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Register a new userLearning to Become an Expert: Deep Networks Applied To Super-Resolution Microscopy
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Louis-\\'Emile Robitaille
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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With super-resolution optical microscopy, it is now possible to observe molecular interactions in living cells. The obtained images have a very high spatial precision but their overall quality can vary a lot depending on the structure of interest and the imaging parameters. Moreover, evaluating this quality is often difficult for non-expert users. In this work, we tackle the problem of learning the quality function of super- resolution images from scores provided by experts. More specifically, we are proposing a system based on a deep neural network that can provide a quantitative quality measure of a STED image of neuronal structures given as input. We conduct a user study in order to evaluate the quality of the predictions of the neural network against those of a human expert. Results show the potential while highlighting some of the limits of the proposed approach.
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Generative Adversarial Networks (GAN) have demonstrated the potential to recover realistic details for single image super-resolution (SISR). To further improve the visual quality of super-resolved results, PIRM2018-SR Challenge employed perceptual metrics to assess the perceptual quality, such as PI, NIQE, and Ma. However, existing methods cannot directly optimize these indifferentiable perceptual metrics, which are shown to be highly correlated with human ratings. To address the problem, we propose Super-Resolution Generative Adversarial Networks with Ranker (RankSRGAN) to optimize generator in the direction of different perceptual metrics. Specifically, we first train a Ranker which can learn the behaviour of perceptual metrics and then introduce a novel rank-content loss to optimize the perceptual quality. The most appealing part is that the proposed method can combine the strengths of different SR methods to generate better results. Furthermore, we extend our method to multiple Rankers to provide multi-dimension constraints for the generator. Extensive experiments show that RankSRGAN achieves visually pleasing results and reaches state-of-the-art performance in perceptual metrics and quality. Project page: https://wenlongzhang0517.github.io/Projects/RankSRGAN
Obtaining magnetic resonance images (MRI) with high resolution and generating quantitative image-based biomarkers for assessing tissue biochemistry is crucial in clinical and research applications. How- ever, acquiring quantitative biomarkers requires high signal-to-noise ratio (SNR), which is at odds with high-resolution in MRI, especially in a single rapid sequence. In this paper, we demonstrate how super-resolution can be utilized to maintain adequate SNR for accurate quantification of the T2 relaxation time biomarker, while simultaneously generating high- resolution images. We compare the efficacy of resolution enhancement using metrics such as peak SNR and structural similarity. We assess accuracy of cartilage T2 relaxation times by comparing against a standard reference method. Our evaluation suggests that SR can successfully maintain high-resolution and generate accurate biomarkers for accelerating MRI scans and enhancing the value of clinical and research MRI.
Matching two different sets of items, called heterogeneous set-to-set matching problem, has recently received attention as a promising problem. The difficulties are to extract features to match a correct pair of different sets and also preserve two types of exchangeability required for set-to-set matching: the pair of sets, as well as the items in each set, should be exchangeable. In this study, we propose a novel deep learning architecture to address the abovementioned difficulties and also an efficient training framework for set-to-set matching. We evaluate the methods through experiments based on two industrial applications: fashion set recommendation and group re-identification. In these experiments, we show that the proposed method provides significant improvements and results compared with the state-of-the-art methods, thereby validating our architecture for the heterogeneous set matching problem.
Volumetric imaging by fluorescence microscopy is often limited by anisotropic spatial resolution from inferior axial resolution compared to the lateral resolution. To address this problem, here we present a deep-learning-enabled unsupervised super-resolution technique that enhances anisotropic images in volumetric fluorescence microscopy. In contrast to the existing deep learning approaches that require matched high-resolution target volume images, our method greatly reduces the effort to put into practice as the training of a network requires as little as a single 3D image stack, without a priori knowledge of the image formation process, registration of training data, or separate acquisition of target data. This is achieved based on the optimal transport driven cycle-consistent generative adversarial network that learns from an unpaired matching between high-resolution 2D images in lateral image plane and low-resolution 2D images in the other planes. Using fluorescence confocal microscopy and light-sheet microscopy, we demonstrate that the trained network not only enhances axial resolution, but also restores suppressed visual details between the imaging planes and removes imaging artifacts.
Fluorescence microscopy has enabled a dramatic development in modern biology by visualizing biological organisms with micrometer scale resolution. However, due to the diffraction limit, sub-micron/nanometer features are difficult to resolve. While various super-resolution techniques are developed to achieve nanometer-scale resolution, they often either require expensive optical setup or specialized fluorophores. In recent years, deep learning has shown the potentials to reduce the technical barrier and obtain super-resolution from diffraction-limited images. For accurate results, conventional deep learning techniques require thousands of images as a training dataset. Obtaining large datasets from biological samples is not often feasible due to the photobleaching of fluorophores, phototoxicity, and dynamic processes occurring within the organism. Therefore, achieving deep learning-based super-resolution using small datasets is challenging. We address this limitation with a new convolutional neural network-based approach that is successfully trained with small datasets and achieves super-resolution images. We captured 750 images in total from 15 different field-of-views as the training dataset to demonstrate the technique. In each FOV, a single target image is generated using the super-resolution radial fluctuation method. As expected, this small dataset failed to produce a usable model using traditional super-resolution architecture. However, using the new approach, a network can be trained to achieve super-resolution images from this small dataset. This deep learning model can be applied to other biomedical imaging modalities such as MRI and X-ray imaging, where obtaining large training datasets is challenging.
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