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The state and behaviour of a cell can be influenced by both genetic and environmental factors. In particular, tumour progression is determined by underlying genetic aberrations1-4 as well as the makeup of the tumour microenvironment5,6. Quantifying the contributions of these factors requires new technologies that can accurately measure the spatial location of genomic sequence together with phenotypic readouts. Here we developed slide-DNA-seq, a method for capturing spatially resolved DNA sequences from intact tissue sections. We demonstrate that this method accurately preserves local tumour architecture and enables the de novo discovery of distinct tumour clones and their copy number alterations. We then apply slide-DNA-seq to a mouse model of metastasis and a primary human cancer, revealing that clonal populations are confined to distinct spatial regions. Moreover, through integration with spatial transcriptomics, we uncover distinct sets of genes that are associated with clone-specific genetic aberrations, the local tumour microenvironment, or both. Together, this multi-modal spatial genomics approach provides a versatile platform for quantifying how cell-intrinsic and cell-extrinsic factors contribute to gene expression, protein abundance and other cellular phenotypes.

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships among cells. mtDNA can be profiled along with measures of cell state, but has not yet been combined with the massively parallel approaches needed to tackle the complexity of human tissue. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), a method that combines high-confidence mtDNA mutation calling in thousands of single cells with their concomitant high-quality accessible chromatin profile. This enables the inference of mtDNA heteroplasmy, clonal relationships, cell state and accessible chromatin variation in individual cells. We reveal single-cell variation in heteroplasmy of a pathologic mtDNA variant, which we associate with intra-individual chromatin variability and clonal evolution. We clonally trace thousands of cells from cancers, linking epigenomic variability to subclonal evolution, and infer cellular dynamics of differentiating hematopoietic cells in vitro and in vivo. Taken together, our approach enables the study of cellular population dynamics and clonal properties in vivo.

This paper reviews the NTIRE 2020 challenge on real world super-resolution. It focuses on the participating methods and final results. The challenge addresses the real world setting, where paired true high and low-resolution images are unavailable. For training, only one set of source input images is therefore provided along with a set of unpaired high-quality target images. In Track 1: Image Processing artifacts, the aim is to super-resolve images with synthetically generated image processing artifacts. This allows for quantitative benchmarking of the approaches \wrt a ground-truth image. In Track 2: Smartphone Images, real low-quality smart phone images have to be super-resolved. In both tracks, the ultimate goal is to achieve the best perceptual quality, evaluated using a human study. This is the second challenge on the subject, following AIM 2019, targeting to advance the state-of-the-art in super-resolution. To measure the performance we use the benchmark protocol from AIM 2019. In total 22 teams competed in the final testing phase, demonstrating new and innovative solutions to the problem.

This paper reviews the NTIRE 2020 challenge on perceptual extreme super-resolution with focus on proposed solutions and results. The challenge task was to super-resolve an input image with a magnification factor 16 based on a set of prior examples of low and corresponding high resolution images. The goal is to obtain a network design capable to produce high resolution results with the best perceptual quality and similar to the ground truth. The track had 280 registered participants, and 19 teams submitted the final results. They gauge the state-of-the-art in single image super-resolution., Comment: CVPRW 2020

Vehicle re-identification (reID) plays an important role in the automatic analysis of the increasing urban surveillance videos, which has become a hot topic in recent years. However, it poses the critical but challenging problem that is caused by various viewpoints of vehicles, diversified illuminations and complicated environments. Till now, most existing vehicle reID approaches focus on learning metrics or ensemble to derive better representation, which are only take identity labels of vehicle into consideration. However, the attributes of vehicle that contain detailed descriptions are beneficial for training reID model. Hence, this paper proposes a novel Attribute-Guided Network (AGNet), which could learn global representation with the abundant attribute features in an end-to-end manner. Specially, an attribute-guided module is proposed in AGNet to generate the attribute mask which could inversely guide to select discriminative features for category classification. Besides that, in our proposed AGNet, an attribute-based label smoothing (ALS) loss is presented to better train the reID model, which can strength the distinct ability of vehicle reID model to regularize AGNet model according to the attributes. Comprehensive experimental results clearly demonstrate that our method achieves excellent performance on both VehicleID dataset and VeRi-776 dataset., Comment: arXiv admin note: text overlap with arXiv:1912.10193

We review the AIM 2020 challenge on virtual image relighting and illumination estimation. This paper presents the novel VIDIT dataset used in the challenge and the different proposed solutions and final evaluation results over the 3 challenge tracks. The first track considered one-to-one relighting; the objective was to relight an input photo of a scene with a different color temperature and illuminant orientation (i.e., light source position). The goal of the second track was to estimate illumination settings, namely the color temperature and orientation, from a given image. Lastly, the third track dealt with any-to-any relighting, thus a generalization of the first track. The target color temperature and orientation, rather than being pre-determined, are instead given by a guide image. Participants were allowed to make use of their track 1 and 2 solutions for track 3. The tracks had 94, 52, and 56 registered participants, respectively, leading to 20 confirmed submissions in the final competition stage., Comment: ECCVW 2020. Data and more information on https://github.com/majedelhelou/VIDIT

This paper introduces the real image Super-Resolution (SR) challenge that was part of the Advances in Image Manipulation (AIM) workshop, held in conjunction with ECCV 2020. This challenge involves three tracks to super-resolve an input image for $\times$2, $\times$3 and $\times$4 scaling factors, respectively. The goal is to attract more attention to realistic image degradation for the SR task, which is much more complicated and challenging, and contributes to real-world image super-resolution applications. 452 participants were registered for three tracks in total, and 24 teams submitted their results. They gauge the state-of-the-art approaches for real image SR in terms of PSNR and SSIM.

This paper reviews the AIM 2020 challenge on efficient single image super-resolution with focus on the proposed solutions and results. The challenge task was to super-resolve an input image with a magnification factor x4 based on a set of prior examples of low and corresponding high resolution images. The goal is to devise a network that reduces one or several aspects such as runtime, parameter count, FLOPs, activations, and memory consumption while at least maintaining PSNR of MSRResNet. The track had 150 registered participants, and 25 teams submitted the final results. They gauge the state-of-the-art in efficient single image super-resolution.

This paper reviews the video extreme super-resolution challenge associated with the AIM 2020 workshop at ECCV 2020. Common scaling factors for learned video super-resolution (VSR) do not go beyond factor 4. Missing information can be restored well in this region, especially in HR videos, where the high-frequency content mostly consists of texture details. The task in this challenge is to upscale videos with an extreme factor of 16, which results in more serious degradations that also affect the structural integrity of the videos. A single pixel in the low-resolution (LR) domain corresponds to 256 pixels in the high-resolution (HR) domain. Due to this massive information loss, it is hard to accurately restore the missing information. Track 1 is set up to gauge the state-of-the-art for such a demanding task, where fidelity to the ground truth is measured by PSNR and SSIM. Perceptually higher quality can be achieved in trade-off for fidelity by generating plausible high-frequency content. Track 2 therefore aims at generating visually pleasing results, which are ranked according to human perception, evaluated by a user study. In contrast to single image super-resolution (SISR), VSR can benefit from additional information in the temporal domain. However, this also imposes an additional requirement, as the generated frames need to be consistent along time.

This paper is the report of the first Under-Display Camera (UDC) image restoration challenge in conjunction with the RLQ workshop at ECCV 2020. The challenge is based on a newly-collected database of Under-Display Camera. The challenge tracks correspond to two types of display: a 4k Transparent OLED (T-OLED) and a phone Pentile OLED (P-OLED). Along with about 150 teams registered the challenge, eight and nine teams submitted the results during the testing phase for each track. The results in the paper are state-of-the-art restoration performance of Under-Display Camera Restoration. Datasets and paper are available at https://yzhouas.github.io/projects/UDC/udc.html., Comment: 15 pages

info:eu-repo/semantics/published

Vehicle re-identification (reID) often requires recognize a target vehicle in large datasets captured from multi-cameras. It plays an important role in the automatic analysis of the increasing urban surveillance videos, which has become a hot topic in recent years. However, the appearance of vehicle images is easily affected by the environment that various illuminations, different backgrounds and viewpoints, which leads to the large bias between different cameras. To address this problem, this paper proposes a cross-camera adaptation framework (CCA), which smooths the bias by exploiting the common space between cameras for all samples. CCA first transfers images from multi-cameras into one camera to reduce the impact of the illumination and resolution, which generates the samples with the similar distribution. Then, to eliminate the influence of background and focus on the valuable parts, we propose an attention alignment network (AANet) to learn powerful features for vehicle reID. Specially, in AANet, the spatial transfer network with attention module is introduced to locate a series of the most discriminative regions with high-attention weights and suppress the background. Moreover, comprehensive experimental results have demonstrated that our proposed CCA can achieve excellent performances on benchmark datasets VehicleID and VeRi-776.

Recently, the progress of learning-by-synthesis has proposed a training model for synthetic images, which can effectively reduce the cost of human and material resources. However, due to the different distribution of synthetic images compared with real images, the desired performance cannot be achieved. To solve this problem, the previous method learned a model to improve the realism of the synthetic images. Different from the previous methods, this paper try to purify real image by extracting discriminative and robust features to convert outdoor real images to indoor synthetic images. In this paper, we first introduce the segmentation masks to construct RGB-mask pairs as inputs, then we design a mask-guided style transfer network to learn style features separately from the attention and bkgd(background) regions and learn content features from full and attention region. Moreover, we propose a novel region-level task-guided loss to restrain the features learnt from style and content. Experiments were performed using mixed studies (qualitative and quantitative) methods to demonstrate the possibility of purifying real images in complex directions. We evaluate the proposed method on various public datasets, including LPW, COCO and MPIIGaze. Experimental results show that the proposed method is effective and achieves the state-of-the-art results., Comment: arXiv admin note: substantial text overlap with arXiv:1903.05820

Vehicle re-identification (reID) is to identify a target vehicle in different cameras with non-overlapping views. When deploy the well-trained model to a new dataset directly, there is a severe performance drop because of differences among datasets named domain bias. To address this problem, this paper proposes an domain adaptation framework which contains an image-to-image translation network named vehicle transfer generative adversarial network (VTGAN) and an attention-based feature learning network (ATTNet). VTGAN could make images from the source domain (well-labeled) have the style of target domain (unlabeled) and preserve identity information of source domain. To further improve the domain adaptation ability for various backgrounds, ATTNet is proposed to train generated images with the attention structure for vehicle reID. Comprehensive experimental results clearly demonstrate that our method achieves excellent performance on VehicleID dataset.

Recently, the progress of learning-by-synthesis has proposed a training model for synthetic images, which can effectively reduce the cost of human and material resources. However, due to the different distribution of synthetic images compared to real images, the desired performance cannot still be achieved. Real images consist of multiple forms of light orientation, while synthetic images consist of a uniform light orientation. These features are considered to be characteristic of outdoor and indoor scenes, respectively. To solve this problem, the previous method learned a model to improve the realism of the synthetic image. Different from the previous methods, this paper takes the first step to purify real images. Through the style transfer task, the distribution of outdoor real images is converted into indoor synthetic images, thereby reducing the influence of light. Therefore, this paper proposes a real-time style transfer network that preserves image content information (eg, gaze direction, pupil center position) of an input image (real image) while inferring style information (eg, image color structure, semantic features) of style image (synthetic image). In addition, the network accelerates the convergence speed of the model and adapts to multi-scale images. Experiments were performed using mixed studies (qualitative and quantitative) methods to demonstrate the possibility of purifying real images in complex directions. Qualitatively, it compares the proposed method with the available methods in a series of indoor and outdoor scenarios of the LPW dataset. In quantitative terms, it evaluates the purified image by training a gaze estimation model on the cross data set. The results show a significant improvement over the baseline method compared to the raw real image.

In Autonomous Driving (AD), detection and tracking of obstacles on the roads is a critical task. Deep-learning based methods using annotated LiDAR data have been the most widely adopted approach for this. Unfortunately, annotating 3D point cloud is a very challenging, time- and money-consuming task. In this paper, we propose a novel LiDAR simulator that augments real point cloud with synthetic obstacles (e.g., cars, pedestrians, and other movable objects). Unlike previous simulators that entirely rely on CG models and game engines, our augmented simulator bypasses the requirement to create high-fidelity background CAD models. Instead, we can simply deploy a vehicle with a LiDAR scanner to sweep the street of interests to obtain the background point cloud, based on which annotated point cloud can be automatically generated. This unique "scan-and-simulate" capability makes our approach scalable and practical, ready for large-scale industrial applications. In this paper, we describe our simulator in detail, in particular the placement of obstacles that is critical for performance enhancement. We show that detectors with our simulated LiDAR point cloud alone can perform comparably (within two percentage points) with these trained with real data. Mixing real and simulated data can achieve over 95% accuracy., Comment: 10 pages

We describe a novel learning-by-synthesis method for estimating gaze direction of an automated intelligent surveillance system. Recently, progress in learning-by-synthesis has proposed training models on synthetic images, which can effectively reduce the cost of manpower and material resources. However, learning from synthetic images still fails to achieve the desired performance compared to naturalistic images due to the different distribution of synthetic images. In an attempt to address this issue, previous method is to improve the realism of synthetic images by learning a model. However, the disadvantage of the method is that the distortion has not been improved and the authenticity level is unstable. To solve this problem, we put forward a new structure to improve synthetic images, via the reference to the idea of style transformation, through which we can efficiently reduce the distortion of pictures and minimize the need of real data annotation. We estimate that this enables generation of highly realistic images, which we demonstrate both qualitatively and with a user study. We quantitatively evaluate the generated images by training models for gaze estimation. We show a significant improvement over using synthetic images, and achieve state-of-the-art results on various datasets including MPIIGaze dataset., Comment: Submit to the journal of Pattern Recognition Letters