Microscopy imaging is vital in biology research and diagnosis. When imaging at the scale of cell or molecule level, mechanical drift on the axial axis can be difficult to correct. Although multi-scale networks have been developed for deblurring, those cascade residual learning approaches fail to accurately capture the end-to-end non-linearity of deconvolution, a relation between in-focus images and their out-of-focus counterparts in microscopy. In our model, we adopt a structure of multi-scale U-Net without cascade residual leaning. Additionally, in contrast to the conventional coarse-to-fine model, our model strengthens the cross-scale interaction by fusing the features from the coarser sub-networks with the finer ones in a head-to-tail manner: the decoder from the coarser scale is fused with the encoder of the finer ones. Such interaction contributes to better feature learning as fusion happens across decoder and encoder at all scales. Numerous experiments demonstrate that our method yields better performance when compared with other existing models.
We propose a novel end-to-end learning-based approach for single image defocus deblurring. The proposed approach is equipped with a novel Iterative Filter Adaptive Network (IFAN) that is specifically designed to handle spatially-varying and large defocus blur. For adaptively handling spatially-varying blur, IFAN predicts pixel-wise deblurring filters, which are applied to defocused features of an input image to generate deblurred features. For effectively managing large blur, IFAN models deblurring filters as stacks of small-sized separable filters. Predicted separable deblurring filters are a…
Tohoku University（东北大学）；RIKEN Center for AIP（理化学研究所人工智能中心）
In this paper, we consider the problem in defocus image deblurring. Previous classical methods follow two-steps approaches, i.e., first defocus map estimation and then the non-blind deblurring. In the era of deep learning, some researchers have tried to address these two problems by CNN. However, the simple concatenation of defocus map, which represents the blur level, leads to suboptimal performance. Considering the spatial variant property of the defocus blur and the blur level indicated in the defocus map, we employ the defocus map as conditional guidance to adjust the features from the inp…
City University of Hong Kong（香港城市大学）；Max-Planck-Institut für Informatik（马克斯·普朗克信息学研究所）；Stanford University（斯坦福大学）
Defocus deblurring is a challenging task due to the spatially varying nature of defocus blur. While deep learning approach shows great promise in solving image restoration problems, defocus deblurring demands accurate training data that consists of all-in-focus and defocus image pairs, which is difficult to collect. Naive two-shot capturing cannot achieve pixel-wise correspondence between the defocused and all-in-focus image pairs. Synthetic aperture of light fields is suggested to be a more reliable way to generate accurate image pairs. However, the defocus blur generated from light field dat…
Harbin Institute of Technology（哈尔滨工业大学）；Wuhan University（武汉大学）
The defocus deblurring raised from the finite aperture size and exposure time is an essential problem in the computational photography. It is very challenging because the blur kernel is spatially varying and difficult to estimate by traditional methods. Due to its great breakthrough in low-level tasks, convolutional neural networks (CNNs) have been introduced to the defocus deblurring problem and achieved significant progress. However, they apply the same kernel for different regions of the defocus blurred images, thus it is difficult to handle these nonuniform blurred images. To this end, thi…
Depth Estimation and Image Restoration by Deep Learning from Defocused Images
CEOSpaceTech；University POLITEHNICA of Bucharest（布加勒斯特理工大学）；Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS)（智能技术卓越研究中心（CiTIUS））；University of Santiago de Compostela（圣地亚哥德孔波斯特拉大学）
Trinity College Dublin（都柏林圣三一学院）；ADAPT: SFI Centre for Digital Media Technology（ADAPT：SFI数字媒体技术中心）；Federal University of Rio Grande Do Sul（南里奥格兰德联邦大学）
Defocus blur is a physical consequence of the optical sensors used in most cameras. Although it can be used as a photographic style, it is commonly viewed as an image degradation modeled as the convolution of a sharp image with a spatially-varying blur kernel. Motivated by the advance of blur estimation methods in the past years, we propose a non-blind approach for image deblurring that can deal with spatially-varying kernels. We introduce two encoder-decoder sub-networks that are fed with the blurry image and the estimated blur map, respectively, and produce as output the deblurred (deconvolv…
We develop a deep convolutional neural networks(CNNs) to deal with the blurry artifacts caused by the defocus of the camera using dual-pixel images. Specifically, we develop a double attention network which consists of attentional encoders, triple locals and global local modules to effectively extract useful information from each image in the dual-pixels and select the useful information from each image and synthesize the final output image. We demonstrate the effectiveness of the proposed deblurring algorithm in terms of both qualitative and quantitative aspects by evaluating on the test set …
Continual Test-Time Adaptation for Single Image Defocus Deblurring via Causal Siamese Networks
Institute of Software Chinese Academy of Sciences（中国科学院软件研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Renmin University of China（中国人民大学）；the Hong Kong University of Science and Technology (Guangzhou)（香港科技大学（广州））；the Hong Kong University of Science and Technology（香港科技大学）
Tencent AI Lab（腾讯AI实验室）；University of Connecticut（康涅狄格大学）；The Fourth Hospital of Hebei Medical University（河北医科大学第四医院）；West China Hospital, Sichuan University（四川大学华西医院）
Artificial Intelligence (AI)-powered pathology is a revolutionary step in the world of digital pathology and shows great promise to increase both diagnosis accuracy and efficiency. However, defocus and motion blur can obscure tissue or cell characteristics hence compromising AI algorithms'accuracy and robustness in analyzing the images. In this paper, we demonstrate a deep-learning-based approach that can alleviate the defocus and motion blur of a microscopic image and output a sharper and cleaner image with retrieved fine details without prior knowledge of the blur type, blur extent and patho…
Skoltech University（斯科尔科沃理工学院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）
Mobile microscopy is a promising technology to assist and to accelerate disease diagnostics, with its widespread adoption being hindered by the mediocre quality of acquired images. Although some paired image translation and super-resolution approaches for mobile microscopy have emerged, a set of essential challenges, necessary for automating it in a high-throughput setting, still await to be addressed. The issues like in-focus/out-of-focus classification, fast scanning deblurring, focus-stacking, etc. -- all have specific peculiarities when the data are recorded using a mobile device. In this …
University of Michigan-Shanghai Jiao Tong University Joint Institute（上海交通大学密西根学院）；Shanghai Jiao Tong University（上海交通大学）
Fluorescence microscopy plays an important role in biomedical research. The depth-variant point spread function (PSF) of a fluorescence microscope produces low-quality images especially in the out-of-focus regions of thick specimens. Traditional deconvolution to restore the out-of-focus images is usually insufficient since a depth-invariant PSF is assumed. This article aims at handling fluorescence microscopy images by learning-based depth-variant PSF and reducing artifacts. We propose adaptive weighting depth-variant deconvolution (AWDVD) with defocus level prediction convolutional neural net…
This Point spread function (PSF) plays a crucial role in many computational imaging applications, such as shape from focus/defocus, depth estimation, and fluorescence microscopy. However, the mathematical model of the defocus process is still unclear. In this work, we develop an alternative method to estimate the precise mathematical model of the point spread function to describe the defocus process. We first derive the mathematical algorithm for the PSF which is used to generate the simulated focused images for different focus depth. Then we compute the loss function of the similarity between…
A practical method utilising three-dimensional image pattern matching is proposed which, in principle, is capable of unambiguous determination of the types and positions of atoms in small molecules from defocus series collected at only a few different angular orientations of the molecule. Numerical tests of the method are presented using multislice calculations of defocus series of small biological molecules. The proposed technique can in future gain from Bayesian or machine-learning approaches and is likely to be useful in cryogenic electron microscopy.
BigFUSE: Global Context-Aware Image Fusion in Dual-View Light-Sheet Fluorescence Microscopy with Image Formation Prior
Technical University of Munich（慕尼黑工业大学）；Georg-August-University Göttingen（哥廷根大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；Institute of AI for Health, Helmholtz Munich - German Research Center for Environmental Health（亥姆霍兹慕尼黑研究中心人工智能健康研究所）；Helmholtz AI, Helmholtz Munich - German Research Center for Environmental Health（亥姆霍兹慕尼黑研究中心亥姆霍兹人工智能）
针对双视角 LSFM 局部融合导致空间不一致的问题，提出 BigFUSE，利用图像形成先验和贝叶斯 EM 估计全局合焦—离焦边界，实现无结构化伪影的自动融合。
Vector Institute（向量研究所）；University of Toronto（多伦多大学）
Deep learning methods are becoming widely used for restoration of defects associated with fluorescence microscopy imaging. One of the major challenges in application of such methods is the availability of training data. In this work, we propose a unified method for reconstruction of multi-defect fluorescence microscopy images when training data is limited. Our approach consists of two stages: first, we perform data augmentation using Generative Adversarial Network (GAN) with conditional instance normalization (CIN); second, we train a conditional GAN (cGAN) on paired ground-truth and defected …
Cornea cell count is an important diagnostic tool commonly used by practitioners to assess the health of a patient's cornea. Unfortunately, clinical specular microscopy requires the acquisition of a large number of images at different focus depths because the curved shape of the cornea makes it impossible to acquire a single all-in-focus image. This paper describes two methods and their implementations to reduce the number of images required to run a cell-counting algorithm, thus shortening the duration of the examination and increasing the patient's comfort. The basic idea is to apply de-blur…
Tsinghua University（清华大学）；University of Connecticut（康涅狄格大学）
Fourier ptychography (FP) is a newly developed computational imaging approach that achieves both high resolution and wide field of view by stitching a series of low-resolution images captured under angle-varied illumination. So far, many supervised data-driven models have been applied to solve inverse imaging problems. These models need massive amounts of data to train, and are limited by the dataset characteristics. In FP problems, generic datasets are always scarce, and the optical aberration varies greatly under different acquisition conditions. To address these dilemmas, we model the forwa…
Structured Illumination Microscopy (SIM) is an imaging technique for achieving both super-resolution (SR) and optical sectioning (OS) in wide-field microscopy. It consists in illuminating the sample with periodic patterns at different orientations and positions. The resulting images are then processed to reconstruct the observed object with SR and/or OS. In this work, we present BOSSA-SIM, a general-purpose SIM reconstruction method, applicable to moving objects such as encountered in in vivo retinal imaging, that enables SR and OS jointly in a fully unsupervised Bayesian framework. By modelin…
Acoustic-resolution photoacoustic microscopy (AR-PAM) is a promising tool for microvascular imaging. In the focal region, resolution of AR-PAM is determined by the ultrasound transducer and ultimately limited by acoustic diffraction. In the out-of-focus region, resolution deteriorates with increasing distance from the focal plane, which restricts depth of focus (DOF). Besides, a trade-off exists between resolution and DOF. Previously, synthetic aperture focusing technique (SAFT) and/or deconvolution methods have been demonstrated to enhance AR-PAM images. However, they suffer from issues in lo…
We report a new lensless microscopy configuration by integrating the concepts of transverse translational ptychography and defocus multi-height phase retrieval. In this approach, we place a tilted image sensor under the specimen for linearly-increasing phase modulation along one lateral direction. Similar to the operation of ptychography, we laterally translate the specimen and acquire the diffraction images for reconstruction. Since the axial distance between the specimen and the sensor varies at different lateral positions, laterally translating the specimen effectively introduces defocus mu…
Fluorescence microscopy plays a vital role in understanding the subcellular structures of living cells. However, it requires considerable effort in sample preparation related to chemical fixation, staining, cost, and time. To reduce those factors, we present a virtual fluorescence staining method based on deep neural networks (VirFluoNet) to transform fluorescence images of molecular labels into other molecular fluorescence labels in the same field-of-view. To achieve this goal, we develop and train a conditional generative adversarial network (cGAN) to perform digital fluorescence imaging dem…
Fourier ptychography microscopy(FP) is a recently developed computational imaging approach for microscopic super-resolution imaging. By turning on each light-emitting-diode (LED) located on different position on the LED array sequentially and acquiring the corresponding images that contain different spatial frequency components, high spatial resolution and quantitative phase imaging can be achieved in the case of large field-of-view. Nevertheless, FPM has high requirements for the system construction and data acquisition processes, such as precise LEDs position, accurate focusing and appropria…
