Structured illumination microscopy (SIM) provides images of fluorescent objects at an enhanced resolution greater than that of conventional epifluorescence wide-field microscopy. Initially demonstrated in 1999 to enhance the lateral resolution two-fold, it has since been extended to enhance axial resolution two-fold (2008), applied to live-cell imaging (2009) and combined with myriad other techniques, including interferometric detection (2008), confocal microscopy (2010) and light sheet illumination (2012). Despite these impressive developments, SIM remains, perhaps, the most poorly understood `super-resolution' method. In this article, we provide answers to the 13 questions regarding SIM proposed by Prakash et al., along with answers to a further three questions. After providing a general overview of the technique and its developments, we explain why SIM as normally used is still diffraction-limited. We then highlight the necessity for a non-polynomial, and not just non-linear, response to the illuminating light in order to make SIM a true, diffraction-unlimited, super-resolution technique. In addition, we present a derivation of a real-space SIM reconstruction approach that can be used to process conventional SIM and image scanning microscopy (ISM) data and extended to process data with quasi-arbitrary illumination patterns. Finally, we provide a simple bibliometric analysis of SIM development over the past two decades and provide a short outlook on potential future work.
Wide-field fluorescence microscopy, while much faster than confocal microscopy, suffers from a lack of optical sectioning and poor axial resolution. 3D structured illumination microscopy (SIM) has been demonstrated to provide optical sectioning and to double the achievable resolution both laterally and axially, but even with this the axial resolution is still worse than the lateral resolution of unmodified wide-field detection. Interferometric schemes using two high numerical aperture objectives, such as 4Pi confocal and I5S microscopy, have improved the axial resolution beyond that of the lat…
Phase contrast techniques, such as differential interference contrast (DIC) microscopy, are widely used to provide morphological images of unstained biological samples. The trans-illumination geometry required for these techniques has restricted their application to thin samples. We introduce oblique back-illumination microscopy (OBM), a method of collecting en face phase gradient images of thick scattering samples, enabling near video-rate in vivo phase imaging with a miniaturized probe suitable for endoscopy.
We propose to enhance the performance of localized plasmon structured illumination microscopy (LP-SIM) via intensity correlations. LP-SIM uses sub-wavelength illumination patterns to encode high spatial frequency information. It can enhance the resolution up to three-fold before gaps in the OTF support arise. For blinking fluorophores or for quantum antibunching an intensity correlation analysis induces higher harmonics of the illumination pattern and enlarges the effective OTF. This enables ultrahigh resolutions without gaps in the OTF support, and thus a fully deterministic imaging scheme. W…
Recently, chiral structured illumination microscopy has been proposed to image fluorescent chiral domains at sub-wavelength resolution. Chiral structured illumination microscopy is based on the combination of structured illumination microscopy, fluorescence-detected circular dichroism, and optical chirality engineering. Since circular dichroism of natural chiral molecules is typically weak, the differential fluorescence is also weak and can be easily buried by the noise, hampering the fidelity of the reconstructed images. In this work, we systematically study the impact of the noise on the qua…
Plasmonic hyperbolic metasurfaces have emerged as an effective platform for manipulating the propagation of light. Here, confined modes on arrays of silver nanoridges that exhibit hyperbolic dispersion are used to demonstrate and model a super-resolution imaging technique based on structured illumination microscopy. A spatial resolution of ~75 nm at 458 nm is demonstrated, which is 3.1 times better than an equivalent diffraction limited image. This work emphasizes the ability to engineer the properties of confined optical modes and to leverage those characteristics for applications in imaging.…
Intensity correlation microscopy (ICM), which is prominently known through antibunching microscopy or super-resolution optical fluctuation imaging (SOFI), provides superresolution through a correlation analysis of antibunching of independent quantum emitters or temporal fluctuations of blinking fluorophores. For correlation order $m$ the PSF in the signal is effectively taken to the $m$th power, and is thus directly shrunk by the factor $\sqrt{m}$. Combined with deconvolution a close to linear resolution improvement of factor $m$ can be obtained. Yet, analysis of high correlation orders is cha…
Differential phase contrast microscopy (DPC) provides high-resolution quantitative phase distribution of thin transparent samples under multi-axis asymmetric illuminations. Typically, illumination in DPC microscopic systems is designed with 2-axis half-circle amplitude patterns, which, however, result in a non-isotropic phase contrast transfer function (PTF). Efforts have been made to achieve isotropic DPC by replacing the conventional half-circle illumination aperture with radially asymmetric patterns with 3-axis illumination or gradient amplitude patterns with 2-axis illumination. Neverthele…
Illumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifi…
In this paper, a method for increasing the temporal resolution of a temporal imaging system has been developed. Analogously to the conventional spatial imaging systems in which resolution limit is due to the finite aperture of the lens, in a temporal imaging system, finite temporal aperture of the time lens is responsible for limited temporal resolution. Based on the method used in spatial structured illumination super-resolution microscopy in spatial optics, we have utilized time prisms, which are temporal versions of conventional prisms, to shift the illusive frequency components of the inpu…
Fluorescence polarization microscopy images both the intensity and orientation of fluorescent dipoles, which plays a vital role in studying the molecular structure and dynamics of bio-complex. However, it is difficult to resolve the dipole assemblies on the subcellular structure and their dynamics in living cells with super-resolution. Here we report polarized structured illumination microscopy (pSIM), which decouples the entangled spatial and angular structured illumination through interpreting the dipoles in spatio-angular hyperspace. We demonstrate its application on a series of biological …
We present a simple and compact approach of structured illumination microscopy by using three $2\times2$ fiber couplers and one $1\times4$ MEMS optics switch. One uniform and three fringe illumination patterns were produced by placing seven output fiber tips at the conjugate Fourier plane of the illumination path. Stable and relatively high-speed illumination switching was achieved by the optics switch. Super-resolution and optical sectioned information was reconstructed from 4-frame data by using algorithms based on a joint Richardson-Lucy deconvolution method and a Hilbert transform method. …
In this work, we present a highly efficient quantitative phase imaging (QPI) approach using programmable annular LED illumination based on traditional bright-field microscope. As a new type of coded illumination, the LED array provides a flexible and compatible way to realize QPI. The proposed method modulates the transfer function of system by changing the LED illumination pattern, which achieves twice resolution of objective NA and gives noise-robust response of transfer function. The phase of a sample could be recovered from the intensity images with the inversion of transfer function. More…
Structured illumination microscopy (SIM) has emerged as an essential technique for 3D and live-cell super-resolution imaging. However, to date, there has not been a dedicated workshop or journal issue covering the various aspects of SIM, from bespoke hardware and software development and the use of commercial instruments to biological applications. This special issue aims to recap recent developments as well as outline future trends. In addition to SIM, we cover related topics such as complementary super-resolution microscopy techniques, computational imaging, visualisation and image processin…
We report a novel extension to structured illumination (SI) microscopy that utilizes the Talbot self-imaging effect to generate a SI pattern on a sample with field-of-view (FOV) and resolution unconstrained by the numerical aperture (NA) of the microscope objective. This enables high-resolution SI pattern generation (up to the free-space propagation limit) across large FOVs, which in turn allows SI microscopy to be efficiently adapted for high-throughput imaging. We demonstrated this concept using a simple prototype microscope to image a large FOV (450 x 350 um) with a diffraction-limited fluo…
Current optoacoustic microscopy configurations often have narrow focal ranges that limit their use for fast volumetric imaging applications. Here, the focal range of optoacoustic microscopes is extended by matching the elongated optical illumination profile of a Bessel beam with the pencil beam acoustic sensitivity profile of a broadband axicon detector. An inverted optoacoustic microscope was developed with interchangeable optical illumination and acoustic detection units to assess the imaging depths and resolutions retained with several combinations of illumination and detection profiles. Ma…
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…
Simultaneous plane illumination and detection in confocal microscopy using a mode-selective photonic lantern
Polytechnique Montréal（蒙特利尔理工学院）；Castor Optics（卡斯托光学）；Peregrine Photon（游隼光子）；Université de Montréal, Institute of Biomedical Engineering（蒙特利尔大学生物医学工程学院）
Quantitative phase microscopy (QPM) is often based on recording an object-reference interference pattern and its further phase demodulation. We propose Pseudo Hilbert Phase Microscopy (PHPM) where we combine pseudo thermal light source illumination and Hilbert spiral transform phase demodulation to achieve hybrid hardware-software-driven noise robustness and increase in resolution of single-shot coherent QPM. Those advantageous features stem from physically altering the laser spatial coherence and numerically restoring spectrally overlapped object spatial frequencies. Capabilities of the PHPM …
We demonstrate a new computational illumination technique that achieves large space-bandwidth-time product, for quantitative phase imaging of unstained live samples in vitro. Microscope lenses can have either large field of view (FOV) or high resolution, not both. Fourier ptychographic microscopy (FPM) is a new computational imaging technique that circumvents this limit by fusing information from multiple images taken with different illumination angles. The result is a gigapixel-scale image having both wide FOV and high resolution, i.e. large space-bandwidth product (SBP). FPM has enormous pot…
Tunable Dynamic Speckle Generation for Random Illumination Microscopy
Aix Marseille Université, CNRS, Centrale Med, Institut Fresnel（艾克斯马赛大学、法国国家科学研究中心、中央理工梅德学院、费斯奈尔研究所）；Department of Engineering Science, University of Oxford（牛津大学工程科学系）；Morgridge Institute for Research（莫格里奇研究所）
This Letter presents the first demonstration of multi-tile stitching for large scale 3D imaging in single objective light-sheet microscopy. We show undistorted 3D imaging spanning complete zebrafish larvae, and over 1 mm3 volumes for thick mouse brain sections. We use remote galvo scanning for light-sheet creation and develop a processing pipeline for 3D tiling across different axes. With the improved one photon (1p) tilt-invariant scanned oblique plane illumination (SOPi) microscope presented here, we demonstrate cellular resolution imaging at depths exceeding 330 um in optically scattering m…
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…
We propose to use intensity correlation microscopy in combination with structured illumination to image quantum emitters that exhibit antibunching with a spatial resolution reaching far beyond the Rayleigh limit. Combining intensity measurements and intensity auto correlations up to order $m$ creates an effective PSF with FWHM shrunk by the factor $\sqrt{m}$. Structured Illumination microscopy on the other hand introduces a resolution improvement of factor 2 by use of the principle of moiré fringes. Here, we show that for linear low-intensity excitation and linear optical detection the simulta…
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…
High SNR 3D Imaging from Millimeter-scale Thick Tissues to Cellular Dynamics via Structured Illumination Microscopy
Xi’an Jiaotong University（西安交通大学）；Chinese Institute for Brain Research（北京脑科学与类脑研究所）；Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences（中国科学院上海有机化学研究所）；Huaxia Imaging Technology Co., Ltd.（华厦成像科技有限公司）；State Key Laboratory of Electrical Insulation and Power Equipment, Xi'an Jiaotong University（西安交通大学电气绝缘与电力设备国家重点实验室）
University of California, Berkeley（加州大学伯克利分校）；Boston University（波士顿大学）
Structured illumination microscopy (SIM) improves resolution by down-modulating high-frequency information of an object to fit within the passband of the optical system. Generally, the reconstruction process requires prior knowledge of the illumination patterns, which implies a well-calibrated and aberration-free system. Here, we propose a new \textit{algorithmic self-calibration} strategy for SIM that does not need to know the exact patterns {\it a priori}, but only their covariance. The algorithm, termed PE-SIMS, includes a Pattern-Estimation (PE) step requiring the uniformity of the sum of …
We propose a chiral imaging modality based on optical chirality engineering, fluorescence-detected circular dichroism and structured illumination microscopy. In this method, the optical chirality of the illumination is structured and the circular dichroism dependent fluorescence is detected. With image reconstruction, the spatial distribution of chiral domains can be obtained at sub-diffraction limited resolution. We theoretically demonstrate this method and discuss the feasibility using an optical chirality engineering approach based on far-field optics.
For quantitative phase imaging (QPI) based on transport-of-intensity equation (TIE), partially coherent illumination provides speckle-free imaging, compatibility with brightfield microscopy, and transverse resolution beyond coherent diffraction limit. Unfortunately, in a conventional microscope with circular illumination aperture, partial coherence tends to diminish the phase contrast, exacerbating the inherent noise-to-resolution tradeoff in TIE imaging, resulting in strong low-frequency artifacts and compromised imaging resolution. Here, we demonstrate how these issues can be effectively add…
Fourier ptychographic (FP) microscope is a coherent imaging method that can synthesize an image with a higher bandwidth using multiple low-bandwidth images captured at different spatial frequency regions. The method's demand for multiple images drives the need for a brighter illumination scheme and a high-frame-rate camera for a faster acquisition. We report the use of a guided laser beam as an illumination source for an FP microscope. It uses a mirror array and a 2-dimensional scanning Galvo mirror system to provide a sample with plane-wave illuminations at diverse incidence angles. The use o…
Phase-resolved wide-field CARS microscopy with speckle illumination
Aix Marseille University, CNRS, Centrale Med, Institut Fresnel（艾克斯-马赛大学、法国国家科学研究中心、中央理工-马赛学院、菲涅耳研究所）；Institut Universitaire de France (IUF)（法兰西学院）；Morgridge Institute for Research（莫格里奇研究所）；XLIM, CNRS UMR 7252, Université de Limoges（XLIM实验室、法国国家科学研究中心UMR 7252、利摩日大学）
In most biological tissues, light scattering due to small differences in refractive index limits the depth of optical imaging systems. Two-photon microscopy (2PM), which significantly reduces the scattering of the excitation light, has emerged as the most common method to image deep within scattering biological tissue. This technique, however, requires high-power pulsed lasers that are both expensive and difficult to integrate into compact portable systems. In this paper, using a combination of theoretical and experimental techniques, we show that Selective Plane Illumination Microscopy (SPIM)…
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…
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…
Modern optical microscopy methods have been advanced to provide super resolution at high imaging speed, but not chirality discriminative. We recently proposed chiral structured-illumination microscopy (SIM) method to image chiral fluorescent domains at sub-wavelength resolution. Chiral SIM is suitable for imaging chiral domains at sub-wavelength resolution but loses the high spatial frequency of the achiral ones. In order to obtain the full picture of all fluorescent domains at sub-wavelength resolution, we propose an advanced version of chiral SIM, termed double SIM, which enables simultaneou…
We present a new two-snapshot structured light illumination (SLI) reconstruction algorithm for fast image acquisition. The new algorithm, which only requires two mutually π phase-shifted raw structured images, is implemented on a custom-built temporal focusing fluorescence microscope (TFFM) to enhance its axial resolution via a digital micromirror device (DMD). First, the orientation of the modulated sinusoidal fringe patterns is automatically identified via spatial frequency vector detection. Subsequently, the modulated in-focal-plane images are obtained via rotation and subtraction. Lastly, …
We present experimental demonstration of tilt-mirror assisted transmission structured illumination microscopy (tSIM) that offers a large field of view super resolution imaging. An assembly of custom-designed tilt-mirrors are employed as the illumination module where the sample is excited with the interference of two beams reflected from the opposite pair of mirror facets. Tunable frequency structured patterns are generated by changing the mirror-tilt angle and the hexagonal-symmetric arrangement is considered for the isotropic resolution in three orientations. Utilizing high numerical aperture…
