Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Extended two-photon microscopy in live samples with Bessel beams: steadier focus, faster volume scans, and simpler stereoscopic imaging.

ABSTRACT: Two-photon microscopy has revolutionized functional cellular imaging in tissue, but although the highly confined depth of field (DOF) of standard set-ups yields great optical sectioning, it also limits imaging speed in volume samples and ease of use. For this reason, we recently presented a simple and retrofittable modification to the two-photon laser-scanning microscope which extends the DOF through the use of an axicon (conical lens). Here we demonstrate three significant benefits of this technique using biological samples commonly employed in the field of neuroscience. First, we use a sample of neurons grown in culture and move it along the z-axis, showing that a more stable focus is achieved without compromise on transverse resolution. Second, we monitor 3D population dynamics in an acute slice of live mouse cortex, demonstrating that faster volumetric scans can be conducted. Third, we acquire a stereoscopic image of neurons and their dendrites in a fixed sample of mouse cortex, using only two scans instead of the complete stack and calculations required by standard systems. Taken together, these advantages, combined with the ease of integration into pre-existing systems, make the extended depth-of-field imaging based on Bessel beams a strong asset for the field of microscopy and life sciences in general.

SUBMITTER: Theriault G

PROVIDER: S-EPMC4032997 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Colloidal density control with Bessel-Gauss beams.

Project description:Optical manipulation of colloidal systems is of high interest for both fundamental studies and practical applications. It has been shown that optically induced thermophoresis and nonlinear interactions can significantly affect the properties of dense colloidal media. However, macroscopic scale phenomena can also be generated at thermal equilibrium. Here, we demonstrate that steady-state variations of particle density can be created over large, three-dimensional regions by appropriately structured external optical fields. We prove analytically and experimentally that an optical vortex beam can dynamically control the spatial density of microscopic particles along the direction of its propagation. We show that these artificial steady-states can be generated at will and can be maintained indefinitely, which can be beneficial for applications such as path clearing and mass transportation.

| S-EPMC8192777 | biostudies-literature

Controllable light capsules employing modified Bessel-Gauss beams.

Project description:We report, in theory and experiment, on a novel class of controlled light capsules with nearly perfect darkness, directly employing intrinsic properties of modified Bessel-Gauss beams. These beams are able to naturally create three-dimensional bottle-shaped region during propagation as long as the parameters are properly chosen. Remarkably, the optical bottle can be controlled to demonstrate various geometries through tuning the beam parameters, thereby leading to an adjustable light capsule. We provide a detailed insight into the theoretical origin and characteristics of the light capsule derived from modified Bessel-Gauss beams. Moreover, a binary digital micromirror device (DMD) based scheme is first employed to shape the bottle beams by precise amplitude and phase manipulation. Further, we demonstrate their ability for optical trapping of core-shell magnetic microparticles, which play a particular role in biomedical research, with holographic optical tweezers. Therefore, our observations provide a new route for generating and controlling bottle beams and will widen the potentials for micromanipulation of absorbing particles, aerosols or even individual atoms.

| S-EPMC4937432 | biostudies-literature

Generation of wavelength-independent subwavelength Bessel beams using metasurfaces.

Project description:Bessel beams are of great interest due to their unique non-diffractive properties. Using a conical prism or an objective paired with an annular aperture are two typical approaches for generating zeroth-order Bessel beams. However, the former approach has a limited numerical aperture (NA), and the latter suffers from low efficiency, as most of the incident light is blocked by the aperture. Furthermore, an additional phase-modulating element is needed to generate higher-order Bessel beams, which in turn adds complexity and bulkiness to the system. We overcome these problems using dielectric metasurfaces to realize meta-axicons with additional functionalities not achievable with conventional means. We demonstrate meta-axicons with high NA up to 0.9 capable of generating Bessel beams with full width at half maximum about as small as ~?/3 (?=405?nm). Importantly, these Bessel beams have transverse intensity profiles independent of wavelength across the visible spectrum. These meta-axicons can enable advanced research and applications related to Bessel beams, such as laser fabrication, imaging and optical manipulation.

| S-EPMC6062187 | biostudies-literature

Cheaper, faster, simpler trypsin digestion for high-throughput targeted protein quantification.

Project description:IntroductionLC-MS-based methods for protein quantification have a stigma of being relatively expensive and low-throughput. This is partly due to the cost and speed of trypsin digestion, which has primarily focused on advancements in research-based biomarker discovery applications that rely on protein/peptide identifications rather than clinical biomarker quantification. However, there is a need for simple, fast, and reproducibly efficient surrogate peptide recovery in clinical biomarker quantification.MethodsMultiple methodologies were evaluated to enhance tryptic digestion for the analysis of thyroglobulin, a prototypical serum protein biomarker. The main criteria for assessment were the yield and speed of formation of surrogate peptides. Various factors such as different additives, types of trypsin, microwave- and pressure-assisted systems, and enzyme concentration were considered as key variables, in addition to digestion time.ResultsIt was observed that digestion additives/denaturants had a significant impact on the speed and yield of digestion for each surrogate peptide. Increasing the concentration of trypsin alone was found to accelerate digestions appreciably for most surrogate peptides, without affecting the yield. However, the use of sequencing-grade trypsins and microwave/pressure-assisted systems did not offer significant advantages over the use of 'standard-grade' TPCK-treated trypsin in combination with a conventional incubator, once digestion time and additive had been optimized.ConclusionWe have dispelled the notion that trypsin digestion is inherently slow and expensive for targeted quantification of serum proteins. Additionally, we have established a groundwork for experimentation that can pave the way for the creation of efficient trypsin digestion protocols, aiming to optimize yield, speed, and cost. It is our hope that these advancements will promote the wider incorporation of such assays in clinical laboratories.

| S-EPMC10716584 | biostudies-literature

Quantifying the influence of Bessel beams on image quality in optical coherence tomography.

Project description:Light scattered by turbid tissue is known to degrade optical coherence tomography (OCT) image contrast progressively with depth. Bessel beams have been proposed as an alternative to Gaussian beams to image deeper into turbid tissue. However, studies of turbid tissue comparing the image quality for different beam types are lacking. We present such a study, using numerically simulated beams and experimental OCT images formed by Bessel or Gaussian beams illuminating phantoms with optical properties spanning a range typical of soft tissue. We demonstrate that, for a given scattering parameter, the higher the scattering anisotropy the lower the OCT contrast, regardless of the beam type. When focusing both beams at the same depth in the sample, we show that, at focus and for equal input power and resolution, imaging with the Gaussian beam suffers less reduction of contrast. This suggests that, whilst Bessel beams offer extended depth of field in a single depth scan, for low numerical aperture (NA < 0.1) and typical soft tissue properties (scattering coefficient, ?s = 3.7 mm(-1) and high scattering anisotropy, g > 0.95), superior contrast (by up to ~40%) may be obtained over an extended depth range by a Gaussian beam combined with dynamic focusing.

| S-EPMC4806300 | biostudies-literature

Tailoring femtosecond 1.5-?m Bessel beams for manufacturing high-aspect-ratio through-silicon vias.

Project description:Three-dimensional integrated circuits (3D ICs) are an attractive replacement for conventional 2D ICs as high-performance, low-power-consumption, and small-footprint microelectronic devices. However, one of the major remaining challenges is the manufacture of high-aspect-ratio through-silicon vias (TSVs), which is a crucial technology for the assembly of 3D Si ICs. Here, we present the fabrication of high-quality TSVs using a femtosecond (fs) 1.5-?m Bessel beam. To eliminate the severe ablation caused by the sidelobes of a conventional Bessel beam, a fs Bessel beam is tailored using a specially designed binary phase plate. We demonstrate that the tailored fs Bessel beam can be used to fabricate a 2D array of approximately ?10-?m TSVs on a 100-?m-thick Si substrate without any sidelobe damage, suggesting potential application in the 3D assembly of 3D Si ICs.

| S-EPMC5241677 | biostudies-literature

Generating Bessel beams with broad depth-of-field by using phase-only acoustic holograms.

Project description:We report zero-th and high-order acoustic Bessel beams with broad depth-of-field generated using acoustic holograms. While the transverse field distribution of Bessel beams generated using traditional passive methods is correctly described by a Bessel function, these methods present a common drawback: the axial distribution of the field is not constant, as required for ideal Bessel beams. In this work, we experimentally, numerically and theoretically report acoustic truncated Bessel beams of flat-intensity along their axis in the ultrasound regime using phase-only holograms. In particular, the beams present a uniform field distribution showing an elongated focal length of about 40 wavelengths, while the transverse width of the beam remains smaller than 0.7 wavelengths. The proposed acoustic holograms were compared with 3D-printed fraxicons, a blazed version of axicons. The performance of both phase-only holograms and fraxicons is studied and we found that both lenses produce Bessel beams in a wide range of frequencies. In addition, high-order Bessel beam were generated. We report first order Bessel beams that show a clear phase dislocation along their axis and a vortex with single topological charge. The proposed method may have potential applications in ultrasonic imaging, biomedical ultrasound and particle manipulation applications using passive lenses.

| S-EPMC6934506 | biostudies-literature

Modal characterization using principal component analysis: application to Bessel, higher-order Gaussian beams and their superposition.

Project description:The modal characterization of various families of beams is a topic of current interest. We recently reported a new method for the simultaneous determination of both the azimuthal and radial mode indices for light fields possessing orbital angular momentum. The method is based upon probing the far-field diffraction pattern from a random aperture and using the recorded data as a 'training set'. We then transform the observed data into uncorrelated variables using the principal component analysis (PCA) algorithm. Here, we show the generic nature of this approach for the simultaneous determination of the modal parameters of Hermite-Gaussian and Bessel beams. This reinforces the widespread applicability of this method for applications including information processing, spectroscopy and manipulation. Additionally, preliminary results demonstrate reliable decomposition of superpositions of Laguerre-Gaussians, yielding the intensities and relative phases of each constituent mode. Thus, this approach represents a powerful method for characterizing the optical multi-dimensional Hilbert space.

| S-EPMC3594757 | biostudies-literature

Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays.

Project description:BackgroundDetection of SARS-CoV-2 infections is important for treatment, isolation of infected and exposed individuals, and contact tracing. RT-qPCR is the "gold-standard" method to sensitively detect SARS-CoV-2 RNA, but most laboratory-developed RT-qPCR assays involve complex steps. Here, we aimed to simplify RT-qPCR assays by streamlining reaction setup, eliminating RNA extraction, and proposing reduced-cost detection workflows that avoid the need for expensive qPCR instruments.MethodA low-cost RT-PCR based "kit" was developed for faster turnaround than the CDC developed protocol. We demonstrated three detection workflows: two that can be deployed in laboratories conducting assays of variable complexity, and one that could be simple enough for point-of-care. Analytical sensitivity was assessed using SARS-CoV-2 RNA spiked in simulated nasal matrix. Clinical performance was evaluated using contrived human nasal matrix (n = 41) and clinical nasal specimens collected from individuals with respiratory symptoms (n = 110).FindingThe analytical sensitivity of the lyophilised RT-PCR was 10 copies/reaction using purified SARS-CoV-2 RNA, and 20 copies/reaction when using direct lysate in simulated nasal matrix. Evaluation of assay performance on contrived human matrix showed 96.7-100% specificity and 100% sensitivity at ≥20 RNA copies. A head-to-head comparison with the standard CDC protocol on clinical specimens showed 83.8-94.6% sensitivity and 96.8-100% specificity. We found 3.6% indeterminate samples (undetected human control), lower than 8.1% with the standard protocol.InterpretationThis preliminary work should support laboratories or commercial entities to develop and expand access to Covid-19 testing. Software guidance development for this assay is ongoing to enable implementation in other settings. FUND: USA NIH R01AI140845 and Seattle Children's Research Institute.

| S-EPMC7878117 | biostudies-literature

High throughput detection of capillary stalling events with Bessel beam two-photon microscopy.

Project description:SignificanceBrief disruptions in capillary flow, commonly referred to as capillary "stalling," have gained interest recently for their potential role in disrupting cerebral blood flow and oxygen delivery. Approaches to studying this phenomenon have been hindered by limited volumetric imaging rates and cumbersome manual analysis. The ability to precisely and efficiently quantify the dynamics of these events will be key in understanding their potential role in stroke and neurodegenerative diseases, such as Alzheimer's disease.AimOur study aimed to demonstrate that the fast volumetric imaging rates offered by Bessel beam two-photon microscopy combined with improved data analysis throughput allows for faster and more precise measurement of capillary stall dynamics.ResultsWe found that while our analysis approach was unable to achieve full automation, we were able to cut analysis time in half while also finding stalling events that were missed in traditional blind manual analysis. The resulting data showed that our Bessel beam system was captured more stalling events compared to optical coherence tomography, particularly shorter stalling events. We then compare differences in stall dynamics between a young and old group of mice as well as a demonstrate changes in stalling before and after photothrombotic model of stroke. Finally, we also demonstrate the ability to monitor arteriole dynamics alongside stall dynamics.ConclusionsBessel beam two-photon microscopy combined with high throughput analysis is a powerful tool for studying capillary stalling due to its ability to monitor hundreds of capillaries simultaneously at high frame rates.

| S-EPMC10495839 | 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