMs) are restricted to a small number of organs or bones or do not adequately represent the general population. Method: To address this, we propose a deformable human shape and pose model that combines skin, internal organs, and bones, learned from CT images. By modeling the statistical variations in a pose-normalized space using probabilistic PCA while also preserving joint kinematics, our approach offers a holistic representation of the body that can benefit various medical applications. Results: We assessed our model's performance on a registered dataset, utilizing the unified shape space, and noted an average error of 3.6 mm for bones and 8.8 mm for organs. To further verify our findings, we conducted additional tests on publicly available datasets with multi-part segmentations, which confirmed the effectiveness of our model. Conclusion: This works shows that anatomically parameterized statistical shape models can be created accurately and in a computationally efficient manner. Significance: The proposed approach enables the construction of shape models that can be directly applied to various medical applications, including biomechanics and reconstruction.

cs.CV↗

arXiv2023

Transient Hemodynamics Prediction Using an Efficient Octree-Based Deep Learning Model

Patient-specific hemodynamics assessment could support diagnosis and treatment of neurovascular diseases. Currently, conventional medical imaging modalities are not able to accurately acquire high-resolution hemodynamic information that would be required to assess complex neurovascular pathologies. Therefore, computational fluid dynamics (CFD) simulations can be applied to tomographic reconstructions to obtain clinically relevant information. However, three-dimensional (3D) CFD simulations require enormous computational resources and simulation-related expert knowledge that are usually not available in clinical environments. Recently, deep-learning-based methods have been proposed as CFD surrogates to improve computational efficiency. Nevertheless, the prediction of high-resolution transient CFD simulations for complex vascular geometries poses a challenge to conventional deep learning models. In this work, we present an architecture that is tailored to predict high-resolution (spatial and temporal) velocity fields for complex synthetic vascular geometries. For this, an octree-based spatial discretization is combined with an implicit neural function representation to efficiently handle the prediction of the 3D velocity field for each time step. The presented method is evaluated for the task of cerebral hemodynamics prediction before and during the injection of contrast agent in the internal carotid artery (ICA). Compared to CFD simulations, the velocity field can be estimated with a mean absolute error of 0.024 m/s, whereas the run time reduces from several hours on a high-performance cluster to a few seconds on a consumer graphical processing unit.

cs.LG↗

arXiv2021

Deep Learning compatible Differentiable X-ray Projections for Inverse Rendering

Many minimally invasive interventional procedures still rely on 2D fluoroscopic imaging. Generating a patient-specific 3D model from these X-ray projection data would allow to improve the procedural workflow, e.g. by providing assistance functions such as automatic positioning. To accomplish this, two things are required. First, a statistical human shape model of the human anatomy and second, a differentiable X-ray renderer. In this work, we propose a differentiable renderer by deriving the distance travelled by a ray inside mesh structures to generate a distance map. To demonstrate its functioning, we use it for simulating X-ray images from human shape models. Then we show its application by solving the inverse problem, namely reconstructing 3D models from real 2D fluoroscopy images of the pelvis, which is an ideal anatomical structure for patient registration. This is accomplished by an iterative optimization strategy using gradient descent. With the majority of the pelvis being in the fluoroscopic field of view, we achieve a mean Hausdorff distance of 30 mm between the reconstructed model and the ground truth segmentation.

eess.IV↗

arXiv2021

X-ray Scatter Estimation Using Deep Splines

Algorithmic X-ray scatter compensation is a desirable technique in flat-panel X-ray imaging and cone-beam computed tomography. State-of-the-art U-net based image translation approaches yielded promising results. As there are no physics constraints applied to the output of the U-Net, it cannot be ruled out that it yields spurious results. Unfortunately, those may be misleading in the context of medical imaging. To overcome this problem, we propose to embed B-splines as a known operator into neural networks. This inherently limits their predictions to well-behaved and smooth functions. In a study using synthetic head and thorax data as well as real thorax phantom data, we found that our approach performed on par with U-net when comparing both algorithms based on quantitative performance metrics. However, our approach not only reduces runtime and parameter complexity, but we also found it much more robust to unseen noise levels. While the U-net responded with visible artifacts, our approach preserved the X-ray signal's frequency characteristics.

physics.med-ph↗

arXiv2020

Simultaneous Estimation of X-ray Back-Scatter and Forward-Scatter using Multi-Task Learning

Scattered radiation is a major concern impacting X-ray image-guided procedures in two ways. First, back-scatter significantly contributes to patient (skin) dose during complicated interventions. Second, forward-scattered radiation reduces contrast in projection images and introduces artifacts in 3-D reconstructions. While conventionally employed anti-scatter grids improve image quality by blocking X-rays, the additional attenuation due to the anti-scatter grid at the detector needs to be compensated for by a higher patient entrance dose. This also increases the room dose affecting the staff caring for the patient. For skin dose quantification, back-scatter is usually accounted for by applying pre-determined scalar back-scatter factors or linear point spread functions to a primary kerma forward projection onto a patient surface point. However, as patients come in different shapes, the generalization of conventional methods is limited. Here, we propose a novel approach combining conventional techniques with learning-based methods to simultaneously estimate the forward-scatter reaching the detector as well as the back-scatter affecting the patient skin dose. Knowing the forward-scatter, we can correct X-ray projections, while a good estimate of the back-scatter component facilitates an improved skin dose assessment. To simultaneously estimate forward-scatter as well as back-scatter, we propose a multi-task approach for joint back- and forward-scatter estimation by combining X-ray physics with neural networks. We show that, in theory, highly accurate scatter estimation in both cases is possible. In addition, we identify research directions for our multi-task framework and learning-based scatter estimation in general.

physics.med-ph↗

arXiv2020

Deep Scatter Splines: Learning-Based Medical X-ray Scatter Estimation Using B-splines

The idea of replacing hardware by software to compensate for scattered radiation in flat-panel X-ray imaging is well established in the literature. Recently, deep-learningbased image translation approaches, most notably the U-Net, have emerged for scatter estimation. These yield considerable improvements over model-based methods. Such networks, however, involve potential drawbacks that need to be considered. First, they are trained in a data-driven fashion without making use of prior knowledge and X-ray physics. Second, due to their high parameter complexity, the validity of deep neural networks is difficult to assess. To circumvent these issues, we introduce here a surrogate function to model X-ray scatter distributions that can be expressed by few parameters. We could show empirically that cubic B-splines are well-suited to model X-ray scatter in the diagnostic energy regime. Based on these findings, we propose a lean convolutional encoder architecture that extracts local scatter characteristics from X-ray projection images. These characteristics are embedded into a global context using a constrained weighting matrix yielding spline coefficients that model the scatter distribution. In a first simulation study with 17 thorax data sets, we could show that our method and the U-Net-based state of the art reach about the same accuracy. However, we could achieve these comparable outcomes with orders of magnitude fewer parameters while ensuring that not high-frequency information gets manipulated.

physics.med-ph↗

arXiv2020

Effects of Tissue Material Properties on X-Ray Image, Scatter and Patient Dose Determined using Monte Carlo Simulations

With increasing patient and staff X-ray radiation awareness, many efforts have been made to develop accurate patient dose estimation methods. To date, Monte Carlo (MC) simulations are considered golden standard to simulate the interaction of X-ray radiation with matter. However, sensitivity of MC simulation results to variations in the experimental or clinical setup of image guided interventional procedures are only limited studied. In particular, the impact of patient material compositions is poorly investigated. This is mainly due to the fact, that these methods are commonly validated in phantom studies utilizing a single anthropomorphic phantom. In this study, we therefore investigate the impact of patient material parameters mapping on the outcome of MC X-ray dose simulations. A computation phantom geometry is constructed and three different commonly used material composition mappings are applied. We used the MC toolkit Geant4 to simulate X-ray radiation in an interventional setup and compared the differences in dose deposition, scatter distributions and resulting X-ray images. The evaluation shows a discrepancy between different material composition mapping up to 20 % concerning directly irradiated organs. These results highlight the need for standardization of material composition mapping for MC simulations in a clinical setup.

physics.med-ph↗

arXiv2020

Tenfold your photons -- a physically-sound approach to filtering-based variance reduction of Monte-Carlo-simulated dose distributions

X-ray dose constantly gains interest in the interventional suite. With dose being generally difficult to monitor reliably, fast computational methods are desirable. A major drawback of the gold standard based on Monte Carlo (MC) methods is its computational complexity. Besides common variance reduction techniques, filter approaches are often applied to achieve conclusive results within a fraction of time. Inspired by these methods, we propose a novel approach. We down-sample the target volume based on the fraction of mass, simulate the imaging situation, and then revert the down-sampling. To this end, the dose is weighted by the mass energy absorption, up-sampled, and distributed using a guided filter. Eventually, the weighting is inverted resulting in accurate high resolution dose distributions. The approach has the potential to considerably speed-up MC simulations since less photons and boundary checks are necessary. First experiments substantiate these assumptions. We achieve a median accuracy of 96.7 % to 97.4 % of the dose estimation with the proposed method and a down-sampling factor of 8 and 4, respectively. While maintaining a high accuracy, the proposed method provides for a tenfold speed-up. The overall findings suggest the conclusion that the proposed method has the potential to allow for further efficiency.

physics.med-ph↗

arXiv2020

Fully-automatic CT data preparation for interventional X-ray skin dose simulation

Recently, deep learning (DL) found its way to interventional X-ray skin dose estimation. While its performance was found to be acceptable, even more accurate results could be achieved if more data sets were available for training. One possibility is to turn to computed tomography (CT) data sets. Typically, computed tomography (CT) scans can be mapped to tissue labels and mass densities to obtain training data. However, care has to be taken to make sure that the different clinical settings are properly accounted for. First, the interventional environment is characterized by wide variety of table setups that are significantly different from the typical patient tables used in conventional CT. This cannot be ignored, since tables play a crucial role in sound skin dose estimation in an interventional setup, e. g., when the X-ray source is directly underneath a patient (posterior-anterior view). Second, due to interpolation errors, most CT scans do not facilitate a clean segmentation of the skin border. As a solution to these problems, we applied connected component labeling (CCL) and Canny edge detection to (a) robustly separate the patient from the table and (b) to identify the outermost skin layer. Our results show that these extensions enable fully-automatic, generalized pre-processing of CT scans for further simulation of both skin dose and corresponding X-ray projections.

physics.med-ph↗

arXiv2020

Pitfalls in interventional X-ray organ dose assessment -- combined experimental and computational phantom study: application to prostatic artery embolization

With X-ray radiation protection and dose management constantly gaining interest in interventional radiology, novel procedures often undergo prospective dose studies using anthropomorphic phantoms to determine expected dose values. Due to inherent uncertainties, these dose values might not allow for patient-specific risk assessment. Therefore, first the aim of this study is to quantify the influence of these parameters on local X-ray dose to evaluate their relevance in the assessment of patient-specific organ doses. Second, this knowledge further enables validating a simulation approach, which allows employing physiological material models and patient-specific geometries. Phantom dosimetry experiments using MOSFET dosimeters were conducted reproducing imaging scenarios in prostatic arterial embolization (PAE). Associated organ-equivalent dose of prostate, bladder, colon and skin was determined. Dose deviation induced by possible small displacements of the patient was reproduced by moving the X-ray source. Dose deviation induced by material differences was investigated by analyzing two different commonly used phantoms. We reconstructed the experiments using Monte Carlo (MC) simulations, a reference male geometry, and different material properties. Overall, MC simulated organ dose values are in accordance with the measured ones for the majority of cases. Marginal displacements of X-ray source relative to the phantoms lead to deviations of 6% to 135% in organ dose values, while skin dose remains relatively constant. Regarding the impact of phantom material composition, underestimation of internal organ dose values by 12% to 20% is prevalent in all simulated phantoms. Skin dose, however, can be estimated with low deviation of 1% to 8% at least for two materials. Prospective reference dose studies might not extend to precise patient-specific dose assessment.

physics.med-ph↗

arXiv2018

Action Learning for 3D Point Cloud Based Organ Segmentation

We propose a novel point cloud based 3D organ segmentation pipeline utilizing deep Q-learning. In order to preserve shape properties, the learning process is guided using a statistical shape model. The trained agent directly predicts piece-wise linear transformations for all vertices in each iteration. This mapping between the ideal transformation for an object outline estimation is learned based on image features. To this end, we introduce aperture features that extract gray values by sampling the 3D volume within the cone centered around the associated vertex and its normal vector. Our approach is also capable of estimating a hierarchical pyramid of non rigid deformations for multi-resolution meshes. In the application phase, we use a marginal approach to gradually estimate affine as well as non-rigid transformations. We performed extensive evaluations to highlight the robust performance of our approach on a variety of challenge data as well as clinical data. Additionally, our method has a run time ranging from 0.3 to 2.7 seconds to segment each organ. In addition, we show that the proposed method can be applied to different organs, X-ray based modalities, and scanning protocols without the need of transfer learning. As we learn actions, even unseen reference meshes can be processed as demonstrated in an example with the Visible Human. From this we conclude that our method is robust, and we believe that our method can be successfully applied to many more applications, in particular, in the interventional imaging space.

cs.CV↗