Optical diffraction tomography (ODT) is an emerging 3D imaging technique that is used for the 3D reconstruction of the refractive index (RI) for semi-transparent samples. Various inverse models have been proposed to reconstruct the 3D RI based on the holographic detection of different samples such as the Born and the Rytov approximations. However, such approximations usually suffer from the so-called missing-cone problem that results in an elongation of the final reconstruction along the optical axis. Different iterative schemes have been proposed to solve the missing cone problem relying on physical forward models and an error function that aims at filling in the k-space and thus eliminating the missing-cone problem and reaching better reconstruction accuracy. In this paper, we propose a different approach where a 3D neural network (NN) is employed. The NN is trained with a cost function derived from a physical model based on the physics of optical wave propagation. The 3D NN starts with an initial guess for the 3D RI reconstruction (i.e. Born, or Rytov) and aims at reconstructing better 3D reconstruction based on an error function. With this technique, the NN can be trained without any examples of the relation between the ill-posed reconstruction (Born or Rytov) and the ground truth (true shape).
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We develop a new type of model for solving the task of inverting the transmission effects of multi-mode optical fibres through the construction of an $\mathrm{SO}^{+}(2,1)$-equivariant neural network. This model takes advantage of the of the azimuthal correlations known to exist in fibre speckle patterns and naturally accounts for the difference in spatial arrangement between input and speckle patterns. In addition, we use a second post-processing network to remove circular artifacts, fill gaps, and sharpen the images, which is required due to the nature of optical fibre transmission. This two stage approach allows for the inspection of the predicted images produced by the more robust physically motivated equivariant model, which could be useful in a safety-critical application, or by the output of both models, which produces high quality images. Further, this model can scale to previously unachievable resolutions of imaging with multi-mode optical fibres and is demonstrated on $256 \times 256$ pixel images. This is a result of improving the trainable parameter requirement from $\mathcal{O}(N^4)$ to $\mathcal{O}(m)$, where $N$ is pixel size and $m$ is number of fibre modes. Finally, this model generalises to new images, outside of the set of training data classes, better than previous models.
Retinal Optical Coherence Tomography Angiography (OCTA) with high-resolution is important for the quantification and analysis of retinal vasculature. However, the resolution of OCTA images is inversely proportional to the field of view at the same sampling frequency, which is not conducive to clinicians for analyzing larger vascular areas. In this paper, we propose a novel Sparse-based domain Adaptation Super-Resolution network (SASR) for the reconstruction of realistic 6x6 mm2/low-resolution (LR) OCTA images to high-resolution (HR) representations. To be more specific, we first perform a simple degradation of the 3x3 mm2/high-resolution (HR) image to obtain the synthetic LR image. An efficient registration method is then employed to register the synthetic LR with its corresponding 3x3 mm2 image region within the 6x6 mm2 image to obtain the cropped realistic LR image. We then propose a multi-level super-resolution model for the fully-supervised reconstruction of the synthetic data, guiding the reconstruction of the realistic LR images through a generative-adversarial strategy that allows the synthetic and realistic LR images to be unified in the feature domain. Finally, a novel sparse edge-aware loss is designed to dynamically optimize the vessel edge structure. Extensive experiments on two OCTA sets have shown that our method performs better than state-of-the-art super-resolution reconstruction methods. In addition, we have investigated the performance of the reconstruction results on retina structure segmentations, which further validate the effectiveness of our approach.
Accurately modeling quadrotor's system dynamics is critical for guaranteeing agile, safe, and stable navigation. The model needs to capture the system behavior in multiple flight regimes and operating conditions, including those producing highly nonlinear effects such as aerodynamic forces and torques, rotor interactions, or possible system configuration modifications. Classical approaches rely on handcrafted models and struggle to generalize and scale to capture these effects. In this paper, we present a novel Physics-Inspired Temporal Convolutional Network (PI-TCN) approach to learning quadrotor's system dynamics purely from robot experience. Our approach combines the expressive power of sparse temporal convolutions and dense feed-forward connections to make accurate system predictions. In addition, physics constraints are embedded in the training process to facilitate the network's generalization capabilities to data outside the training distribution. Finally, we design a model predictive control approach that incorporates the learned dynamics for accurate closed-loop trajectory tracking fully exploiting the learned model predictions in a receding horizon fashion. Experimental results demonstrate that our approach accurately extracts the structure of the quadrotor's dynamics from data, capturing effects that would remain hidden to classical approaches. To the best of our knowledge, this is the first time physics-inspired deep learning is successfully applied to temporal convolutional networks and to the system identification task, while concurrently enabling predictive control.
We propose FiberNet, a method to estimate \emph{in-vivo} the cardiac fiber architecture of the human atria from multiple catheter recordings of the electrical activation. Cardiac fibers play a central role in the electro-mechanical function of the heart, yet they are difficult to determine in-vivo, and hence rarely truly patient-specific in existing cardiac models. FiberNet learns the fiber arrangement by solving an inverse problem with physics-informed neural networks. The inverse problem amounts to identifying the conduction velocity tensor of a cardiac propagation model from a set of sparse activation maps. The use of multiple maps enables the simultaneous identification of all the components of the conduction velocity tensor, including the local fiber angle. We extensively test FiberNet on synthetic 2-D and 3-D examples, diffusion tensor fibers, and a patient-specific case. We show that 3 maps are sufficient to accurately capture the fibers, also in the presence of noise. With fewer maps, the role of regularization becomes prominent. Moreover, we show that the fitted model can robustly reproduce unseen activation maps. We envision that FiberNet will help the creation of patient-specific models for personalized medicine. The full code is available at //github.com/fsahli/FiberNet.
Fasteners play a critical role in securing various parts of machinery. Deformations such as dents, cracks, and scratches on the surface of fasteners are caused by material properties and incorrect handling of equipment during production processes. As a result, quality control is required to ensure safe and reliable operations. The existing defect inspection method relies on manual examination, which consumes a significant amount of time, money, and other resources; also, accuracy cannot be guaranteed due to human error. Automatic defect detection systems have proven impactful over the manual inspection technique for defect analysis. However, computational techniques such as convolutional neural networks (CNN) and deep learning-based approaches are evolutionary methods. By carefully selecting the design parameter values, the full potential of CNN can be realised. Using Taguchi-based design of experiments and analysis, an attempt has been made to develop a robust automatic system in this study. The dataset used to train the system has been created manually for M14 size nuts having two labeled classes: Defective and Non-defective. There are a total of 264 images in the dataset. The proposed sequential CNN comes up with a 96.3% validation accuracy, 0.277 validation loss at 0.001 learning rate.
Implicit neural representations have shown compelling results in offline 3D reconstruction and also recently demonstrated the potential for online SLAM systems. However, applying them to autonomous 3D reconstruction, where robots are required to explore a scene and plan a view path for the reconstruction, has not been studied. In this paper, we explore for the first time the possibility of using implicit neural representations for autonomous 3D scene reconstruction by addressing two key challenges: 1) seeking a criterion to measure the quality of the candidate viewpoints for the view planning based on the new representations, and 2) learning the criterion from data that can generalize to different scenes instead of hand-crafting one. For the first challenge, a proxy of Peak Signal-to-Noise Ratio (PSNR) is proposed to quantify a viewpoint quality. The proxy is acquired by treating the color of a spatial point in a scene as a random variable under a Gaussian distribution rather than a deterministic one; the variance of the distribution quantifies the uncertainty of the reconstruction and composes the proxy. For the second challenge, the proxy is optimized jointly with the parameters of an implicit neural network for the scene. With the proposed view quality criterion, we can then apply the new representations to autonomous 3D reconstruction. Our method demonstrates significant improvements on various metrics for the rendered image quality and the geometry quality of the reconstructed 3D models when compared with variants using TSDF or reconstruction without view planning.
Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.
A variety of deep neural networks have been applied in medical image segmentation and achieve good performance. Unlike natural images, medical images of the same imaging modality are characterized by the same pattern, which indicates that same normal organs or tissues locate at similar positions in the images. Thus, in this paper we try to incorporate the prior knowledge of medical images into the structure of neural networks such that the prior knowledge can be utilized for accurate segmentation. Based on this idea, we propose a novel deep network called knowledge-based fully convolutional network (KFCN) for medical image segmentation. The segmentation function and corresponding error is analyzed. We show the existence of an asymptotically stable region for KFCN which traditional FCN doesn't possess. Experiments validate our knowledge assumption about the incorporation of prior knowledge into the convolution kernels of KFCN and show that KFCN can achieve a reasonable segmentation and a satisfactory accuracy.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
Image segmentation is still an open problem especially when intensities of the interested objects are overlapped due to the presence of intensity inhomogeneity (also known as bias field). To segment images with intensity inhomogeneities, a bias correction embedded level set model is proposed where Inhomogeneities are Estimated by Orthogonal Primary Functions (IEOPF). In the proposed model, the smoothly varying bias is estimated by a linear combination of a given set of orthogonal primary functions. An inhomogeneous intensity clustering energy is then defined and membership functions of the clusters described by the level set function are introduced to rewrite the energy as a data term of the proposed model. Similar to popular level set methods, a regularization term and an arc length term are also included to regularize and smooth the level set function, respectively. The proposed model is then extended to multichannel and multiphase patterns to segment colourful images and images with multiple objects, respectively. It has been extensively tested on both synthetic and real images that are widely used in the literature and public BrainWeb and IBSR datasets. Experimental results and comparison with state-of-the-art methods demonstrate that advantages of the proposed model in terms of bias correction and segmentation accuracy.
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