Featured Researches

Image And Video Processing

ASIST: Annotation-free Synthetic Instance Segmentation and Tracking by Adversarial Simulations

Background: The quantitative analysis of microscope videos often requires instance segmentation and tracking of cellular and subcellular objects. The traditional method consists of two stages: (1) performing instance object segmentation of each frame, and (2) associating objects frame-by-frame. Recently, pixel-embedding-based deep learning approaches these two steps simultaneously as a single stage holistic solution. In computer vision, annotated training data with consistent segmentation and tracking is resource intensive, the severity of which is multiplied in microscopy imaging due to (1) dense objects (e.g., overlapping or touching), and (2) high dynamics (e.g., irregular motion and mitosis). Adversarial simulations have provided successful solutions to alleviate the lack of such annotations in dynamics scenes in computer vision, such as using simulated environments (e.g., computer games) to train real-world self-driving systems. Methods: In this paper, we propose an annotation-free synthetic instance segmentation and tracking (ASIST) method with adversarial simulation and single-stage pixel-embedding based learning. Contribution: The contribution of this paper is three-fold: (1) the proposed method aggregates adversarial simulations and single-stage pixel-embedding based deep learning; (2) the method is assessed with both the cellular (i.e., HeLa cells) and subcellular (i.e., microvilli) objects; and (3) to the best of our knowledge, this is the first study to explore annotation-free instance segmentation and tracking study for microscope videos. Results: The ASIST method achieved an important step forward, when compared with fully supervised approaches: ASIST shows 7% to 11% higher segmentation, detection and tracking performance on microvilli relative to fully supervised methods, and comparable performance on Hela cell videos.

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Image And Video Processing

Active millimeter wave three-dimensional scan real-time imaging mechanism with a line antenna array

Active Millimeter wave (AMMW) imaging is of interest as it has played important roles in wide variety of applications, from nondestructive test to medical diagnosis. Current AMMW imaging systems have a high spatial resolution and can realize three-dimensional (3D) imaging. However, conventional AMMW imaging systems based on the synthetic aperture require either time-consume acquisition or reconstruction. The AMMW imaging systems based on real-aperture are able to real-time imaging but they need a large aperture and a complex two-dimensional (2D) scan structure to get 3D images. Besides, most AMMW imaging systems need the targets keep still and hold a special posture while screening, limiting the throughput. Here, by using beam control techniques and fast post-processing algorithms, we demonstrate the AMMW 3D scan real-time imaging mechanism with a line antenna array, which can realize 3D real-time imaging by a simple one-dimensional (1D) linear moving, simultaneously, with a satisfactory throughput (over 2000 people per-hour, 10 times than the commercial AMMW imaging systems) and a low system cost. First, the original spherical beam lines generated by the linear antenna array are modulated to fan beam lines via a bi-convex cylindrical lens. Then the holographic imaging algorithm is used to primarily focus the echo data of the imaged object. Finally, the defocus blur is corrected rapidly to get high resolution images by deconvolution. Since our method does not need targets to keep still, has a low system cost, can achieve 3D real-time imaging with a satisfactory throughput simultaneously, this work has the potential to serve as a foundation for future short-range AMMW imaging systems, which can be used in a variety of fields such as security inspection, medical diagnosis, etc.

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Image And Video Processing

Adaptive Debanding Filter

Banding artifacts, which manifest as staircase-like color bands on pictures or video frames, is a common distortion caused by compression of low-textured smooth regions. These false contours can be very noticeable even on high-quality videos, especially when displayed on high-definition screens. Yet, relatively little attention has been applied to this problem. Here we consider banding artifact removal as a visual enhancement problem, and accordingly, we solve it by applying a form of content-adaptive smoothing filtering followed by dithered quantization, as a post-processing module. The proposed debanding filter is able to adaptively smooth banded regions while preserving image edges and details, yielding perceptually enhanced gradient rendering with limited bit-depths. Experimental results show that our proposed debanding filter outperforms state-of-the-art false contour removing algorithms both visually and quantitatively.

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Image And Video Processing

Adaptive Video Configuration and Bitrate Allocation for Teleoperated Vehicles

Vehicles with autonomous driving capabilities are present on public streets. However, edge cases remain that still require a human in-vehicle driver. Assuming the vehicle manages to come to a safe state in an automated fashion, teleoperated driving technology enables a human to resolve the situation remotely by a control interface connected via a mobile network. While this is a promising solution, it also introduces technical challenges, one of them being the necessity to transmit video data of multiple cameras from the vehicle to the human operator. In this paper, an adaptive video streaming framework specifically designed for teleoperated vehicles is proposed and demonstrated. The framework enables automatic reconfiguration of the video streams of the multi-camera system at runtime. Predictions of variable transmission service quality are taken into account. With the objective to improve visual quality, the framework uses so-called rate-quality models to dynamically allocate bitrates and select resolution scaling factors. Results from deploying the proposed framework on an actual teleoperated driving system are presented.

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Image And Video Processing

Adaptively Sparse Regularization for Blind Image Restoration

Image quality is the basis of image communication and understanding tasks. Due to the blur and noise effects caused by imaging, transmission and other processes, the image quality is degraded. Blind image restoration is widely used to improve image quality, where the main goal is to faithfully estimate the blur kernel and the latent sharp image. In this study, based on experimental observation and research, an adaptively sparse regularized minimization method is originally proposed. The high-order gradients combine with low-order ones to form a hybrid regularization term, and an adaptive operator derived from the image entropy is introduced to maintain a good convergence. Extensive experiments were conducted on different blur kernels and images. Compared with existing state-of-the-art blind deblurring methods, our method demonstrates superiority on the recovery accuracy.

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Image And Video Processing

Advances In Video Compression System Using Deep Neural Network: A Review And Case Studies

Significant advances in video compression system have been made in the past several decades to satisfy the nearly exponential growth of Internet-scale video traffic. From the application perspective, we have identified three major functional blocks including pre-processing, coding, and post-processing, that have been continuously investigated to maximize the end-user quality of experience (QoE) under a limited bit rate budget. Recently, artificial intelligence (AI) powered techniques have shown great potential to further increase the efficiency of the aforementioned functional blocks, both individually and jointly. In this article, we review extensively recent technical advances in video compression system, with an emphasis on deep neural network (DNN)-based approaches; and then present three comprehensive case studies. On pre-processing, we show a switchable texture-based video coding example that leverages DNN-based scene understanding to extract semantic areas for the improvement of subsequent video coder. On coding, we present an end-to-end neural video coding framework that takes advantage of the stacked DNNs to efficiently and compactly code input raw videos via fully data-driven learning. On post-processing, we demonstrate two neural adaptive filters to respectively facilitate the in-loop and post filtering for the enhancement of compressed frames. Finally, a companion website hosting the contents developed in this work can be accessed publicly at this https URL.

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Image And Video Processing

Advances in Electron Microscopy with Deep Learning

This doctoral thesis covers some of my advances in electron microscopy with deep learning. Highlights include a comprehensive review of deep learning in electron microscopy; large new electron microscopy datasets for machine learning, dataset search engines based on variational autoencoders, and automatic data clustering by t-distributed stochastic neighbour embedding; adaptive learning rate clipping to stabilize learning; generative adversarial networks for compressed sensing with spiral, uniformly spaced and other fixed sparse scan paths; recurrent neural networks trained to piecewise adapt sparse scan paths to specimens by reinforcement learning; improving signal-to-noise; and conditional generative adversarial networks for exit wavefunction reconstruction from single transmission electron micrographs. This thesis adds to my publications by presenting their relationships, reflections, and holistic conclusions. This version of my thesis is typeset for online dissemination to improve readability, whereas the thesis submitted to the University of Warwick in support of my application for the degree of Doctor of Philosophy in Physics is typeset for physical printing and binding.

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Image And Video Processing

Advancing Eosinophilic Esophagitis Diagnosis and Phenotype Assessment with Deep Learning Computer Vision

Eosinophilic Esophagitis (EoE) is an inflammatory esophageal disease which is increasing in prevalence. The diagnostic gold-standard involves manual review of a patient's biopsy tissue sample by a clinical pathologist for the presence of 15 or greater eosinophils within a single high-power field (400x magnification). Diagnosing EoE can be a cumbersome process with added difficulty for assessing the severity and progression of disease. We propose an automated approach for quantifying eosinophils using deep image segmentation. A U-Net model and post-processing system are applied to generate eosinophil-based statistics that can diagnose EoE as well as describe disease severity and progression. These statistics are captured in biopsies at the initial EoE diagnosis and are then compared with patient metadata: clinical and treatment phenotypes. The goal is to find linkages that could potentially guide treatment plans for new patients at their initial disease diagnosis. A deep image classification model is further applied to discover features other than eosinophils that can be used to diagnose EoE. This is the first study to utilize a deep learning computer vision approach for EoE diagnosis and to provide an automated process for tracking disease severity and progression.

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Image And Video Processing

Adversarial Brain Multiplex Prediction From a Single Network for High-Order Connectional Gender-Specific Brain Mapping

Brain connectivity networks, derived from magnetic resonance imaging (MRI), non-invasively quantify the relationship in function, structure, and morphology between two brain regions of interest (ROIs) and give insights into gender-related connectional differences. However, to the best of our knowledge, studies on gender differences in brain connectivity were limited to investigating pairwise (i.e., low-order) relationship ROIs, overlooking the complex high-order interconnectedness of the brain as a network. To address this limitation, brain multiplexes have been introduced to model the relationship between at least two different brain networks. However, this inhibits their application to datasets with single brain networks such as functional networks. To fill this gap, we propose the first work on predicting brain multiplexes from a source network to investigate gender differences. Recently, generative adversarial networks (GANs) submerged the field of medical data synthesis. However, although conventional GANs work well on images, they cannot handle brain networks due to their non-Euclidean topological structure. Differently, in this paper, we tap into the nascent field of geometric-GANs (G-GAN) to design a deep multiplex prediction architecture comprising (i) a geometric source to target network translator mimicking a U-Net architecture with skip connections and (ii) a conditional discriminator which classifies predicted target intra-layers by conditioning on the multiplex source intra-layers. Such architecture simultaneously learns the latent source network representation and the deep non-linear mapping from the source to target multiplex intra-layers. Our experiments on a large dataset demonstrated that predicted multiplexes significantly boost gender classification accuracy compared with source networks and identifies both low and high-order gender-specific multiplex connections.

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Image And Video Processing

Adversarial Robustness Study of Convolutional Neural Network for Lumbar Disk Shape Reconstruction from MR images

Machine learning technologies using deep neural networks (DNNs), especially convolutional neural networks (CNNs), have made automated, accurate, and fast medical image analysis a reality for many applications, and some DNN-based medical image analysis systems have even been FDA-cleared. Despite the progress, challenges remain to build DNNs as reliable as human expert doctors. It is known that DNN classifiers may not be robust to noises: by adding a small amount of noise to an input image, a DNN classifier may make a wrong classification of the noisy image (i.e., in-distribution adversarial sample), whereas it makes the right classification of the clean image. Another issue is caused by out-of-distribution samples that are not similar to any sample in the training set. Given such a sample as input, the output of a DNN will become meaningless. In this study, we investigated the in-distribution (IND) and out-of-distribution (OOD) adversarial robustness of a representative CNN for lumbar disk shape reconstruction from spine MR images. To study the relationship between dataset size and robustness to IND adversarial attacks, we used a data augmentation method to create training sets with different levels of shape variations. We utilized the PGD-based algorithm for IND adversarial attacks and extended it for OOD adversarial attacks to generate OOD adversarial samples for model testing. The results show that IND adversarial training can improve the CNN robustness to IND adversarial attacks, and larger training datasets may lead to higher IND robustness. However, it is still a challenge to defend against OOD adversarial attacks.

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