Algorithm-driven Advances for Scientific CT Instruments: From Model-based to Deep Learning-based Approaches

Multi-scale 3D characterization is widely used by materials scientists to further their understanding of the relationships between microscopic structure and macroscopic function. Scientific computed tomography (CT) instruments are one of the most popular choices for 3D non-destructive characterization of materials at length scales ranging from the angstrom-scale to the micron-scale. These instruments typically have a source of radiation that interacts with the sample to be studied and a detector assembly to capture the result of this interaction. A collection of such high-resolution measurements are made by re-orienting the sample which is mounted on a specially designed stage/holder after which reconstruction algorithms are used to produce the final 3D volume of interest. The end goal of scientific CT scans include determining the morphology,chemical composition or dynamic behavior of materials when subjected to external stimuli. In this article, we will present an overview of recent advances in reconstruction algorithms that have enabled significant improvements in the performance of scientific CT instruments - enabling faster, more accurate and novel imaging capabilities. In the first part, we will focus on model-based image reconstruction algorithms that formulate the inversion as solving a high-dimensional optimization problem involving a data-fidelity term and a regularization term. In the last part of the article, we will present an overview of recent approaches using deep-learning based algorithms for improving scientific CT instruments.

Cross-View Regularization for Domain Adaptive Panoptic Segmentation

Panoptic segmentation unifies semantic segmentation and instance segmentation which has been attracting increasing attention in recent years. However, most existing research was conducted under a supervised learning setup whereas unsupervised domain adaptive panoptic segmentation which is critical in different tasks and applications is largely neglected. We design a domain adaptive panoptic segmentation network that exploits inter-style consistency and inter-task regularization for optimal domain adaptive panoptic segmentation. The inter-style consistency leverages geometric invariance across the same image of the different styles which fabricates certain self-supervisions to guide the network to learn domain-invariant features. The inter-task regularization exploits the complementary nature of instance segmentation and semantic segmentation and uses it as a constraint for better feature alignment across domains. Extensive experiments over multiple domain adaptive panoptic segmentation tasks (e.g., synthetic-to-real and real-to-real) show that our proposed network achieves superior segmentation performance as compared with the state-of-the-art.

Underwater Single Image Color Restoration Using Haze-Lines and a New Quantitative Dataset

Underwater images suffer from color distortion and low contrast, because light is attenuated while it propagates through water. Attenuation under water varies with wavelength, unlike terrestrial images where attenuation is assumed to be spectrally uniform. The attenuation depends both on the water body and the 3D structure of the scene, making color restoration difficult. Unlike existing single underwater image enhancement techniques, our method takes into account multiple spectral profiles of different water types. By estimating just two additional global parameters: the attenuation ratios of the blue-red and blue-green color channels, the problem is reduced to single image dehazing, where all color channels have the same attenuation coefficients. Since the water type is unknown, we evaluate different parameters out of an existing library of water types. Each type leads to a different restored image and the best result is automatically chosen based on color distribution. We collected a dataset of images taken in different locations with varying water properties, showing color charts in the scenes. Moreover, to obtain ground truth, the 3D structure of the scene was calculated based on stereo imaging. This dataset enables a quantitative evaluation of restoration algorithms on natural images and shows the advantage of our method.

Generative Adversarial Networks for MR-CT Deformable Image Registration

Deformable Image Registration (DIR) of MR and CT images is one of the most challenging registration task, due to the inherent structural differences of the modalities and the missing dense ground truth. Recently cycle Generative Adversarial Networks (cycle-GANs) have been used to learn the intensity relationship between these 2 modalities for unpaired brain data. Yet its usefulness for DIR was not assessed. In this study we evaluate the DIR performance for thoracic and abdominal organs after synthesis by cycle-GAN. We show that geometric changes, which differentiate the two populations (e.g. inhale vs. exhale), are readily synthesized as well. This causes substantial problems for any application which relies on spatial correspondences being preserved between the real and the synthesized image (e.g. plan, segmentation, landmark propagation). To alleviate this problem, we investigated reducing the spatial information provided to the discriminator by decreasing the size of its receptive fields. Image synthesis was learned from 17 unpaired subjects per modality. Registration performance was evaluated with respect to manual segmentations of 11 structures for 3 subjects from the VISERAL challenge. State-of-the-art DIR methods based on Normalized Mutual Information (NMI), Modality Independent Neighborhood Descriptor (MIND) and their novel combination achieved a mean segmentation overlap ratio of 76.7, 67.7, 76.9%, respectively. This dropped to 69.1% or less when registering images synthesized by cycle-GAN based on local correlation, due to the poor performance on the thoracic region, where large lung volume changes were synthesized. Performance for the abdominal region was similar to that of CT-MRI NMI registration (77.4 vs. 78.8%) when using 3D synthesizing MRIs (12 slices) and medium sized receptive fields for the discriminator.

Image Super-Resolution Using VDSR-ResNeXt and SRCGAN

Over the past decade, many Super Resolution techniques have been developed using deep learning. Among those, generative adversarial networks (GAN) and very deep convolutional networks (VDSR) have shown promising results in terms of HR image quality and computational speed. In this paper, we propose two approaches based on these two algorithms: VDSR-ResNeXt, which is a deep multi-branch convolutional network inspired by VDSR and ResNeXt; and SRCGAN, which is a conditional GAN that explicitly passes class labels as input to the GAN. The two methods were implemented on common SR benchmark datasets for both quantitative and qualitative assessment.

EvoSplit: An evolutionary approach to split a multi-label data set into disjoint subsets

This paper presents a new evolutionary approach, EvoSplit, for the distribution of multi-label data sets into disjoint subsets for supervised machine learning. Currently, data set providers either divide a data set randomly or using iterative stratification, a method that aims to maintain the label (or label pair) distribution of the original data set into the different subsets. Following the same aim, this paper first introduces a single-objective evolutionary approach that tries to obtain a split that maximizes the similarity between those distributions independently. Second, a new multi-objective evolutionary algorithm is presented to maximize the similarity considering simultaneously both distributions (label and label pair). Both approaches are validated using well-known multi-label data sets as well as large image data sets currently used in computer vision and machine learning applications. EvoSplit improves the splitting of a data set in comparison to the iterative stratification following different measures: Label Distribution, Label Pair Distribution, Examples Distribution, folds and fold-label pairs with zero positive examples.

Image Retrieval with Mixed Initiative and Multimodal Feedback

How would you search for a unique, fashionable shoe that a friend wore and you want to buy, but you didn't take a picture? Existing approaches propose interactive image search as a promising venue. However, they either entrust the user with taking the initiative to provide informative feedback, or give all control to the system which determines informative questions to ask. Instead, we propose a mixed-initiative framework where both the user and system can be active participants, depending on whose initiative will be more beneficial for obtaining high-quality search results. We develop a reinforcement learning approach which dynamically decides which of three interaction opportunities to give to the user: drawing a sketch, providing free-form attribute feedback, or answering attribute-based questions. By allowing these three options, our system optimizes both the informativeness and exploration capabilities allowing faster image retrieval. We outperform three baselines on three datasets and extensive experimental settings.

ISP4ML: Understanding the Role of Image Signal Processing in Efficient Deep Learning Vision Systems

Convolutional neural networks (CNNs) are now predominant components in a variety of computer vision (CV) systems. These systems typically include an image signal processor (ISP), even though the ISP is traditionally designed to produce images that look appealing to humans. In CV systems, it is not clear what the role of the ISP is, or if it is even required at all for accurate prediction. In this work, we investigate the efficacy of the ISP in CNN classification tasks, and outline the system-level trade-offs between prediction accuracy and computational cost. To do so, we build software models of a configurable ISP and an imaging sensor in order to train CNNs on ImageNet with a range of different ISP settings and functionality. Results on ImageNet show that an ISP improves accuracy by 4.6%-12.2% on MobileNet architectures of different widths. Results using ResNets demonstrate that these trends also generalize to deeper networks. An ablation study of the various processing stages in a typical ISP reveals that the tone mapper is the most significant stage when operating on high dynamic range (HDR) images, by providing 5.8% average accuracy improvement alone. Overall, the ISP benefits system efficiency because the memory and computational costs of the ISP is minimal compared to the cost of using a larger CNN to achieve the same accuracy.

Embedded Self-Distillation in Compact Multi-Branch Ensemble Network for Remote Sensing Scene Classification

Remote sensing (RS) image scene classification task faces many challenges due to the interference from different characteristics of different geographical elements. To solve this problem, we propose a multi-branch ensemble network to enhance the feature representation ability by fusing features in final output logits and intermediate feature maps. However, simply adding branches will increase the complexity of models and decline the inference efficiency. On this issue, we embed self-distillation (SD) method to transfer knowledge from ensemble network to main-branch in it. Through optimizing with SD, main-branch will have close performance as ensemble network. During inference, we can cut other branches to simplify the whole model. In this paper, we first design compact multi-branch ensemble network, which can be trained in an end-to-end manner. Then, we insert SD method on output logits and feature maps. Compared to previous methods, our proposed architecture (ESD-MBENet) performs strongly on classification accuracy with compact design. Extensive experiments are applied on three benchmark RS datasets AID, NWPU-RESISC45 and UC-Merced with three classic baseline models, VGG16, ResNet50 and DenseNet121. Results prove that our proposed ESD-MBENet can achieve better accuracy than previous state-of-the-art (SOTA) complex models. Moreover, abundant visualization analysis make our method more convincing and interpretable.

DeepTag: An Unsupervised Deep Learning Method for Motion Tracking on Cardiac Tagging Magnetic Resonance Images

Cardiac tagging magnetic resonance imaging (t-MRI) is the gold standard for regional myocardium deformation and cardiac strain estimation. However, this technique has not been widely used in clinical diagnosis, as a result of the difficulty of motion tracking encountered with t-MRI images. In this paper, we propose a novel deep learning-based fully unsupervised method for in vivo motion tracking on t-MRI images. We first estimate the motion field (INF) between any two consecutive t-MRI frames by a bi-directional generative diffeomorphic registration neural network. Using this result, we then estimate the Lagrangian motion field between the reference frame and any other frame through a differentiable composition layer. By utilizing temporal information to perform reasonable estimations on spatio-temporal motion fields, this novel method provides a useful solution for motion tracking and image registration in dynamic medical imaging. Our method has been validated on a representative clinical t-MRI dataset; the experimental results show that our method is superior to conventional motion tracking methods in terms of landmark tracking accuracy and inference efficiency.