Browse
Submit Data
Databases
API
Help

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lensless Three-Dimensional Quantitative Phase Imaging Using Phase Retrieval Algorithm.

ABSTRACT: Quantitative phase imaging (QPI) techniques are widely used for the label-free examining of transparent biological samples. QPI techniques can be broadly classified into interference-based and interferenceless methods. The interferometric methods which record the complex amplitude are usually bulky with many optical components and use coherent illumination. The interferenceless approaches which need only the intensity distribution and works using phase retrieval algorithms have gained attention as they require lesser resources, cost, space and can work with incoherent illumination. With rapid developments in computational optical techniques and deep learning, QPI has reached new levels of applications. In this tutorial, we discuss one of the basic optical configurations of a lensless QPI technique based on the phase-retrieval algorithm. Simulative studies on QPI of thin, thick, and greyscale phase objects with assistive pseudo-codes and computational codes in Octave is provided. Binary phase samples with positive and negative resist profiles were fabricated using lithography, and a single plane and two plane phase objects were constructed. Light diffracted from a point object is modulated by phase samples and the corresponding intensity patterns are recorded. The phase retrieval approach is applied for 2D and 3D phase reconstructions. Commented codes in Octave for image acquisition and automation using a web camera in an open source operating system are provided.

SUBMITTER: Anand V

PROVIDER: S-EPMC8321078 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Three dimensional imaging of gold-nanoparticles tagged samples using phase retrieval with two focus planes.

Project description:Optical sectioning microscopy can provide highly detailed three dimensional (3D) images of biological samples. However, it requires acquisition of many images per volume, and is therefore time consuming, and may not be suitable for live cell 3D imaging. We propose the use of the modified Gerchberg-Saxton phase retrieval algorithm to enable full 3D imaging of gold-particle tagged samples using only two images. The reconstructed field is free space propagated to all other focus planes using post processing, and the 2D z-stack is merged to create a 3D image of the sample with high fidelity. Because we propose to apply the phase retrieving on nano particles, the regular ambiguities typical to the Gerchberg-Saxton algorithm, are eliminated. The proposed concept is presented and validated both on simulated data as well as experimentally.

| S-EPMC4620448 | biostudies-other

Quantitative phase imaging through an ultra-thin lensless fiber endoscope.

Project description:Quantitative phase imaging (QPI) is a label-free technique providing both morphology and quantitative biophysical information in biomedicine. However, applying such a powerful technique to in vivo pathological diagnosis remains challenging. Multi-core fiber bundles (MCFs) enable ultra-thin probes for in vivo imaging, but current MCF imaging techniques are limited to amplitude imaging modalities. We demonstrate a computational lensless microendoscope that uses an ultra-thin bare MCF to perform quantitative phase imaging with microscale lateral resolution and nanoscale axial sensitivity of the optical path length. The incident complex light field at the measurement side is precisely reconstructed from the far-field speckle pattern at the detection side, enabling digital refocusing in a multi-layer sample without any mechanical movement. The accuracy of the quantitative phase reconstruction is validated by imaging the phase target and hydrogel beads through the MCF. With the proposed imaging modality, three-dimensional imaging of human cancer cells is achieved through the ultra-thin fiber endoscope, promising widespread clinical applications.

| S-EPMC9255502 | biostudies-literature

X-ray Phase Contrast Allows Three Dimensional, Quantitative Imaging of Hydrogel Implants.

Project description:Three dimensional imaging techniques are needed for the evaluation and assessment of biomaterials used for tissue engineering and drug delivery applications. Hydrogels are a particularly popular class of materials for medical applications but are difficult to image in tissue using most available imaging modalities. Imaging techniques based on X-ray Phase Contrast (XPC) have shown promise for tissue engineering applications due to their ability to provide image contrast based on multiple X-ray properties. In this manuscript, we investigate the use of XPC for imaging a model hydrogel and soft tissue structure. Porous fibrin loaded poly(ethylene glycol) hydrogels were synthesized and implanted in a rodent subcutaneous model. Samples were explanted and imaged with an analyzer-based XPC technique and processed and stained for histology for comparison. Both hydrogel and soft tissues structures could be identified in XPC images. Structure in skeletal muscle adjacent could be visualized and invading fibrovascular tissue could be quantified. There were no differences between invading tissue measurements from XPC and the gold-standard histology. These results provide evidence of the significant potential of techniques based on XPC for 3D imaging of hydrogel structure and local tissue response.

| S-EPMC4792647 | biostudies-literature

Long-term label-free assessments of individual bacteria using three-dimensional quantitative phase imaging and hydrogel-based immobilization.

Project description:Three-dimensional (3D) quantitative phase imaging (QPI) enables long-term label-free tomographic imaging and quantitative analysis of live individual bacteria. However, the Brownian motion or motility of bacteria in a liquid medium produces motion artifacts during 3D measurements and hinders precise cell imaging and analysis. Meanwhile, existing cell immobilization methods produce noisy backgrounds and even alter cellular physiology. Here, we introduce a protocol that utilizes hydrogels for high-quality 3D QPI of live bacteria maintaining bacterial physiology. We demonstrate long-term high-resolution quantitative imaging and analysis of individual bacteria, including measuring the biophysical parameters of bacteria and responses to antibiotic treatments.

| S-EPMC9806822 | biostudies-literature

Three-dimensional MR Fingerprinting for Quantitative Breast Imaging.

Project description:Purpose To develop a fast three-dimensional method for simultaneous T1 and T2 quantification for breast imaging by using MR fingerprinting. Materials and Methods In this prospective study, variable flip angles and magnetization preparation modules were applied to acquire MR fingerprinting data for each partition of a three-dimensional data set. A fast postprocessing method was implemented by using singular value decomposition. The proposed technique was first validated in phantoms and then applied to 15 healthy female participants (mean age, 24.2 years ± 5.1 [standard deviation]; range, 18-35 years) and 14 female participants with breast cancer (mean age, 55.4 years ± 8.8; range, 39-66 years) between March 2016 and April 2018. The sensitivity of the method to B1 field inhomogeneity was also evaluated by using the Bloch-Siegert method. Results Phantom results showed that accurate and volumetric T1 and T2 quantification was achieved by using the proposed technique. The acquisition time for three-dimensional quantitative maps with a spatial resolution of 1.6 × 1.6 × 3 mm3 was approximately 6 minutes. For healthy participants, averaged T1 and T2 relaxation times for fibroglandular tissues at 3.0 T were 1256 msec ± 171 and 46 msec ± 7, respectively. Compared with normal breast tissues, higher T2 relaxation time (68 msec ± 13) was observed in invasive ductal carcinoma (P < .001), whereas no statistical difference was found in T1 relaxation time (1183 msec ± 256; P = .37). Conclusion A method was developed for breast imaging by using the MR fingerprinting technique, which allows simultaneous and volumetric quantification of T1 and T2 relaxation times for breast tissues. © RSNA, 2018 Online supplemental material is available for this article.

| S-EPMC6312432 | biostudies-literature

Three-dimensional propagation in near-field tomographic X-ray phase retrieval.

Project description:This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.

| S-EPMC4770872 | biostudies-other

A super-resolution scanning algorithm for lensless microfluidic imaging using the dual-line array image sensor.

Project description:The lensless optical fluid microscopy is of great significance to the miniaturization, portability and low cost development of cell detection instruments. However, the resolution of the cell image collected directly is low, because the physical pixel size of the image sensor is the same order of magnitude as the cell size. To solve this problem, this paper proposes a super-resolution scanning algorithm using a dual-line array sensor and a microfluidic chip. For dual-line array sensor images, the multi-group velocity and acceleration of cells flowing through the line array sensor are calculated. Then the reconstruction model of the super-resolution image is constructed with variable acceleration. By changing the angle between the line array image sensor and the direction of cell flow, the super-resolution image scanning and reconstruction are achieved in both horizontal and vertical directions. In addition, it is necessary to study the row by row extraction algorithm for cell foreground image. In this paper, the dual-line array sensor is implemented by adjusting the acquisition window of the image sensor with a pixel size of 2.2?m. When the tilt angle is 21 degrees, the equivalent pixel size is 0.79?m, improved 2.8 times, and after de-diffraction its average size error was 3.249%. As the angle decreases, the image resolution is higher, but the amount of information is less. This super-resolution scanning algorithm can be integrated on the chip and used with a microfluidic chip to realize on-chip instrument.

| S-EPMC7316336 | biostudies-literature

Pixel Super-Resolution Phase Retrieval for Lensless On-Chip Microscopy via Accelerated Wirtinger Flow.

Project description:Empowered by pixel super-resolution (PSR) and phase retrieval techniques, lensless on-chip microscopy opens up new possibilities for high-throughput biomedical imaging. However, the current PSR phase retrieval approaches are time consuming in terms of both the measurement and reconstruction procedures. In this work, we present a novel computational framework for PSR phase retrieval to address these concerns. Specifically, a sparsity-promoting regularizer is introduced to enhance the well posedness of the nonconvex problem under limited measurements, and Nesterov's momentum is used to accelerate the iterations. The resulting algorithm, termed accelerated Wirtinger flow (AWF), achieves at least an order of magnitude faster rate of convergence and allows a twofold reduction in the measurement number while maintaining competitive reconstruction quality. Furthermore, we provide general guidance for step size selection based on theoretical analyses, facilitating simple implementation without the need for complicated parameter tuning. The proposed AWF algorithm is compatible with most of the existing lensless on-chip microscopes and could help achieve label-free rapid whole slide imaging of dynamic biological activities at subpixel resolution.

| S-EPMC9265759 | biostudies-literature

Quantitative volumetric Raman imaging of three dimensional cell cultures.

Project description:The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

| S-EPMC5364421 | biostudies-literature

Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging.

Project description:Novel methods for quantitative, transient-state multiparametric imaging are increasingly being demonstrated for assessment of disease and treatment efficacy. Here, we build on these by assessing the most common Non-Cartesian readout trajectories (2D/3D radials and spirals), demonstrating efficient anti-aliasing with a k-space view-sharing technique, and proposing novel methods for parameter inference with neural networks that incorporate the estimation of proton density. Our results show good agreement with gold standard and phantom references for all readout trajectories at 1.5 T and 3 T. Parameters inferred with the neural network were within 6.58% difference from the parameters inferred with a high-resolution dictionary. Concordance correlation coefficients were above 0.92 and the normalized root mean squared error ranged between 4.2 and 12.7% with respect to gold-standard phantom references for T1 and T2. In vivo acquisitions demonstrate sub-millimetric isotropic resolution in under five minutes with reconstruction and inference times < 7 min. Our 3D quantitative transient-state imaging approach could enable high-resolution multiparametric tissue quantification within clinically acceptable acquisition and reconstruction times.

| S-EPMC7427097 | 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