Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Point spread function estimation from projected speckle illumination.

ABSTRACT: 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.

SUBMITTER: Meitav N

PROVIDER: S-EPMC6059898 | biostudies-other | 2016 Mar

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Point spread function estimation from projected speckle illumination.

Meitav Nizan N Ribak Erez N EN Shoham Shy S

Light, science & applications 20160325 3

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 ...[more]

PMID: 30167151

Similar Datasets

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

Project description: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.

| S-EPMC8016956 | biostudies-literature

Speckle illumination holographic non-scanning fluorescence endoscopy.

Project description:Optical sectioning endoscopy such as confocal endoscopy offers capabilities to obtain three-dimensional (3D) information from various biological samples by discriminating between the desired in-focus signals and out-of-focus background. However, in general confocal images are formed through point-by-point scanning and the scanning time is proportional to the 3D space-bandwidth product. Recently, structured illumination endoscopy has been utilized for optically sectioned wide-field imaging, but it still needs axial scanning to acquire images from different depths of focal plane. Here, we report wide-field, multiplane, optical sectioning endoscopic imaging, incorporating 3D active speckle-based illumination and multiplexed volume holographic gratings, to simultaneously obtain images of fluorescently labeled tissue structures from different depths, without the need of scanning. We present the design, and implementation, as well as experimental data, demonstrating this endoscopic system's ability to obtain optically sectioned multiplane fluorescent images of tissue samples, with cellular level resolution in wide-field fashion, and no need for mechanical or optical axial scanning.(A) Schematic drawing of the SIHN endoscopy to simultaneously acquire multiplane images from different depths. (B) Uniform, and (C) SIHN illuminated images of standard fluorescence beads (25 μm in diameter) for the two axial planes. (D) Intensity profile on fluorescently labeled signal (ie, in-focus) and background (ie, out-of-focus) of microspheres.

| S-EPMC6466634 | biostudies-literature

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

Optimal point spread function design for 3D imaging.

Project description:To extract from an image of a single nanoscale object maximum physical information about its position, we propose and demonstrate a framework for pupil-plane modulation for 3D imaging applications requiring precise localization, including single-particle tracking and superresolution microscopy. The method is based on maximizing the information content of the system, by formulating and solving the appropriate optimization problem--finding the pupil-plane phase pattern that would yield a point spread function (PSF) with optimal Fisher information properties. We use our method to generate and experimentally demonstrate two example PSFs: one optimized for 3D localization precision over a 3 μm depth of field, and another with an unprecedented 5 μm depth of field, both designed to perform under physically common conditions of high background signals.

| S-EPMC4381866 | biostudies-literature

A Portable Compact System for Laser Speckle Correlation Imaging of Artworks Using Projected Speckle Pattern.

Project description:Artworks have a layered structure subjected to alterations caused by various factors. The monitoring of defects at sub-millimeter scale may be performed by laser interferometric techniques. The aim of this work was to develop a compact system to perform laser speckle imaging in situ for effective mapping of subsurface defects in paintings. The device was designed to be versatile with the possibility of optimizing the performance by easy parameters adjustment. The system exploits a laser speckle pattern generated through an optical diffuser and projected onto the artworks and image correlation techniques for the analysis of the speckle intensity pattern. A protocol for the optimal measurement was suggested, based on calibration curves for tuning the mean speckle size in the acquired intensity pattern. The system was validated in the analysis of detachments in an ancient painting model using a short pulse thermal stimulus to induce a surface deformation field and standard decorrelation algorithms for speckle pattern matching. The device is equipped with a compact thermal camera for preventing any overheating effects during the phase of the stimulus. The developed system represents a valuable nondestructive tool for artwork diagnostics, allowing the monitoring of subsurface defects in paintings in out-of-laboratory environment.

| S-EPMC8321176 | biostudies-literature

Superresolution imaging with optical fluctuation using speckle patterns illumination.

Project description:Superresolution fluorescence microscopy possesses an important role for the study of processes in biological cells with subdiffraction resolution. Recently, superresolution methods employing the emission properties of fluorophores have rapidly evolved due to their technical simplicity and direct applicability to existing microscopes. However, the application of these methods has been limited to samples labeled with fluorophores that can exhibit intrinsic emission properties at a restricted timescale, especially stochastic blinking. Here, we present a superresolution method that can be performed using general fluorophores, regardless of this intrinsic property. Utilizing speckle patterns illumination, temporal emission fluctuation of fluorophores is induced and controlled, from which a superresolution image can be obtained exploiting its statistical property. Using this method, we demonstrate, theoretically and experimentally, the capability to produce subdiffraction resolution images. A spatial resolution of 500?nm, 300?nm and 140?nm with 0.4, 0.5 and 1.4 NA objective lenses respectively was achieved in various samples with an enhancement factor of 1.6 compared to conventional fluorescence microscopy.

| S-EPMC4648106 | biostudies-literature

Speckle illumination SFDI for projector-free optical property mapping.

Project description:Spatial frequency domain imaging can map tissue scattering and absorption properties over a wide field of view, making it useful for clinical applications such as wound assessment and surgical guidance. This technique has previously required the projection of fully characterized illumination patterns. Here, we show that random and unknown speckle illumination can be used to sample the modulation transfer function of tissues at known spatial frequencies, allowing the quantitative mapping of optical properties with simple laser diode illumination. We compute low- and high-spatial frequency response parameters from the local power spectral density for each pixel and use a lookup table to accurately estimate absorption and scattering coefficients in tissue phantoms, in vivo human hand, and ex vivo swine esophagus. Because speckle patterns can be generated over a large depth of field and field of view with simple coherent illumination, this approach may enable optical property mapping in new form-factors and applications, including endoscopy.

| S-EPMC8285059 | biostudies-literature

Point spread function of the polarized light field microscope.

Project description:We examined the point spread function of the polarized light field microscope and established a computational framework to solve the forward problem in polarized light field imaging, for the purpose of furthering its use as a quantitative tool for measuring three-dimensional maps of the birefringence of transparent objects. We recorded experimental polarized light field images of small calcite crystals and of larger birefringent objects and compared our experimental results to numerical simulations based on polarized light ray tracing. We find good agreement between all our experiments and simulations, which leads us to propose polarized light ray tracing as one solution to the forward problem for the complex, nonlinear imaging mode of the polarized light field microscope. Solutions to the ill-posed inverse problem might be found in analytical methods and/or deep learning approaches that are based on training data generated by the forward solution presented here.

| S-EPMC10024342 | biostudies-literature

Measuring light transport properties using speckle patterns as structured illumination.

Project description:The measurement of light absorption and scattering properties of biological materials has several diagnostic and therapeutic applications. We can measure these properties for skin without contact using structured illumination and imaging. However, building simple handheld devices remains challenging due to motion artefacts and moving targets. To overcome this limitation, we project random speckle patterns instead of discrete spatial frequencies on the target. Since random patterns are spatially broadband, they capture more information per image, enabling frame-by-frame analysis. In this paper, we describe the statistics of objective speckles and demonstrate how the optical system is designed for spatially bandlimited illumination. Next, we use a diverse set of liquid tissue phantom to validate the method. We successfully demonstrate that a calibrated instrument can independently predict the two primary light transport properties of a homogeneous turbid system. This work is a starting point for analysing skin and other heterogeneous biological media in the future.

| S-EPMC6672017 | biostudies-literature

Accurate determination of CT point-spread-function with high precision.

Project description:The measurement of modulation transfer functions (MTFs) in computed tomography (CT) is often performed by scanning a point source phantom such as a thin wire or a microbead. In these methods the region of interest (ROI) is generally placed on the scanned image to crop the point source response. The aim of the present study was to examine the effect of ROI size on MTF measurement, and to optimize the ROI size. Using a 4 multidetector-row CT, MTFs were measured by the wire and bead methods for three types of reconstruction kernels designated as 'smooth', 'standard', and 'edge-enhancement' kernels. The size of a square ROI was changed from 30 to 50 pixels (approximately 2.9 to 4.9 mm). The accuracies of the MTFs were evaluated using the verification method. The MTFs measured by the wire and bead methods were dependent on ROI size, particularly in MTF measurement for the 'edge-enhancement' kernel. MTF accuracy evaluated by the verification method changed with ROI size, and we were able to determine the optimum ROI size for each method (wire/bead) and for each kernel. Using these optimal ROI sizes, the MTF obtained by the wire method was in strong agreement with the MTF obtained by the bead method in each kernel. Our data demonstrate that the difficulties in obtaining accurate MTFs for some kernels such as edge-enhancement can be overcome by incorporating the verification method into the wire and bead methods, allowing optimization of the ROI size to accurately determine the MTF.

| S-EPMC5714539 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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