Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Wide-field fluorescence molecular tomography with compressive sensing based preconditioning.

ABSTRACT: Wide-field optical tomography based on structured light illumination and detection strategies enables efficient tomographic imaging of large tissues at very fast acquisition speeds. However, the optical inverse problem based on such instrumental approach is still ill-conditioned. Herein, we investigate the benefit of employing compressive sensing-based preconditioning to wide-field structured illumination and detection approaches. We assess the performances of Fluorescence Molecular Tomography (FMT) when using such preconditioning methods both in silico and with experimental data. Additionally, we demonstrate that such methodology could be used to select the subset of patterns that provides optimal reconstruction performances. Lastly, we compare preconditioning data collected using a normal base that offers good experimental SNR against that directly acquired with optimal designed base. An experimental phantom study is provided to validate the proposed technique.

SUBMITTER: Yao R

PROVIDER: S-EPMC4679262 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Wide-field fluorescence molecular tomography with compressive sensing based preconditioning.

Yao Ruoyang R Pian Qi Q Intes Xavier X

Biomedical optics express 20151117 12

Wide-field optical tomography based on structured light illumination and detection strategies enables efficient tomographic imaging of large tissues at very fast acquisition speeds. However, the optical inverse problem based on such instrumental approach is still ill-conditioned. Herein, we investigate the benefit of employing compressive sensing-based preconditioning to wide-field structured illumination and detection approaches. We assess the performances of Fluorescence Molecular Tomography ( ...[more]

PMID: 26713202

Similar Datasets

Compressive hyperspectral time-resolved wide-field fluorescence lifetime imaging.

Project description:Spectrally resolved fluorescence lifetime imaging1-3 and spatial multiplexing1,4,5 have offered information content and collection-efficiency boosts in microscopy, but efficient implementations for macroscopic applications are still lacking. An imaging platform based on time-resolved structured light and hyperspectral single-pixel detection has been developed to perform quantitative macroscopic fluorescence lifetime imaging (MFLI) over a large field of view (FOV) and multiple spectral bands simultaneously. The system makes use of three digital micromirror device (DMD)-based spatial light modulators (SLMs) to generate spatial optical bases and reconstruct N by N images over 16 spectral channels with a time-resolved capability (~40 ps temporal resolution) using fewer than N2 optical measurements. We demonstrate the potential of this new imaging platform by quantitatively imaging near-infrared (NIR) Förster resonance energy transfer (FRET) both in vitro and in vivo. The technique is well suited for quantitative hyperspectral lifetime imaging with a high sensitivity and paves the way for many important biomedical applications.

| S-EPMC5726531 | biostudies-literature

Wide-Field Fluorescence Microscopy of Real-Time Bioconjugation Sensing.

Project description:We apply wide-field fluorescence microscopy to measure real-time attachment of photosynthetic proteins to plasmonically active silver nanowires. The observation of this effect is enabled, on the one hand, by sensitive detection of fluorescence and, on the other hand, by plasmonic enhancement of protein fluorescence. We examined two sample configurations with substrates being a bare glass coverslip and a coverslip functionalized with a monolayer of streptavidin. The different preparation of the substrate changes the observed behavior as far as attachment of the protein is concerned as well as its subsequent photobleaching. For the latter substrate the conjugation process is measurably slower. The described method can be universally applied in studying protein-nanostructure interactions for real-time fluorescence-based sensing.

| S-EPMC5796375 | biostudies-literature

Real-time compressive sensing spectral domain optical coherence tomography.

Project description:We developed and demonstrated real-time compressive sensing (CS) spectral domain optical coherence tomography (SD-OCT) B-mode imaging at excess of 70 fps. The system was implemented using a conventional desktop computer architecture having three graphics processing units. This result shows speed gain of 459 and 112 times compared to the best CS implementations based on the MATLAB and C++, respectively, and that real-time CS SD-OCT imaging can finally be realized.

| S-EPMC4114772 | biostudies-literature

Separation of Spacecraft Noise From Geomagnetic Field Observations Through Density-Based Cluster Analysis and Compressive Sensing.

Project description:The use of magnetometers for space exploration is inhibited by magnetic noise generated by spacecraft electrical systems. Mechanical booms are traditionally used to extend magnetometers away from noise sources. If a spacecraft is equipped with multiple magnetometers, signal processing algorithms can be used to compare magnetometer measurements and remove stray magnetic noise signals. We propose the use of density-based cluster analysis to identify spacecraft noise signals and compressive sensing to separate spacecraft noise from geomagnetic field data. This method assumes no prior knowledge of the number, location, or amplitude of noise signals, but assumes that they have minimal overlapping spectral properties. We demonstrate the validity of this algorithm by separating high latitude magnetic perturbations recorded by the low-Earth orbiting satellite, SWARM, from noise signals in simulation and in a laboratory experiment using a mock CubeSat apparatus. In the case of more noise sources than magnetometers, this problem is an instance of underdetermined blind source separation (UBSS). This work presents a UBSS signal processing algorithm to remove spacecraft noise and minimize the need for a mechanical boom.

| S-EPMC9541872 | biostudies-literature

GPU-accelerated non-uniform fast Fourier transform-based compressive sensing spectral domain optical coherence tomography.

Project description:We implemented the graphics processing unit (GPU) accelerated compressive sensing (CS) non-uniform in k-space spectral domain optical coherence tomography (SD OCT). Kaiser-Bessel (KB) function and Gaussian function are used independently as the convolution kernel in the gridding-based non-uniform fast Fourier transform (NUFFT) algorithm with different oversampling ratios and kernel widths. Our implementation is compared with the GPU-accelerated modified non-uniform discrete Fourier transform (MNUDFT) matrix-based CS SD OCT and the GPU-accelerated fast Fourier transform (FFT)-based CS SD OCT. It was found that our implementation has comparable performance to the GPU-accelerated MNUDFT-based CS SD OCT in terms of image quality while providing more than 5 times speed enhancement. When compared to the GPU-accelerated FFT based-CS SD OCT, it shows smaller background noise and less side lobes while eliminating the need for the cumbersome k-space grid filling and the k-linear calibration procedure. Finally, we demonstrated that by using a conventional desktop computer architecture having three GPUs, real-time B-mode imaging can be obtained in excess of 30 fps for the GPU-accelerated NUFFT based CS SD OCT with frame size 2048(axial) × 1,000(lateral).

| S-EPMC4083058 | biostudies-other

Wide-field optical coherence tomography based microangiography for retinal imaging.

Project description:Optical coherence tomography angiography (OCTA) allows for the evaluation of functional retinal vascular networks without a need for contrast dyes. For sophisticated monitoring and diagnosis of retinal diseases, OCTA capable of providing wide-field and high definition images of retinal vasculature in a single image is desirable. We report OCTA with motion tracking through an auxiliary real-time line scan ophthalmoscope that is clinically feasible to image functional retinal vasculature in patients, with a coverage of more than 60 degrees of retina while still maintaining high definition and resolution. We demonstrate six illustrative cases with unprecedented details of vascular involvement in retinal diseases. In each case, OCTA yields images of the normal and diseased microvasculature at all levels of the retina, with higher resolution than observed with fluorescein angiography. Wide-field OCTA technology will be an important next step in augmenting the utility of OCT technology in clinical practice.

| S-EPMC4766473 | biostudies-literature

Adaptive wide-field optical tomography.

Project description:We describe a wide-field optical tomography technique, which allows the measurement-guided optimization of illumination patterns for enhanced reconstruction performances. The iterative optimization of the excitation pattern aims at reducing the dynamic range in photons transmitted through biological tissue. It increases the number of measurements collected with high photon counts resulting in a dataset with improved tomographic information. Herein, this imaging technique is applied to time-resolved fluorescence molecular tomography for preclinical studies. First, the merit of this approach is tested by in silico studies in a synthetic small animal model for typical illumination patterns. Second, the applicability of this approach in tomographic imaging is validated in vitro using a small animal phantom with two fluorescent capillaries occluded by a highly absorbing inclusion. The simulation study demonstrates an improvement of signal transmitted (?2 orders of magnitude) through the central portion of the small animal model for all patterns considered. A corresponding improvement in the signal at the emission wavelength by 1.6 orders of magnitude demonstrates the applicability of this technique for fluorescence molecular tomography. The successful discrimination and localization (?1??mm error) of the two objects with higher resolution using the optimized patterns compared with nonoptimized illumination establishes the improvement in reconstruction performance when using this technique.

| S-EPMC3591745 | biostudies-literature

Wide-field Optical Coherence Tomography Imaging of Excised Breast Tissue.

Project description:This is a single-arm, multi-center data collection study designed to collect WF-OCT imaging data of excised breast tissue margins with corresponding margin status from histopathology.

| 2328012 | ecrin-mdr-crc

Wide field-of-view Talbot grid-based microscopy for multicolor fluorescence imaging.

Project description:The capability to perform multicolor, wide field-of-view (FOV) fluorescence microscopy imaging is important in screening and pathology applications. We developed a microscopic slide-imaging system that can achieve multicolor, wide FOV, fluorescence imaging based on the Talbot effect. In this system, a light-spot grid generated by the Talbot effect illuminates the sample. By tilting the excitation beam, the Talbot-focused spot scans across the sample. The images are reconstructed by collecting the fluorescence emissions that correspond to each focused spot with a relay optics arrangement. The prototype system achieved an FOV of 12 × 10 mm(2) at an acquisition time as fast as 23 s for one fluorescence channel. The resolution is fundamentally limited by spot size, with a demonstrated full-width at half-maximum spot diameter of 1.2 μm. The prototype was used to nimage green fluorescent beads, double-stained human breast cancer SK-BR-3 cells, Giardia lamblia cysts, and the Cryptosporidium parvum oocysts. This imaging method is scalable and simple for implementation of high-speed wide FOV fluorescence microscopy.

| S-EPMC3726246 | biostudies-other

Net-FLICS: fast quantitative wide-field fluorescence lifetime imaging with compressed sensing - a deep learning approach.

Project description:Macroscopic fluorescence lifetime imaging (MFLI) via compressed sensed (CS) measurements enables efficient and accurate quantification of molecular interactions in vivo over a large field of view (FOV). However, the current data-processing workflow is slow, complex and performs poorly under photon-starved conditions. In this paper, we propose Net-FLICS, a novel image reconstruction method based on a convolutional neural network (CNN), to directly reconstruct the intensity and lifetime images from raw time-resolved CS data. By carefully designing a large simulated dataset, Net-FLICS is successfully trained and achieves outstanding reconstruction performance on both in vitro and in vivo experimental data and even superior results at low photon count levels for lifetime quantification.

| S-EPMC6400960 | 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