ML-SIM: A deep neural network for reconstruction of structured illumination microscopy images
University of Cambridge（剑桥大学）；Department of Chemical Engineering and Biotechnology（化学工程与生物技术系）；Department of Computer Science and Technology（计算机科学与技术系）
Charles N. Christensen, Edward N. Ward, Pietro Lio, Clemens F. Kaminski
Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible for live-cell imaging. However, the reconstruction of SIM images is often slow and prone to artefacts. Here we propose a versatile reconstruction method, ML-SIM, which makes use of machine learning. The model is an end-to-end deep residual neural network that is trained on a simulated data set to be free of common SIM artefacts. ML-SIM is thus robust to noise and irregularities in the illumination patterns of the raw SIM input frames. The reconstruction method is widely applicable and does not require the acquisition of experimental training data. Since the training data are generated from simulations of the SIM process on images from generic libraries the method can be efficiently adapted to specific experimental SIM implementations. The reconstruction quality enabled by our method is compared with traditional SIM reconstruction methods, and we demonstrate advantages in terms of noise, reconstruction fidelity and contrast for both simulated and experimental inputs. In addition, reconstruction of one SIM frame typically only takes ~100ms to perform on PCs with modern Nvidia graphics cards, making the technique compatible with real-time imaging. The full implementation and the trained networks are available at http://ML-SIM.com.
This paper introduces a new method of data-driven microscope design for virtual fluorescence microscopy. Our results show that by including a model of illumination within the first layers of a deep convolutional neural network, it is possible to learn task-specific LED patterns that substantially improve the ability to infer fluorescence image information from unstained transmission microscopy images. We validated our method on two different experimental setups, with different magnifications and different sample types, to show a consistent improvement in performance as compared to conventional…
Structured illumination microscopy (SIM) is a very important super-resolution microscopy technique, which provides high speed super-resolution with about two-fold spatial resolution enhancement. Several attempts aimed at improving the performance of SIM reconstruction algorithm have been reported. However, most of these highlight only one specific aspect of the SIM reconstruction -- such as the determination of the illumination pattern phase shift accurately -- whereas other key elements -- such as determination of modulation factor, estimation of object power spectrum, Wiener filtering freque…
The trade-off between throughput and image quality is an inherent challenge in microscopy. To improve throughput, compressive imaging under-samples image signals; the images are then computationally reconstructed by solving a regularized inverse problem. Compared to traditional regularizers, Deep Learning based methods have achieved greater success in compression and image quality. However, the information loss in the acquisition process sets the compression bounds. Further improvement in compression, without compromising the reconstruction quality is thus a challenge. In this work, we propose…
This work presents the development of a flexible microscopic chemical imaging platform for cultural heritage that utilizes wavelength-tunable oblique illumination from a point source to obtain per-pixel reflectance spectra in the VIS-NIR range. The microscope light source can be adjusted on two axes allowing for a hemisphere of possible illumination directions. The synthesis of multiple illumination angles allows for the calculation of surface normal vectors, similar to phase gradients, and axial optical sectioning. The extraction of spectral reflectance images with high spatial resolutions fr…
In recent years there has been great interest in using deep neural networks (DNN) for super-resolution image reconstruction including for structured illumination microscopy (SIM). While these methods have shown very promising results, they all rely on data-driven, supervised training strategies that need a large number of ground truth images, which is experimentally difficult to realize. For SIM imaging, there exists a need for a flexible, general, and open-source reconstruction method that can be readily adapted to different forms of structured illumination. We demonstrate that we can combine…
High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resoluti…
Nanjing University of Science and Technology（南京理工大学）；Soochow University（苏州大学）
Structured illumination microscopy (SIM) is an important super-resolution based microscopy technique that breaks the diffraction limit and enhances optical microscopy systems. With the development of biology and medical engineering, there is a high demand for real-time and robust SIM imaging under extreme low light and short exposure environments. Existing SIM techniques typically require multiple structured illumination frames to produce a high-resolution image. In this paper, we propose a single-frame structured illumination microscopy (SF-SIM) based on deep learning. Our SF-SIM only needs o…
A method is proposed for assessing the temporal resolution of Structured Illumination Microscopy (SIM), by tracking the amplitude of different spatial frequency components over time, and comparing them to a temporally-oscillating ground-truth. This method is used to gain insight into the performance limits of SIM, along with alternative reconstruction techniques (termed 'rolling SIM') that claim to improve temporal resolution. Results show that the temporal resolution of SIM varies considerably between low and high spatial frequencies, and that, despite being used in several high profile paper…
Structured illumination microscopy (SIM) can double the resolution beyond the light diffraction limit, but it comes at the cost of multiple camera exposures and the heavy computation burden of multiple Fourier transforms. In this paper, we report a novel technique termed single-shot SIM, to overcome these limitations. A multi-task joint deep-learning strategy is proposed. Generative adversative networks (GAN) are employed to generate five structured illumination images based on the single-shot structured illumination image. U-Net is employed to reconstruct the super-resolution image from these…
Structured illumination microscopy (SIM) achieves doubled spatial resolution by exciting the specimen with a high-contrast, high-frequency sinusoidal pattern. Such an excitation pattern can be generated by interference between multiple laser beams, which are diffracted from a grating. In SIM, 2D imaging requires 9 patterns and 3D imaging requires 15 patterns. Compared to mechanical movement of gratings, opti-electro devices provide rapid switch of the excitation patterns, in which Digital Micro-mirror Device (DMD) is most common in industry. Here we model DMD as the blazed grating and report a…
Fourier ptychographic microscopy allows for the collection of images with a high space-bandwidth product at the cost of temporal resolution. In Fourier ptychographic microscopy, the light source of a conventional widefield microscope is replaced with a light-emitting diode (LED) matrix, and multiple images are collected with different LED illumination patterns. From these images, a higher-resolution image can be computationally reconstructed without sacrificing field-of-view. We use deep learning to achieve single-shot imaging without sacrificing the space-bandwidth product, reducing the acqui…
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…
The structured illumination microscopy using unknown speckle patterns has shown the capacity to surpass the Abbe's diffraction barrier, giving the possibility to design cheap and versatile SIM devices. However, the state-of-the-art joint reconstruction methods in this framework has a relatively low contrast in super-resolution part in comparison to conventional SIM and the hyper-parameter is not easy to tune. In this paper, a unified joint reconstruction approach is proposed with the hyper-parameter proportional to the noise level. Different regularization terms could be evaluated under the sa…
The performance of light-field microscopy is improved by selectively illuminating the relevant subvolume of the specimen with a second objective lens [1-3]. Here we advance this approach to a single-objective geometry, using an oblique one-photon illumination path or two-photon illumination to accomplish selective-volume excitation. The elimination of the second orthogonally oriented objective to selectively excite the volume of interest simplifies specimen mounting; yet, this single-objective approach still reduces out-of-volume background, resulting in improvements in image contrast, effecti…
Many optical microscopy techniques rely on structured illumination by way of a projected image (eg. structured illumination microscopy) or a tailored angular distribution of light (eg. ptychography). Electro-optical equipment such as spatial light modulators and light emitting diode (LED) arrays are commonly used to sculpt light for these imaging schemes. However, these high-tech devices are not a requirement for light crafting. Patterned diffusely reflecting surfaces also imprint a spatio-angular structure onto reflected light. We demonstrate that paper patterned with a standard commercial pr…
Previous studies have shown that the frequency content of an illumination affects the convergence rate and reconstruction quality of ptychographic reconstructions. In this numerical study, we demonstrate that structuring a large illumination as a modified uniformly redundant array (MURA) can yield higher resolution and faster convergence for ptychography by improving the signal-to-noise ratio of high spatial frequencies in the far-field diffraction pattern.
Digital two-dimensional (2D) spatial sampling devices (such as charge-coupled device) have been widely used in various imaging systems, especially in computational imaging systems. However, the undersampling of digital sampling devices is a problem that limits the resolution of the acquired images. In this study, we present a synthetic sampling imaging (SSI) concept to solve the undersampling problem. It combines the structured illumination system and conventional 2D image detection system to simultaneously sample the specimen from the illumination and the detection sides. Then, we synthesize …
The transport-of-intensity equation (TIE) is a well-established non-interferometric phase retrieval approach, which enables quantitative phase imaging (QPI) of transparent sample simply by measuring the intensities at multiple axially displaced planes. Nevertheless, it still suffers from two fundamentally limitations. First, it is quite susceptible to low-frequency errors (such as \cloudy" artifacts), which results from the poor contrast of the phase transfer function (PTF) near the zero frequency. Second, the reconstructed phase tends to blur under spatially low-coherent illumination, especia…
The wavefront is scrambled when coherent light propagates through a random scattering medium and which makes direct use of the conventional optical methods ineffective. In this paper, we propose and demonstrate a structured light illumination for imaging through an opaque scattering layer. Proposed technique is reference free and capable to recover the complex field from intensities of the speckle patterns. This is realized by making use of the phase-shifting in the structured light illumination and applying spatial averaging of the speckle pattern in the intensity correlation measurement. An …
Conventional approaches for 3D imaging in or through scattering media are usually limited to 2D reconstruction of objects at some discontinuous locations, although the time-consuming iteration, guide-star, or complex system are implemented. How to quickly visualize dynamic 3D objects behind scattering media is still an open issue. Here, by using structured light illumination, we propose a single-shot technique that can quickly acquire continuous 3D surfaces of objects hidden behind the diffuser. The proposed method can realize the 3D imaging of single, multiple, and dynamic targets from the sp…
Fourier ptychographic microscopy (FPM) can achieve quantitative phase imaging with a large space-bandwidth product by synthesizing a set of low-resolution intensity images captured under angularly varying illuminations. Determining accurate illumination angles is critical because the consistency between actual systematic parameters and those used in the recovery algorithm is essential for high-quality imaging. This paper presents a full-pose-parameter and physics-based method for calibrating illumination angles. Using a physics-based model constructed with general knowledge of the employed mic…
A generic computational imaging setup is considered which assumes sequential illumination of a semi-transparent object by an arbitrary set of structured illumination patterns. For each incident illumination pattern, all transmitted light is collected by a photon-counting bucket (single-pixel) detector. The transmission coefficients measured in this way are then used to reconstruct the spatial distribution of the object's projected transmission. It is demonstrated that the squared spatial resolution of such a setup is usually equal to the ratio of the image area to the number of linearly indepe…
We report a compact, cost-effective and field-portable lensless imaging platform for quantitative microscopy. In this platform, the object is placed on top of an image sensor chip without using any lens. We use a low-cost galvo scanner to rapidly scan an unknown laser speckle pattern on the object. To address the positioning repeatability and accuracy issues, we directly recover the positional shifts of the speckle pattern based on the phase correlation of the captured images. To bypass the resolution limit set by the imager pixel size, we employ a sub-sampled ptychographic phase retrieval pro…
Deconvolution phase microscopy enables high-contrast visualization of transparent samples through reconstructions of their transmitted phases or refractive indexes. Herein, we propose a method to extend 2D deconvolution phase microscopy to thick 3D samples. The refractive index distribution of a sample can be obtained at a specific axial plane by measuring only four intensity images obtained under optimized illumination patterns. Also, the optical phase delay of a sample can be measured using different illumination patterns.
We report a novel microscopy platform, termed Multi-Aperture Fourier ptychographic microscopy (MA-FPM), capable of realizing gigapixel complex field images with large data acquisition bandwidths - in gigapixels per second. MA-FPM is a synthetic aperture technique- an array of objectives together with tilt-shift illumination are used to synthesize high-resolution, wide field-of-view images. Here, the phase is recovered using Fourier ptychography (FP) algorithms, unlike conventional optical synthetic aperture techniques where holographic measurements are used. The parallel data-acquisition capab…
Coherent diffractive imaging (CDI) is widely used to characterize structured samples from measurements of diffracting intensity patterns. We introduce a numerical framework to quantify the precision that can be achieved when estimating any given set of parameters characterizing the sample from measured data. The approach, based on the calculation of the Fisher information matrix, provides a clear benchmark to assess the performance of CDI methods. Moreover, by optimizing the Fisher information metric using deep learning optimization libraries, we demonstrate how to identify the optimal illumin…
Stanford University（斯坦福大学）；Nanjing University（南京大学）；Snap Research（Snap研究院）；University of Alberta（阿尔伯塔大学）；University of Manitoba（曼尼托巴大学）
Structured light (SL) systems acquire high-fidelity 3D geometry with active illumination projection. Conventional systems exhibit challenges when working in environments with strong ambient illumination, global illumination and cross-device interference. This paper proposes a general-purposed technique to improve the robustness of SL by projecting redundant optical signals in addition to the native SL patterns. In this way, projected signals become more distinguishable from errors. Thus the geometry information can be more easily recovered using simple signal processing and the ``coding gain" …
Fourier ptychography microscopy (FPM), sharing its roots with synthetic aperture technique and phase retrieval method, is a recently developed computational microscopic super-resolution technique. By turning on the light-emitting diode (LED) elements sequentially and acquiring the corresponding images that contain different spatial frequencies, FPM can achieve a wide field-of-view (FOV), high-spatial-resolution imaging, and phase recovery simultaneously. Conventional FPM assumes that the sample is sufficiently thin and strictly in focus. Nevertheless, even for a relatively thin sample, the non…
