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Register a new userEnd-to-End Simultaneous Learning of Single-particle Orientation and 3D Map Reconstruction from Cryo-electron Microscopy Data
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Cryogenic electron microscopy (cryo-EM) provides images from different copies of the same biomolecule in arbitrary orientations. Here, we present an end-to-end unsupervised approach that learns individual particle orientations from cryo-EM data while reconstructing the average 3D map of the biomolecule, starting from a random initialization. The approach relies on an auto-encoder architecture where the latent space is explicitly interpreted as orientations used by the decoder to form an image according to the linear projection model. We evaluate our method on simulated data and show that it is able to reconstruct 3D particle maps from noisy- and CTF-corrupted 2D projection images of unknown particle orientations.
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Accelerated MRI shortens acquisition time by subsampling in the measurement k-space. Recovering a high-fidelity anatomical image from subsampled measurements requires close cooperation between two components: (1) a sampler that chooses the subsampling pattern and (2) a reconstructor that recovers images from incomplete measurements. In this paper, we leverage the sequential nature of MRI measurements, and propose a fully differentiable framework that jointly learns a sequential sampling policy simultaneously with a reconstruction strategy. This co-designed framework is able to adapt during acquisition in order to capture the most informative measurements for a particular target (Figure 1). Experimental results on the fastMRI knee dataset demonstrate that the proposed approach successfully utilizes intermediate information during the sampling process to boost reconstruction performance. In particular, our proposed method outperforms the current state-of-the-art learned k-space sampling baseline on up to 96.96% of test samples. We also investigate the individual and collective benefits of the sequential sampling and co-design strategies. Code and more visualizations are available at http://imaging.cms.caltech.edu/seq-mri
The slow acquisition speed of magnetic resonance imaging (MRI) has led to the development of two complementary methods: acquiring multiple views of the anatomy simultaneously (parallel imaging) and acquiring fewer samples than necessary for traditional signal processing methods (compressed sensing). While the combination of these methods has the potential to allow much faster scan times, reconstruction from such undersampled multi-coil data has remained an open problem. In this paper, we present a new approach to this problem that extends previously proposed variational methods by learning fully end-to-end. Our method obtains new state-of-the-art results on the fastMRI dataset for both brain and knee MRIs.
Breast CT provides image volumes with isotropic resolution in high contrast, enabling detection of small calcification (down to a few hundred microns in size) and subtle density differences. Since breast is sensitive to x-ray radiation, dose reduction of breast CT is an important topic, and for this purpose, few-view scanning is a main approach. In this article, we propose a Deep Efficient End-to-end Reconstruction (DEER) network for few-view breast CT image reconstruction. The major merits of our network include high dose efficiency, excellent image quality, and low model complexity. By the design, the proposed network can learn the reconstruction process with as few as O(N) parameters, where N is the side length of an image to be reconstructed, which represents orders of magnitude improvements relative to the state-of-the-art deep-learning-based reconstruction methods that map raw data to tomographic images directly. Also, validated on a cone-beam breast CT dataset prepared by Koning Corporation on a commercial scanner, our method demonstrates a competitive performance over the state-of-the-art reconstruction networks in terms of image quality. The source code of this paper is available at: https://github.com/HuidongXie/DEER.
Image compression is one of the most fundamental techniques and commonly used applications in the image and video processing field. Earlier methods built a well-designed pipeline, and efforts were made to improve all modules of the pipeline by handcrafted tuning. Later, tremendous contributions were made, especially when data-driven methods revitalized the domain with their excellent modeling capacities and flexibility in incorporating newly designed modules and constraints. Despite great progress, a systematic benchmark and comprehensive analysis of end-to-end learned image compression methods are lacking. In this paper, we first conduct a comprehensive literature survey of learned image compression methods. The literature is organized based on several aspects to jointly optimize the rate-distortion performance with a neural network, i.e., network architecture, entropy model and rate control. We describe milestones in cutting-edge learned image-compression methods, review a broad range of existing works, and provide insights into their historical development routes. With this survey, the main challenges of image compression methods are revealed, along with opportunities to address the related issues with recent advanced learning methods. This analysis provides an opportunity to take a further step towards higher-efficiency image compression. By introducing a coarse-to-fine hyperprior model for entropy estimation and signal reconstruction, we achieve improved rate-distortion performance, especially on high-resolution images. Extensive benchmark experiments demonstrate the superiority of our model in rate-distortion performance and time complexity on multi-core CPUs and GPUs. Our project website is available at https://huzi96.github.io/compression-bench.html.
One of the core components of conventional (i.e., non-learned) video codecs consists of predicting a frame from a previously-decoded frame, by leveraging temporal correlations. In this paper, we propose an end-to-end learned system for compressing video frames. Instead of relying on pixel-space motion (as with optical flow), our system learns deep embeddings of frames and encodes their difference in latent space. At decoder-side, an attention mechanism is designed to attend to the latent space of frames to decide how different parts of the previous and current frame are combined to form the final predicted current frame. Spatially-varying channel allocation is achieved by using importance masks acting on the feature-channels. The model is trained to reduce the bitrate by minimizing a loss on importance maps and a loss on the probability output by a context model for arithmetic coding. In our experiments, we show that the proposed system achieves high compression rates and high objective visual quality as measured by MS-SSIM and PSNR. Furthermore, we provide ablation studies where we highlight the contribution of different components.
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