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1. Automating Model Generation for Image-Based Cardiac Flow Simulation

   https://doi.org/10.1115/1.4048032  

   Kong, Fanwei ; Shadden, Shawn C. ( November 2020 , Journal of Biomechanical Engineering)

   Abstract Computational fluid dynamics (CFD) modeling of left ventricle (LV) flow combined with patient medical imaging data has shown great potential in obtaining patient-specific hemodynamics information for functional assessment of the heart. A typical model construction pipeline usually starts with segmentation of the LV by manual delineation followed by mesh generation and registration techniques using separate software tools. However, such approaches usually require significant time and human efforts in the model generation process, limiting large-scale analysis. In this study, we propose an approach toward fully automating the model generation process for CFD simulation of LV flow to significantly reduce LVmore »CFD model generation time. Our modeling framework leverages a novel combination of techniques including deep-learning based segmentation, geometry processing, and image registration to reliably reconstruct CFD-suitable LV models with little-to-no user intervention.1 We utilized an ensemble of two-dimensional (2D) convolutional neural networks (CNNs) for automatic segmentation of cardiac structures from three-dimensional (3D) patient images and our segmentation approach outperformed recent state-of-the-art segmentation techniques when evaluated on benchmark data containing both magnetic resonance (MR) and computed tomography(CT) cardiac scans. We demonstrate that through a combination of segmentation and geometry processing, we were able to robustly create CFD-suitable LV meshes from segmentations for 78 out of 80 test cases. Although the focus on this study is on image-to-mesh generation, we demonstrate the feasibility of this framework in supporting LV hemodynamics modeling by performing CFD simulations from two representative time-resolved patient-specific image datasets.« less
2. Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction

   https://doi.org/10.1186/s12859-020-03885-9  

   Al-Azzawi, Adil ; Ouadou, Anes ; Duan, Ye ; Cheng, Jianlin ( December 2020 , BMC Bioinformatics)

   Abstract Background Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D density map of a protein structure. However, low contrast and high noise in particle images make it challenging to build 3D density maps at intermediate to high resolution (1–3 Å). To overcome this problem, we propose a fully automated cryo-EM 3D density map reconstruction approach based on deep learning particle picking. Results A perfect 2D particle mask is fully automatically generated for every single particle. Then, it uses a computermore »vision image alignment algorithm (image registration) to fully automatically align the particle masks. It calculates the difference of the particle image orientation angles to align the original particle image. Finally, it reconstructs a localized 3D density map between every two single-particle images that have the largest number of corresponding features. The localized 3D density maps are then averaged to reconstruct a final 3D density map. The constructed 3D density map results illustrate the potential to determine the structures of the molecules using a few samples of good particles. Also, using the localized particle samples (with no background) to generate the localized 3D density maps can improve the process of the resolution evaluation in experimental maps of cryo-EM. Tested on two widely used datasets, Auto3DCryoMap is able to reconstruct good 3D density maps using only a few thousand protein particle images, which is much smaller than hundreds of thousands of particles required by the existing methods. Conclusions We design a fully automated approach for cryo-EM 3D density maps reconstruction (Auto3DCryoMap). Instead of increasing the signal-to-noise ratio by using 2D class averaging, our approach uses 2D particle masks to produce locally aligned particle images. Auto3DCryoMap is able to accurately align structural particle shapes. Also, it is able to construct a decent 3D density map from only a few thousand aligned particle images while the existing tools require hundreds of thousands of particle images. Finally, by using the pre-processed particle images,Auto3DCryoMap reconstructs a better 3D density map than using the original particle images.« less
3. On cross-correlations, averages and noise in electron microscopy

   https://doi.org/10.1107/S2053230X18014036  

   Radermacher, Michael ; Ruiz, Teresa ( January 2019 , Acta Crystallographica Section F Structural Biology Communications)

   Biological samples are radiation-sensitive and require imaging under low-dose conditions to minimize damage. As a result, images contain a high level of noise and exhibit signal-to-noise ratios that are typically significantly smaller than 1. Averaging techniques, either implicit or explicit, are used to overcome the limitations imposed by the high level of noise. Averaging of 2D images showing the same molecule in the same orientation results in highly significant projections. A high-resolution structure can be obtained by combining the information from many single-particle images to determine a 3D structure. Similarly, averaging of multiple copies of macromolecular assembly subvolumes extracted frommore »tomographic reconstructions can lead to a virtually noise-free high-resolution structure. Cross-correlation methods are often used in the alignment and classification steps of averaging processes for both 2D images and 3D volumes. However, the high noise level can bias alignment and certain classification results. While other approaches may be implicitly affected, sensitivity to noise is most apparent in multireference alignments, 3D reference-based projection alignments and projection-based volume alignments. Here, the influence of the image signal-to-noise ratio on the value of the cross-correlation coefficient is analyzed and a method for compensating for this effect is provided.« less
4. Traffic4D: Single View Longitudinal 4D Reconstruction of Repetitious Activity using Self-Supervised Experts

   Li, Fangyu ; Reddy, N. Dinesh ; Chen, Xudong ; Narasimhan, Srinivasa G. ( July 2021 , IEEE Intelligent Vehicles Symposium)

   Reconstructing 4D vehicular activity (3D space and time) from cameras is useful for autonomous vehicles, commuters and local authorities to plan for smarter and safer cities. Traffic is inherently repetitious over long periods, yet current deep learning-based 3D reconstruction methods have not considered such repetitions and have difficulty generalizing to new intersection-installed cameras. We present a novel approach exploiting longitudinal (long-term) repetitious motion as self-supervision to reconstruct 3D vehicular activity from a video captured by a single fixed camera. Starting from off-the-shelf 2D keypoint detections, our algorithm optimizes 3D vehicle shapes and poses, and then clusters their trajectories in 3Dmore »space. The 2D keypoints and trajectory clusters accumulated over long-term are later used to improve the 2D and 3D keypoints via self-supervision without any human annotation. Our method improves reconstruction accuracy over state of the art on scenes with a significant visual difference from the keypoint detector’s training data, and has many applications including velocity estimation, anomaly detection and vehicle counting. We demonstrate results on traffic videos captured at multiple city intersections, collected using our smartphones, YouTube, and other public datasets.« less
5. Mesh Reconstruction from Aerial Images for Outdoor Terrain Mapping Using Joint 2D-3D Learning

   Feng, Qiaojun ; Atanasov, Nikolay ( January 2021 , IEEE International Conference on Robotics and Automation)

   This paper addresses outdoor terrain mapping using overhead images obtained from an unmanned aerial vehicle. Dense depth estimation from aerial images during flight is challenging. While feature-based localization and mapping techniques can deliver real-time odometry and sparse points reconstruction, a dense environment model is generally recovered offline with significant computation and storage. This paper develops a joint 2D-3D learning approach to reconstruct local meshes at each camera keyframe, which can be assembled into a global environment model. Each local mesh is initialized from sparse depth measurements. We associate image features with the mesh vertices through camera projection and apply graphmore »convolution to refine the mesh vertices based on joint 2-D reprojected depth and 3-D mesh supervision. Quantitative and qualitative evaluations using real aerial images show the potential of our method to support environmental monitoring and surveillance applications.« less