Gradient-based geometry learning for fan-beam CT reconstruction.

Objective.Incorporating computed tomography (CT) reconstruction operators into differentiable pipelines has proven beneficial in many applications. Such approaches usually focus on the projection data and keep the acquisition geometry fixed. However, precise knowledge of the acquisition geometry is essential for high quality reconstruction results. In this paper, the differentiable formulation of fan-beam CT reconstruction is extended to the acquisition geometry.Approach.The CT fan-beam reconstruction is analytically derived with respect to the acquisition geometry. This allows to propagate gradient information from a loss function on the reconstructed image into the geometry parameters. As a proof-of-concept experiment, this idea is applied to rigid motion compensation. The cost function is parameterized by a trained neural network which regresses an image quality metric from the motion-affected reconstruction alone.Main results.The algorithm improves the structural similarity index measure (SSIM) from 0.848 for the initial motion-affected reconstruction to 0.946 after compensation. It also generalizes to real fan-beam sinograms which are rebinned from a helical trajectory where the SSIM increases from 0.639 to 0.742.Significance.Using the proposed method, we are the first to optimize an autofocus-inspired algorithm based on analytical gradients. Next to motion compensation, we see further use cases of our differentiable method for scanner calibration or hybrid techniques employing deep models.

SEMPAI: a Self-Enhancing Multi-Photon Artificial Intelligence for Prior-Informed Assessment of Muscle Function and Pathology.

Deep learning (DL) shows notable success in biomedical studies. However, most DL algorithms work as black boxes, exclude biomedical experts, and need extensive data. This is especially problematic for fundamental research in the laboratory, where often only small and sparse data are available and the objective is knowledge discovery rather than automation. Furthermore, basic research is usually hypothesis-driven and extensive prior knowledge (priors) exists. To address this, the Self-Enhancing Multi-Photon Artificial Intelligence (SEMPAI) that is designed for multiphoton microscopy (MPM)-based laboratory research is presented. It utilizes meta-learning to optimize prior (and hypothesis) integration, data representation, and neural network architecture simultaneously. By this, the method allows hypothesis testing with DL and provides interpretable feedback about the origin of biological information in 3D images. SEMPAI performs multi-task learning of several related tasks to enable prediction for small datasets. SEMPAI is applied on an extensive MPM database of single muscle fibers from a decade of experiments, resulting in the largest joint analysis of pathologies and function for single muscle fibers to date. It outperforms state-of-the-art biomarkers in six of seven prediction tasks, including those with scarce data. SEMPAI's DL models with integrated priors are superior to those without priors and to prior-only approaches.

Fast 3D YOLOv3 based standard plane regression of vertebral bodies in intra-operative CBCT volumes.

Purpose: Mobile C-arm systems represent the standard imaging devices within the field of spine surgery. In addition to 2D imaging, they allow for 3D scans while preserving unrestricted patient access. For viewing, the acquired volumes are adjusted such that their anatomical standard planes align with the axes of the viewing modality. This difficult and time-consuming step is currently performed manually by the leading surgeon. This process is automatized within this work to improve the usability of C-arm systems. Thereby, the spinal region consisting of multiple vertebrae and the standard planes of all vertebrae being of interest to the surgeon need to be taken into account. Approach: An object detection algorithm based on the you only look once version 3 architecture, adapted to 3D inputs, is compared with a segmentation-based approach employing a 3D U-Net. Both algorithms are trained on a dataset of 440 and tested on 218 spinal volumes. Results: Although the detection-based algorithm is slightly inferior concerning the detection (91% versus 97% accuracy), localization (1.26 mm versus 0.74 mm error) and alignment accuracy (5.00 deg versus 4.73 deg error), it outperforms the segmentation-based one in terms of speed (5 s versus 38 s). Conclusions: Both algorithms show similar good results. However, the speed gain of the detection-based algorithm, resulting in a run time of 5 s, makes it more suitable for usage in an intra-operative scenario.

Evaluation of perivascular fat attenuation with coronary CT angiography in cardiac transplantation patients: an imaging biomarker candidate for prediction of cardiac mortality and re-transplantation.

OBJECTIVES: In cardiac transplant recipients, non-invasive allograft surveillance for identifying patients at risk for graft failure remains challenging. The fat attenuation index (FAI) of the perivascular adipose tissue in coronary computed tomography angiography (CCTA) predicts outcomes in coronary artery disease in non-transplanted hearts; however, it has not been evaluated in cardiac transplant patients. METHODS: We followed 39 cardiac transplant patients with two or more CCTAs obtained between 2010 and 2021. We performed FAI measurements around the proximal 4 cm segments of the left anterior descending (LAD), right coronary artery (RCA), and left circumflex artery (LCx) using a previously validated methodology. The FAI was analyzed at a threshold of - 30 to - 190 Hounsfield units. RESULTS: FAI measurements were completed in 113 CCTAs, obtained on two same-vendor CT models. Within each CCTA, the FAI values between coronary vessels were strongly correlated (RCA and LAD R = 0.67 (p < 0.0001), RCA and LCx R = 0.58 (p < 0.0001), LAD and LCx R = 0.67 (p < 0.0001)). The FAIs of each coronary vessel between the patient's first and last CCTA completed at 120 kV were also correlated (RCA R = 0.73 (p < 0.0001), LAD R = 0.81 (p < 0.0001), LCx R = 0.55 (p = 0.0069). Finally, a high mean FAI value of all three coronary vessels at baseline (mean ≥ - 71 HU) was predictive of cardiac mortality or re-transplantation, however, not predictive of all cause-mortality. CONCLUSION: High baseline FAI values may identify a higher-risk cardiac transplant population; thus, FAI may support the implementation of CCTA in post-transplant surveillance. KEY POINT: • Perivascular fat attenuation measured with coronary CT is feasible in cardiac transplant patients and may predict cardiac mortality or need for re-transplantation.

How scan parameter choice affects deep learning-based coronary artery disease assessment from computed tomography.

Recently, algorithms capable of assessing the severity of Coronary Artery Disease (CAD) in form of the Coronary Artery Disease-Reporting and Data System (CAD-RADS) grade from Coronary Computed Tomography Angiography (CCTA) scans using Deep Learning (DL) were proposed. Before considering to apply these algorithms in clinical practice, their robustness regarding different commonly used Computed Tomography (CT)-specific image formation parameters-including denoising strength, slab combination, and reconstruction kernel-needs to be evaluated. For this study, we reconstructed a data set of 500 patient CCTA scans under seven image formation parameter configurations. We select one default configuration and evaluate how varying individual parameters impacts the performance and stability of a typical algorithm for automated CAD assessment from CCTA. This algorithm consists of multiple preprocessing and a DL prediction step. We evaluate the influence of the parameter changes on the entire pipeline and additionally on only the DL step by propagating the centerline extraction results of the default configuration to all others. We consider the standard deviation of the CAD severity prediction grade difference between the default and variation configurations to assess the stability w.r.t. parameter changes. For the full pipeline we observe slight instability (± 0.226 CAD-RADS) for all variations. Predictions are more stable with centerlines propagated from the default to the variation configurations (± 0.122 CAD-RADS), especially for differing denoising strengths (± 0.046 CAD-RADS). However, stacking slabs with sharp boundaries instead of mixing slabs in overlapping regions (called true stack ± 0.313 CAD-RADS) and increasing the sharpness of the reconstruction kernel (± 0.150 CAD-RADS) leads to unstable predictions. Regarding the clinically relevant tasks of excluding CAD (called rule-out; AUC default 0.957, min 0.937) and excluding obstructive CAD (called hold-out; AUC default 0.971, min 0.964) the performance remains on a high level for all variations. Concluding, an influence of reconstruction parameters on the predictions is observed. Especially, scans reconstructed with the true stack parameter need to be treated with caution when using a DL-based method. Also, reconstruction kernels which are underrepresented in the training data increase the prediction uncertainty.

Trainable joint bilateral filters for enhanced prediction stability in low-dose CT.

Low-dose computed tomography (CT) denoising algorithms aim to enable reduced patient dose in routine CT acquisitions while maintaining high image quality. Recently, deep learning (DL)-based methods were introduced, outperforming conventional denoising algorithms on this task due to their high model capacity. However, for the transition of DL-based denoising to clinical practice, these data-driven approaches must generalize robustly beyond the seen training data. We, therefore, propose a hybrid denoising approach consisting of a set of trainable joint bilateral filters (JBFs) combined with a convolutional DL-based denoising network to predict the guidance image. Our proposed denoising pipeline combines the high model capacity enabled by DL-based feature extraction with the reliability of the conventional JBF. The pipeline's ability to generalize is demonstrated by training on abdomen CT scans without metal implants and testing on abdomen scans with metal implants as well as on head CT data. When embedding RED-CNN/QAE, two well-established DL-based denoisers in our pipeline, the denoising performance is improved by 10%/82% (RMSE) and 3%/81% (PSNR) in regions containing metal and by 6%/78% (RMSE) and 2%/4% (PSNR) on head CT data, compared to the respective vanilla model. Concluding, the proposed trainable JBFs limit the error bound of deep neural networks to facilitate the applicability of DL-based denoisers in low-dose CT pipelines.

Automatic plane adjustment of orthopedic intraoperative flat panel detector CT-volumes.

Purpose: To assess the result in orthopedic trauma surgery, usually three-dimensional volume data of the treated region is acquired. With mobile C-arm systems, these acquisitions can be performed intraoperatively, reducing the number of required revision surgeries. However, the acquired volumes are typically not aligned to the anatomical regions. Thus, the multiplanar reconstructed (MPR) planes need to be adjusted manually during the review of the volume. To speed up and ease the workflow, an automatic parameterization of these planes is needed. Approach: We present a detailed study of multitask learning (MTL) regression networks to estimate the parameters of the MPR planes. First, various mathematical descriptions for rotation, including Euler angle, quaternion, and matrix representation, are revised. Then, two different MTL network architectures based on the PoseNet are compared with a single task learning network. Results: Using a matrix description rather than the Euler angle description, the accuracy of the regressed normals improves from 7.7 deg to 7.3 deg in the mean value for single anatomies. The multihead approach improves the regression of the plane position from 7.4 to 6.1 mm, whereas the orientation does not benefit from this approach. Thus, the achieved accuracy meets the reported interrater variance in similarly complex body regions of up to 6.3 deg for the normals and up to 9.3 mm for the plane position. Conclusions: The use of a multihead approach with shared features leads to more accurate plane regression compared with the use of individual networks for each task. It also improves the angle estimation for the ankle region. The reported results are in the same range as manual plane adjustments. The use of a combined network with shared parameters requires less memory, which is a great benefit for the implementation of an application for the surgical environment.