Weak-signal extraction enabled by deep-neural-network denoising of diffraction data
Physik-Institut, Universität Zürich（苏黎世大学物理研究所）；Department of Physics, The Chinese University of Hong Kong（香港中文大学物理系）；Deutsches Elektronen-Synchrotron DESY（德国电子同步加速器研究所）；AGH University of Science and Technology（AGH科技大学）；Collège de France, PSL University（巴黎文理研究大学法兰西学院）
Jens Oppliger, M. Michael Denner, Julia Küspert, Ruggero Frison, Qisi Wang, Alexander Morawietz, Oleh Ivashko, Ann-Christin Dippel, Martin von Zimmermann, Izabe… 展开作者
Jens Oppliger, M. Michael Denner, Julia Küspert, Ruggero Frison, Qisi Wang, Alexander Morawietz, Oleh Ivashko, Ann-Christin Dippel, Martin von Zimmermann, Izabela Biało, Leonardo Martinelli, Benoît Fauqué, Jaewon Choi, Mirian Garcia-Fernandez, Ke-Jin Zhou, Niels B. Christensen, Tohru Kurosawa, Naoki Momono, Migaku Oda, Fabian D. Natterer, Mark H. Fischer, Titus Neupert, Johan Chang
Removal or cancellation of noise has wide-spread applications for imaging and acoustics. In every-day-life applications, denoising may even include generative aspects, which are unfaithful to the ground truth. For scientific use, however, denoising must reproduce the ground truth accurately. Here, we show how data can be denoised via a deep convolutional neural network such that weak signals appear with quantitative accuracy. In particular, we study X-ray diffraction on crystalline materials. We demonstrate that weak signals stemming from charge ordering, insignificant in the noisy data, become visible and accurate in the denoised data. This success is enabled by supervised training of a deep neural network with pairs of measured low- and high-noise data. We demonstrate that using artificial noise does not yield such quantitatively accurate results. Our approach thus illustrates a practical strategy for noise filtering that can be applied to challenging acquisition problems.
We present a deep neural network to reduce coherent noise in three-dimensional quantitative phase imaging. Inspired by the cycle generative adversarial network, the denoising network was trained to learn a transform between two image domains: clean and noisy refractive index tomograms. The unique feature of this network, distinct from previous machine learning approaches employed in the optical imaging problem, is that it uses unpaired images. The learned network quantitatively demonstrated its performance and generalization capability through denoising experiments of various samples. We concl…
In tomographic reconstruction, the image quality of the reconstructed images can be significantly degraded by defects in the measured two-dimensional (2D) raw image data. Despite the importance of screening defective 2D images for robust tomographic reconstruction, manual inspection and rule-based automation suffer from low-throughput and insufficient accuracy, respectively. Here, we present deep learning-enabled quality control for holographic data to produce robust and high-throughput optical diffraction tomography (ODT). The key idea is to distill the knowledge of an expert into a deep conv…
In this manuscript we demonstrate a method to reconstruct the wavefront of focused beams from a measured diffraction pattern behind a diffracting mask in real-time. The phase problem is solved by means of a neural network, which is trained with simulated data and verified with experimental data. The neural network allows live reconstructions within a few milliseconds, which previously with iterative phase retrieval took several seconds, thus allowing the adjustment of complex systems and correction by adaptive optics in real time. The neural network additionally outperforms iterative phase ret…
Fluorescence microscopy has enabled a dramatic development in modern biology. Due to its inherently weak signal, fluorescence microscopy is not only much noisier than photography, but also presented with Poisson-Gaussian noise where Poisson noise, or shot noise, is the dominating noise source. To get clean fluorescence microscopy images, it is highly desirable to have effective denoising algorithms and datasets that are specifically designed to denoise fluorescence microscopy images. While such algorithms exist, no such datasets are available. In this paper, we fill this gap by constructing a …
Plug-and-Play Priors (PnP) and Regularization by Denoising (RED) are widely-used frameworks for solving imaging inverse problems by computing fixed-points of operators combining physical measurement models and learned image priors. While traditional PnP/RED formulations have focused on priors specified using image denoisers, there is a growing interest in learning PnP/RED priors that are end-to-end optimal. The recent Deep Equilibrium Models (DEQ) framework has enabled memory-efficient end-to-end learning of PnP/RED priors by implicitly differentiating through the fixed-point equations without…
York University（约克大学）；Weizmann Institute of Science（魏茨曼科学研究所）
While deep learning (DL) architectures like convolutional neural networks (CNNs) have enabled effective solutions in image denoising, in general their implementations overly rely on training data, lack interpretability, and require tuning of a large parameter set. In this paper, we combine classical graph signal filtering with deep feature learning into a competitive hybrid design -- one that utilizes interpretable analytical low-pass graph filters and employs 80% fewer network parameters than state-of-the-art DL denoising scheme DnCNN. Specifically, to construct a suitable similarity graph fo…
Two features desired in a three-dimensional (3D) optical tomographic image reconstruction algorithm are the ability to reduce imaging artifacts and to do fast processing of large data volumes. Traditional iterative inversion algorithms are impractical in this context due to their heavy computational and memory requirements. We propose and experimentally validate a novel scalable iterative mini-batch algorithm (SIMBA) for fast and high-quality optical tomographic imaging. SIMBA enables high-quality imaging by combining two complementary information sources: the physics of the imaging system cha…
Max-Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）；Center for Systems Biology Dresden (CSBD)（德累斯顿系统生物学中心）；Fondazione Human Technopole（人类技术城基金会）；Max Planck Institute for the Physics of Complex Systems（马克斯·普朗克复杂系统物理研究所）
Many microscopy applications are limited by the total amount of usable light and are consequently challenged by the resulting levels of noise in the acquired images. This problem is often addressed via (supervised) deep learning based denoising. Recently, by making assumptions about the noise statistics, self-supervised methods have emerged. Such methods are trained directly on the images that are to be denoised and do not require additional paired training data. While achieving remarkable results, self-supervised methods can produce high-frequency artifacts and achieve inferior results compar…
Centrum Wiskunde & Informatica（荷兰国家数学与计算机科学研究中心）；Leiden Institute of Advanced Computer Science, Leiden Universiteit（莱顿大学高级计算机科学研究所）
Recovering a high-quality image from noisy indirect measurements is an important problem with many applications. For such inverse problems, supervised deep convolutional neural network (CNN)-based denoising methods have shown strong results, but the success of these supervised methods critically depends on the availability of a high-quality training dataset of similar measurements. For image denoising, methods are available that enable training without a separate training dataset by assuming that the noise in two different pixels is uncorrelated. However, this assumption does not hold for inve…
The success of ptychographic imaging experiments strongly depends on achieving high signal-to-noise ratio. This is particularly important in nanoscale imaging experiments when diffraction signals are very weak and the experiments are accompanied by significant parasitic scattering (background), outliers or correlated noise sources. It is also critical when rare events such as cosmic rays, or bad frames caused by electronic glitches or shutter timing malfunction take place. In this paper, we propose a novel iterative algorithm with rigorous analysis that exploits the direct forward model for pa…
Low-dose computed tomography (CT) denoising algorithms aim to enable reduced patient dose in routine CT acquisitions while maintaining high image quality. Recently, deep learning~(DL)-based methods were introduced, outperforming conventional denoising algorithms on this task due to their high model capacity. However, for the transition of DL-based denoising to clinical practice, these data-driven approaches must generalize robustly beyond the seen training data. We, therefore, propose a hybrid denoising approach consisting of a set of trainable joint bilateral filters (JBFs) combined with a co…
A Zero-Shot Deep Image Prior Framework for Denoising and Deconvolution in Fluorescence Microscopy
Wenzhou Key Laboratory of Biomedical Imaging（温州生物医学成像重点实验室）；Zhejiang Key Laboratory of Soft Matter Biomedical Materials（浙江软物质生物医学材料重点实验室）；Wenzhou Institute, University of Chinese Academy of Sciences（中国科学院大学温州研究院）；Postgraduate Training Base Alliance of Wenzhou Medical University（温州医学院研究生联合培养基地联盟）
King's College London（伦敦国王学院）；University of Groningen（格罗宁根大学）；University of Ottawa（渥太华大学）；Imperial College London（伦敦帝国理工学院）
Raman spectroscopy enables non-destructive, label-free imaging with unprecedented molecular contrast but is limited by slow data acquisition, largely preventing high-throughput imaging applications. Here, we present a comprehensive framework for higher-throughput molecular imaging via deep learning enabled Raman spectroscopy, termed DeepeR, trained on a large dataset of hyperspectral Raman images, with over 1.5 million spectra (400 hours of acquisition) in total. We firstly perform denoising and reconstruction of low signal-to-noise ratio Raman molecular signatures via deep learning, with a 9x…
Recent development of Under-Display Camera (UDC) systems provides a true bezel-less and notch-free viewing experience on smartphones (and TV, laptops, tablets), while allowing images to be captured from the selfie camera embedded underneath. In a typical UDC system, the microstructure of the semi-transparent organic light-emitting diode (OLED) pixel array attenuates and diffracts the incident light on the camera, resulting in significant image quality degradation. Oftentimes, noise, flare, haze, and blur can be observed in UDC images. In this work, we aim to analyze and tackle the aforemention…
Phase can be reliably estimated from a single diffracted intensity image, if a faithful prior information about the object is available. Examples include amplitude bounds, object support, sparsity in the spatial or a transform domain, deep image prior and the prior learnt from the labelled datasets by a deep neural network. Deep learning facilitates state of art reconstruction quality but requires a large labelled dataset (ground truth-measurement pair acquired in the same experimental conditions) for training. To alleviate this data requirement problem, this letter proposes a zero-shot learni…
