Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Three-dimensional label-free histological imaging of whole organs by microtomy-assisted autofluorescence tomography.

ABSTRACT: Three-dimensional (3D) histology is vitally important to characterize disease-induced tissue heterogeneity at the individual cell level. However, it remains challenging for both high-throughput 3D imaging and volumetric reconstruction. Here we propose a label-free, cost-effective, and ready-to-use 3D histological imaging technique, termed microtomy-assisted autofluorescence tomography with ultraviolet excitation (MATE). With the combination of block-face imaging and serial microtome sectioning, MATE can achieve rapid and label-free imaging of paraffin-embedded whole organs at an acquisition speed of 1 cm³ per 4 h with a voxel resolution of 1.2 × 1.2 × 10 μm³. We demonstrate that MATE enables simultaneous visualization of cell nuclei, fiber tracts, and blood vessels in mouse/human brains without tissue staining or clearing. Moreover, diagnostic features, including nuclear size and packing density, can be quantitatively extracted with high accuracy. MATE is augmented to the current slide-based 2D histology, holding great promise to facilitate histopathological interpretation at the organelle level.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC8786675 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Label-free automated three-dimensional imaging of whole organs by microtomy-assisted photoacoustic microscopy.

Project description:Three-dimensional (3D) optical imaging of whole biological organs with microscopic resolution has remained a challenge. Most versions of such imaging techniques require special preparation of the tissue specimen. Here we demonstrate microtomy-assisted photoacoustic microscopy (mPAM) of mouse brains and other organs, which automatically acquires serial distortion-free and registration-free images with endogenous absorption contrasts. Without tissue staining or clearing, mPAM generates micrometer-resolution 3D images of paraffin- or agarose-embedded whole organs with high fidelity, achieved by label-free simultaneous sensing of DNA/RNA, hemoglobins, and lipids. mPAM provides histology-like imaging of cell nuclei, blood vessels, axons, and other anatomical structures, enabling the application of histopathological interpretation at the organelle level to analyze a whole organ. Its deep tissue imaging capability leads to less sectioning, resulting in negligible sectioning artifact. mPAM offers a new way to better understand complex biological organs.

| S-EPMC5680318 | biostudies-literature

Three-dimensional label-free imaging and analysis of Pinus pollen grains using optical diffraction tomography.

Project description:The structure of pollen grains is related to the reproductive function of the plants. Here, three-dimensional (3D) refractive index maps were obtained for individual conifer pollen grains using optical diffraction tomography (ODT). The 3D morphological features of pollen grains from pine trees were investigated using measured refractive index maps, in which distinct substructures were clearly distinguished and analyzed. Morphological and physiochemical parameters of the pollen grains were quantified from the obtained refractive index (RI) maps and used to quantitatively study the interspecific differences of pollen grains from different strains. Our results demonstrate that ODT can assess the structure of pollen grains. This label-free and rapid 3D imaging approach may provide a new platform for understanding the physiology of pollen grains.

| S-EPMC5788986 | biostudies-literature

In vivo, label-free, three-dimensional quantitative imaging of kidney microcirculation using Doppler optical coherence tomography.

Project description:Doppler optical coherence tomography (DOCT) is a functional extension of optical coherence tomography (OCT) and is currently being employed in several clinical arenas to quantify blood flow in vivo. In this study, the objective was to investigate the feasibility of DOCT to image kidney microcirculation, specifically, glomerular blood flow. DOCT is able to capture three-dimensional (3D) data sets consisting of a series of cross-sectional images in real time, which enables label-free and non-destructive quantification of glomerular blood flow. The kidneys of adult, male Munich-Wistar rats were exposed through laparotomy procedure after being anesthetized. Following exposure of the kidney beneath the DOCT microscope, glomerular blood flow was observed. The effects of acute mannitol and angiotensin II infusion were also observed. Glomerular blood flow was quantified for the induced physiological states and compared with baseline measurements. Glomerular volume, cumulative Doppler volume, and Doppler flow range parameters were computed from 3D OCT/DOCT data sets. Glomerular size was determined from OCT, and DOCT readily revealed glomerular blood flow. After infusion of mannitol, a significant increase in blood flow was observed and quantified, and following infusion of angiontensin II, a significant decrease in blood flow was observed and quantified. Also, blood flow histograms were produced to illustrate differences in blood flow rate and blood volume among the induced physiological states. We demonstrated 3D DOCT imaging of rat kidney microcirculation in the glomerulus in vivo. Dynamic changes in blood flow were detected under altered physiological conditions demonstrating the real-time imaging capability of DOCT. This method holds promise to allow non-invasive imaging of kidney blood flow for transplant graft evaluation or monitoring of altered-renal hemodynamics related to disease progression.

| S-EPMC3312876 | biostudies-literature

Transport of intensity diffraction tomography with non-interferometric synthetic aperture for three-dimensional label-free microscopy.

Project description:We present a new label-free three-dimensional (3D) microscopy technique, termed transport of intensity diffraction tomography with non-interferometric synthetic aperture (TIDT-NSA). Without resorting to interferometric detection, TIDT-NSA retrieves the 3D refractive index (RI) distribution of biological specimens from 3D intensity-only measurements at various illumination angles, allowing incoherent-diffraction-limited quantitative 3D phase-contrast imaging. The unique combination of z-scanning the sample with illumination angle diversity in TIDT-NSA provides strong defocus phase contrast and better optical sectioning capabilities suitable for high-resolution tomography of thick biological samples. Based on an off-the-shelf bright-field microscope with a programmable light-emitting-diode (LED) illumination source, TIDT-NSA achieves an imaging resolution of 206 nm laterally and 520 nm axially with a high-NA oil immersion objective. We validate the 3D RI tomographic imaging performance on various unlabeled fixed and live samples, including human breast cancer cell lines MCF-7, human hepatocyte carcinoma cell lines HepG2, mouse macrophage cell lines RAW 264.7, Caenorhabditis elegans (C. elegans), and live Henrietta Lacks (HeLa) cells. These results establish TIDT-NSA as a new non-interferometric approach to optical diffraction tomography and 3D label-free microscopy, permitting quantitative characterization of cell morphology and time-dependent subcellular changes for widespread biological and medical applications.

| S-EPMC9160286 | biostudies-literature

Label-free drug response evaluation of human derived tumor spheroids using three-dimensional dynamic optical coherence tomography.

Project description:This study aims at demonstrating label-free drug-response-patterns assessment of different tumor spheroids and drug types by dynamic optical coherence tomography (D-OCT). The study involved human breast cancer (MCF-7) and colon cancer (HT-29) spheroids. The MCF-7 and HT-29 spheroids were treated with paclitaxel (Taxol; PTX) and the active metabolite of irinotecan SN-38, respectively. The drugs were applied with 0 (control), 0.1, 1, and 10 μM concentrations and the treatment durations were 1, 3, and 6 days. A swept-source OCT microscope equipped with a repeated raster scanning protocol was used to scan the spheroids. Logarithmic intensity variance (LIV) and late OCT correlation decay speed (OCDS[Formula: see text]) algorithms were used to visualize the tumor spheroid dynamics. LIV and OCDS[Formula: see text] images visualized different response patterns of the two types of spheroids. In addition, spheroid morphology, LIV, and OCDS[Formula: see text] quantification showed different time-courses among the spheroid and drug types. These results may indicate different action mechanisms of the drugs. The results showed the feasibility of D-OCT for the evaluation of drug response patterns of different cell spheroids and drug types and suggest that D-OCT can perform anti-cancer drug testing.

| S-EPMC10505213 | biostudies-literature

Photoimprint photoacoustic microscopy for three-dimensional label-free subdiffraction imaging.

Project description:Subdiffraction optical microscopy allows the imaging of cellular and subcellular structures with a resolution finer than the diffraction limit. Here, combining the absorption-based photoacoustic effect and intensity-dependent photobleaching effect, we demonstrate a simple method for subdiffraction photoacoustic imaging of both fluorescent and nonfluorescent samples. Our method is based on a double-excitation process, where the first excitation pulse partially and inhomogeneously bleaches the molecules in the diffraction-limited excitation volume, thus biasing the signal contributions from a second excitation pulse striking the same region. The differential signal between the two excitations preserves the signal contribution mostly from the center of the excitation volume, and dramatically sharpens the lateral resolution. Moreover, due to the nonlinear nature of the signal, our method offers an inherent optical sectioning capability, which is lacking in conventional photoacoustic microscopy. By scanning the excitation beam, we performed three-dimensional subdiffraction imaging of varied fluorescent and nonfluorescent species. As any molecules have absorption, this technique has the potential to enable label-free subdiffraction imaging, and can be transferred to other optical imaging modalities or combined with other subdiffraction methods.

| S-EPMC3957272 | biostudies-literature

Label-free photoacoustic tomography of whole mouse brain structures ex vivo.

Project description:Capitalizing on endogenous hemoglobin contrast, photoacoustic-computed tomography (PACT), a deep-tissue high-resolution imaging modality, has drawn increasing interest in neuroimaging. However, most existing studies are limited to functional imaging on the cortical surface and the deep brain structural imaging capability of PACT has never been demonstrated. Here, we explicitly studied the limiting factors of deep brain PACT imaging. We found that the skull distorted the acoustic signal and blood suppressed the structural contrast from other chromophores. When the two effects are mitigated, PACT can potentially provide high-resolution label-free imaging of structures in the entire mouse brain. With [Formula: see text] in-plane resolution, we can clearly identify major structures of the brain, which complements magnetic resonance microscopy for imaging small-animal brain structures. Spectral PACT studies indicate that structural contrasts mainly originate from cytochrome distribution and that the presence of lipid sharpens the image contrast; brain histology results provide further validation. The feasibility of imaging the structure of the brain in vivo is also discussed. Our results demonstrate that PACT is a promising modality for both structural and functional brain imaging.

| S-EPMC5696384 | biostudies-literature

Simultaneous label-free autofluorescence-multiharmonic microscopy and beyond.

Project description:Without sophisticated data inversion algorithms, nonlinear optical microscopy can acquire images at subcellular resolution and relatively large depth, with plausible endogenous contrasts indicative of authentic biological and pathological states. Although independent contrasts have been derived by sequentially imaging the same sample plane or volume under different and often optimized excitation conditions, new laser source engineering with inputs from key biomolecules surprisingly enable real-time simultaneous acquisition of multiple endogenous molecular contrasts to segment a rich set of cellular and extracellular components. Since this development allows simple single-beam single-shot excitation and simultaneous multicontrast epidirected signal detection, the resulting platform avoids perturbative sample pretreatments such as fluorescent labeling, mechanical sectioning, scarce or interdependent contrast generation, constraints to the sample or imaging geometry, and intraimaging motion artifacts that have limited in vivo nonlinear optical molecular imaging.

| S-EPMC7880241 | biostudies-literature

Rationalisation and Validation of an Acrylamide-Free Procedure in Three-Dimensional Histological Imaging.

Project description:Three-dimensional visualization of intact tissues is now being achieved by turning tissues transparent. CLARITY is a unique tissue clearing technique, which features the use of detergents to remove lipids from fixed tissues to achieve optical transparency. To preserve tissue integrity, an acrylamide-based hydrogel has been proposed to embed the tissue. In this study, we examined the rationale behind the use of acrylamide in CLARITY, and presented evidence to suggest that the omission of acrylamide-hydrogel embedding in CLARITY does not alter the preservation of tissue morphology and molecular information in fixed tissues. We therefore propose a novel and simplified workflow for formaldehyde-fixed tissue clearing, which will facilitate the laboratory implementation of this technique. Furthermore, we have investigated the basic tissue clearing process in detail and have highlighted some areas for targeted improvement of technologies essential for the emerging subject of three-dimensional histology.

| S-EPMC4928791 | biostudies-literature

Intravital imaging by simultaneous label-free autofluorescence-multiharmonic microscopy.

Project description:Intravital microscopy (IVM) emerged and matured as a powerful tool for elucidating pathways in biological processes. Although label-free multiphoton IVM is attractive for its non-perturbative nature, its wide application has been hindered, mostly due to the limited contrast of each imaging modality and the challenge to integrate them. Here we introduce simultaneous label-free autofluorescence-multiharmonic (SLAM) microscopy, a single-excitation source nonlinear imaging platform that uses a custom-designed excitation window at 1110?nm and shaped ultrafast pulses at 10?MHz to enable fast (2-orders-of-magnitude improvement), simultaneous, and efficient acquisition of autofluorescence (FAD and NADH) and second/third harmonic generation from a wide array of cellular and extracellular components (e.g., tumor cells, immune cells, vesicles, and vessels) in living tissue using only 14?mW for extended time-lapse investigations. Our work demonstrates the versatility and efficiency of SLAM microscopy for tracking cellular events in vivo, and is a major enabling advance in label-free IVM.

| S-EPMC5974075 | 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