Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-fidelity structured illumination microscopy by point-spread-function engineering.

ABSTRACT: Structured illumination microscopy (SIM) has become a widely used tool for insight into biomedical challenges due to its rapid, long-term, and super-resolution (SR) imaging. However, artifacts that often appear in SIM images have long brought into question its fidelity, and might cause misinterpretation of biological structures. We present HiFi-SIM, a high-fidelity SIM reconstruction algorithm, by engineering the effective point spread function (PSF) into an ideal form. HiFi-SIM can effectively reduce commonly seen artifacts without loss of fine structures and improve the axial sectioning for samples with strong background. In particular, HiFi-SIM is not sensitive to the commonly used PSF and reconstruction parameters; hence, it lowers the requirements for dedicated PSF calibration and complicated parameter adjustment, thus promoting SIM as a daily imaging tool.

SUBMITTER: Wen G

PROVIDER: S-EPMC8016956 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Multicolour localization microscopy by point-spread-function engineering.

Project description:Super-resolution microscopy has revolutionized cellular imaging in recent years1-4. Methods relying on sequential localization of single point emitters enable spatial tracking at ~10-40 nm resolution. Moreover, tracking and imaging in three dimensions is made possible by various techniques, including point-spread-function (PSF) engineering5-9 -namely, encoding the axial (z) position of a point source in the shape that it creates in the image plane. However, a remaining challenge for localization-microscopy is efficient multicolour imaging - a task of the utmost importance for contextualizing biological data. Normally, multicolour imaging requires sequential imaging10, 11, multiple cameras12, or segmented dedicated fields of view13, 14. Here, we demonstrate an alternate strategy, the encoding of spectral information (colour), in addition to 3D position, directly in the image. By exploiting chromatic dispersion, we design a new class of optical phase masks that simultaneously yield controllably different PSFs for different wavelengths, enabling simultaneous multicolour tracking or super-resolution imaging in a single optical path.

| S-EPMC5391844 | biostudies-literature

Point spread function estimation from projected speckle illumination.

Project description:The resolution of an imaging apparatus is ideally limited by the diffraction properties of the light passing through the system aperture, but in many practical cases, inhomogeneities in the light propagating medium or imperfections in the optics degrade the image resolution. Here we introduce a powerful and practical new approach for estimating the point spread function (PSF) of an imaging system on the basis of PSF Estimation from Projected Speckle Illumination (PEPSI). PEPSI uses the fact that the speckles' phase randomness cancels the effects of the aberrations in the illumination path, thereby providing an objective pattern for measuring the deformation of the imaging path. Using this approach, both wide-field-of-view and local-PSF estimation can be obtained by calibration-free, single-speckle-pattern projection. Finally, we demonstrate the feasibility of using PEPSI estimates for resolution improvement in iterative maximum likelihood deconvolution.

| S-EPMC6059898 | biostudies-other

Structured line illumination Raman microscopy.

Project description:In the last couple of decades, the spatial resolution in optical microscopy has increased to unprecedented levels by exploiting the fluorescence properties of the probe. At about the same time, Raman imaging techniques have emerged as a way to image inherent chemical information in a sample without using fluorescent probes. However, in many applications, the achievable resolution is limited to about half the wavelength of excitation light. Here we report the use of structured illumination to increase the spatial resolution of label-free spontaneous Raman microscopy, generating highly detailed spatial contrast from the ensemble of molecular information in the sample. Using structured line illumination in slit-scanning Raman microscopy, we demonstrate a marked improvement in spatial resolution and show the applicability to a range of samples, including both biological and inorganic chemical component mapping. This technique is expected to contribute towards greater understanding of chemical component distributions in organic and inorganic materials.

| S-EPMC4686755 | biostudies-literature

Multifocal structured illumination optoacoustic microscopy.

Project description:Optoacoustic (OA) imaging has the capacity to effectively bridge the gap between macroscopic and microscopic realms in biological imaging. High-resolution OA microscopy has so far been performed via point-by-point scanning with a focused laser beam, thus greatly restricting the achievable imaging speed and/or field of view. Herein we introduce multifocal structured illumination OA microscopy (MSIOAM) that attains real-time 3D imaging speeds. For this purpose, the excitation laser beam is shaped to a grid of focused spots at the tissue surface by means of a beamsplitting diffraction grating and a condenser and is then scanned with an acousto-optic deflector operating at kHz rates. In both phantom and in vivo mouse experiments, a 10 mm wide volumetric field of view was imaged with 15 Hz frame rate at 28 μm spatial resolution. The proposed method is expected to greatly aid in biological investigations of dynamic functional, kinetic, and metabolic processes across multiple scales.

| S-EPMC7459102 | biostudies-literature

Full-color structured illumination optical sectioning microscopy.

Project description:In merits of super-resolved resolution and fast speed of three-dimensional (3D) optical sectioning capability, structured illumination microscopy (SIM) has found variety of applications in biomedical imaging. So far, most SIM systems use monochrome CCD or CMOS cameras to acquire images and discard the natural color information of the specimens. Although multicolor integration scheme are employed, multiple excitation sources and detectors are required and the spectral information is limited to a few of wavelengths. Here, we report a new method for full-color SIM with a color digital camera. A data processing algorithm based on HSV (Hue, Saturation, and Value) color space is proposed, in which the recorded color raw images are processed in the Hue, Saturation, Value color channels, and then reconstructed to a 3D image with full color. We demonstrated some 3D optical sectioning results on samples such as mixed pollen grains, insects, micro-chips and the surface of coins. The presented technique is applicable to some circumstance where color information plays crucial roles, such as in materials science and surface morphology.

| S-EPMC4586488 | biostudies-literature

Concepts for structured illumination microscopy with extended axial resolution through mirrored illumination.

Project description: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 resolution limit both laterally and axially, but even with this the axial resolution is still worse than the lateral resolution of unmodified wide-field microscopy. Interferometric schemes using two high numerical aperture objectives, such as 4Pi confocal and I5M microscopy, have improved the axial resolution beyond that of the lateral, but at the cost of a significantly more complex optical setup. Here, we theoretically and numerically investigate a simpler dual-objective scheme which we propose can be easily added to an existing 3D-SIM microscope, providing lateral and axial resolutions in excess of 125 nm with conventional fluorophores and without the need for interferometric detection.

| S-EPMC7173891 | biostudies-literature

Structured illumination microscopy with noise-controlled image reconstructions.

Project description:Super-resolution structured illumination microscopy (SIM) has become a widely used method for biological imaging. Standard reconstruction algorithms, however, are prone to generate noise-specific artifacts that limit their applicability for lower signal-to-noise data. Here we present a physically realistic noise model that explains the structured noise artifact, which we then use to motivate new complementary reconstruction approaches. True-Wiener-filtered SIM optimizes contrast given the available signal-to-noise ratio, and flat-noise SIM fully overcomes the structured noise artifact while maintaining resolving power. Both methods eliminate ad hoc user-adjustable reconstruction parameters in favor of physical parameters, enhancing objectivity. The new reconstructions point to a trade-off between contrast and a natural noise appearance. This trade-off can be partly overcome by further notch filtering but at the expense of a decrease in signal-to-noise ratio. The benefits of the proposed approaches are demonstrated on focal adhesion and tubulin samples in two and three dimensions, and on nanofabricated fluorescent test patterns.

| S-EPMC7611169 | biostudies-literature

Characterization of neurite dystrophy after trauma by high speed structured illumination microscopy and lattice light sheet microscopy.

Project description:BACKGROUND:Unbiased screening studies have repeatedly identified actin-related proteins as one of the families of proteins most influenced by neurotrauma. Nevertheless, the status quo model of cytoskeletal reorganization after neurotrauma excludes actin and incorporates only changes in microtubules and intermediate filaments. Actin is excluded in part because it is difficult to image with conventional techniques. However, recent innovations in fluorescent microscopy provide an opportunity to image the actin cytoskeleton at super-resolution resolution in living cells. This study applied these innovations to an in vitro model of neurotrauma. NEW METHOD:New methods are introduced for traumatizing neurons before imaging them with high speed structured illumination microscopy or lattice light sheet microscopy. Also, methods for analyzing structured illumination microscopy images to quantify post-traumatic neurite dystrophy are presented. RESULTS:Human induced pluripotent stem cell-derived neurons exhibited actin organization typical of immature neurons. Neurite dystrophy increased after trauma but was not influenced by jasplakinolide treatment. The F-actin content of dystrophies varied greatly from one dystrophy to another. COMPARISON WITH EXISTING METHODS:In contrast to fixation dependent methods, these methods capture the evolution of the actin cytoskeleton over time in a living cell. In contrast to prior methods based on counting dystrophies, this quantification scheme parameterizes the severity of a given dystrophy as it evolves from a local swelling to an almost-perfect spheroid that threatens to transect the neurite. CONCLUSIONS:These methods can be used to investigate genetic factors and therapeutic interventions that modulate the course of neurite dystrophy after trauma.

| S-EPMC6342006 | biostudies-literature

Nonsmooth Convex Optimization for Structured Illumination Microscopy Image Reconstruction.

Project description:In this paper, we propose a new approach for structured illumination microscopy image reconstruction. We first introduce the principles of this imaging modality and describe the forward model. We then propose the minimization of nonsmooth convex objective functions for the recovery of the unknown image. In this context, we investigate two data-fitting terms for Poisson-Gaussian noise and introduce a new patch-based regularization method. This approach is tested against other regularization approaches on a realistic benchmark. Finally, we perform some test experiments on images acquired on two different microscopes.

| S-EPMC6075701 | biostudies-literature

QSIM: quantitative structured illumination microscopy image processing in ImageJ.

Project description:BackgroundStructured illumination microscopy has been extensively used in biological imaging due to its low cost and easy implementation. However, the lack of quantitative imaging capability limits its application in absolute irradiance measurements.MethodWe have developed a quantitative structured illumination microscopy image processing algorithm (QSIM) as a plugin for the widely used ImageJ software. QSIM can work with the raw images acquired by a traditional structured illumination microscope and can quantitatively measure photon numbers, with noise estimates for both wide-field images and sectioned images.Results and conclusionWe demonstrated the quantitative image processing capability of QSIM by imaging a mouse kidney section in 3D. The results show that QSIM can transform structured illumination microscopy from qualitative to quantitative, which is essential for demanding fluorescence imaging applications.

| S-EPMC4360942 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data