Characterization of optical clearing mechanisms in muscle during treatment with glycerol and gadobutrol solutions

The recent increasing interest in the application of radiology contrasting agents to create transparency in biological tissues implies that the diffusion properties of those agents need evaluation. The comparison of those properties with the ones obtained for other optical clearing agents allows to perform an optimized agent selection to create optimized transparency in clinical applications. In this study, the evaluation and comparison of the diffusion properties of gadobutrol and glycerol in skeletal muscle was made, showing that although gadobutrol has a higher molar mass than glycerol, its low viscosity allows for a faster diffusion in the muscle. The characterization of the tissue dehydration and refractive index matching mechanisms of optical clearing was made in skeletal muscle, namely by the estimation of the diffusion coefficients for water, glycerol and gadobutrol. The estimated tortuosity values of glycerol (2.2) and of gadobutrol (1.7) showed a longer path-length for glycerol in the muscle.

Time-Resolved PIV Measurements and Turbulence Characteristics of Flow Inside an Open-Cell Metal Foam

Open-cell metal foams are porous medium for thermo-fluidic systems. However, their complex geometry makes it difficult to perform time-resolved (TR) measurements inside them. In this study, a TR particle image velocimetry (PIV) method is introduced for use inside open-cell metal foam structures. Stereolithography 3D printing methods and conventional post-processing methods cannot be applied to metal foam structures; therefore, PolyJet 3D printing and post-processing methods were employed to fabricate a transparent metal foam replica. The key to obtaining acceptable transparency in this method is the complete removal of the support material from the printing surfaces. The flow characteristics inside a 10-pore-per-inch (PPI) metal foam were analyzed in which porosity is 0.92 while laminar flow condition is applied to inlet. The flow inside the foam replica is randomly divided and combined by the interconnected pore network. Robust crosswise motion occurs inside foam with approximately 23% bulk speed. Strong influence on transverse motion by metal foam is evident. In addition, span-wise vorticity evolution is similar to the integral time length scale of the stream-wise center plane. The span-wise vorticity fluctuation through the foam arrangement is presented. It is believed that this turbulent characteristic is caused by the interaction of jets that have different flow directions inside the metal foam structure. The finite-time Lyapunov exponent method is employed to visualize the vortex ridges. Fluctuating attracting and repelling material lines are expected to enhance the heat and mass transfer. The results presented in this study could be useful for understanding the flow characteristics inside metal foams.

Fabrication and Bonding of Refractive Index Matched Microfluidics for Precise Measurements of Cell Mass

The optical properties of polymer materials used for microfluidic device fabrication can impact device performance when used for optical measurements. In particular, conventional polymer materials used for microfluidic devices have a large difference in refractive index relative to aqueous media generally used for biomedical applications. This can create artifacts when used for microscopy-based assays. Fluorination can reduce polymer refractive index, but at the cost of reduced adhesion, creating issues with device bonding. Here, we present a novel fabrication technique for bonding microfluidic devices made of NOA1348, which is a fluorinated, UV-curable polymer with a refractive index similar to that of water, to a glass substrate. This technique is compatible with soft lithography techniques, making this approach readily integrated into existing microfabrication workflows. We also demonstrate that this material is compatible with quantitative phase imaging, which we used to validate the refractive index of the material post-fabrication. Finally, we demonstrate the use of this material with a novel image processing approach to precisely quantify the mass of cells in the microchannel without the use of cell segmentation or tracking. The novel image processing approach combined with this low refractive index material eliminates an important source of error, allowing for high-precision measurements of cell mass with a coefficient of variance of 1%.

Experimental Investigation of the Pumping of a Model-Concrete through Pipes

Many practical aspects of processing fresh concrete depend on its rheology, such as the pumping of the material. It is known that a lubricating layer is formed in the process, which significantly reduces the pumping pressure. However, these phenomena can hardly be considered in the usual rheological measurements. A main problem is the optical inaccessibility of the material, which prevents estimations about, e.g., the thickness of the plug flow or particle migration. In this paper, the pneumatic pumping of a transparent model concrete is performed by means of a test plant. The flow profile over the entire pipe cross-section is resolved in time and space via Particle Image Velocimetry (PIV) measurements. This allows the comparison with the analytical flow profile from rheological measurements of the material using the Buckingham–Reiner equation. A reduction of the pressure loss to around 60% induced through segregation of the material is found. These measurements reflect the rheology of the material under realistic pumping conditions including particle migration. This makes it possible for the first time to observe a transparent material with concrete-like rheology under pulsating pumping conditions and to compare the true and calculated time-resolved pressure loss.

Fabrication of Refractive-index-matched Devices for Biomedical Microfluidics

The use of microfluidic devices has emerged as a defining tool for biomedical applications. When combined with modern microscopy techniques, these devices can be implemented as part of a robust platform capable of making simultaneous complementary measurements. The primary challenge created by the combination of these two techniques is the mismatch in refractive index between the materials traditionally used to make microfluidic devices and the aqueous solutions typically used in biomedicine. This mismatch can create optical artifacts near the channel or device edges. One solution is to reduce the refractive index of the material used to fabricate the device by using a fluorinated polymer such as MY133-V2000 whose refractive index is similar to that of water (n = 1.33). Here, the construction of a microfluidic device made out of MY133-V2000 using soft lithography techniques is demonstrated, using O2 plasma in conjunction with an acrylic holder to increase the adhesion between the MY133-V2000 fabricated device and the polydimethylsiloxane (PDMS) substrate. The device is then tested by incubating it filled with cell culture media for 24 h to demonstrate the ability of the device to maintain cell culture conditions during the course of a typical imaging experiment. Finally, quantitative phase microscopy (QPM) is used to measure the distribution of mass within the live adherent cells in the microchannel. This way, the increased precision, enabled by fabricating the device from a low index of refraction polymer such as MY133-V2000 in lieu of traditional soft lithography materials such as PDMS, is demonstrated. Overall, this approach for fabricating microfluidic devices can be readily integrated into existing soft lithography workflows in order to reduce optical artifacts and increase measurement precision.

Skeletal muscle dispersion (400-1000 nm) and kinetics at optical clearing

Skeletal muscle dispersion and optical clearing (OC) kinetics were studied experimentally to prove the existence of the refractive index (RI) matching mechanism of OC. Sample thickness and collimated transmittance spectra were measured during treatments with glucose (40%) and ethylene glycol (EG; 99%) solutions and used to obtain the time dependence of the RI of tissue fluids based on the proposed theoretical model. Calculated results demonstrated an increase of RI of tissue fluids and consequently proved the occurrence of the RI matching mechanism. The RI increase was observed for the wavelength range between 400 and 1000 nm and for the 2 probing molecules explored. We found that for 30 min treatment with 40% glucose and 99% EG, RI of sarcoplasm plus interstitial fluid was increased at 800 nm from 1.328 to 1.348 and from 1.328 to 1.369, respectively.

Live imaging looks deeper

Iodixanol provides an easy and affordable solution to a problem that has limited resolution and brightness when imaging living samples.

A tunable refractive index matching medium for live imaging cells, tissues and model organisms

In light microscopy, refractive index mismatches between media and sample cause spherical aberrations that often limit penetration depth and resolution. Optical clearing techniques can alleviate these mismatches, but they are so far limited to fixed samples. We present Iodixanol as a non-toxic medium supplement that allows refractive index matching in live specimens and thus substantially improves image quality in live-imaged primary cell cultures, planarians, zebrafish and human cerebral organoids.

DOI:http://dx.doi.org/10.7554/eLife.27240.001

Light microscopy is a key tool in biomedical research. For perfect images, light needs to be able to pass through the sample, the material (or “mounting medium”) that holds the sample in place, and finally the image-detecting equipment in a straight line. However, in practice, light rays often deviate away from this line because they move at different speeds in different materials; how much the speed of light changes is related to a property called the refractive index of the material. This is exactly the effect that causes a stick stuck into water to look bent at the water’s surface. In light microscopy, mismatches in refractive index significantly reduce quality of the images that can be obtained.

Live specimens are particularly challenging to image because different specimens have very different refractive indices compared to the mounting medium, which holds specimens in place but must also keep them alive. Although the addition of chemical compounds can theoretically match the refractive index of the mounting medium to that of the specimen, this approach has so far not been practical because such manipulations tend to kill the specimen. An important challenge has therefore been to identify a compound that can adjust, or “tune”, the refractive index of mounting media over a wide range, yet without harming the specimens.

Now, Boothe et al. have identified a chemical called Iodixanol as an ideal and easy to use supplement for tuning the refractive index of water-based live imaging media. Adding Iodixanol to the mounting media did not appear to have any toxic effects on cell cultures, developing zebrafish embryos or regenerating planarian flatworms. Importantly, Boothe et al. found that Iodixanol significantly improved the quality of the images collected from all of these different specimens.

It is important to stress that Iodixanol does not change the refractive index of the sample or cancel out refractive index differences within the sample – so it cannot render opaque specimens transparent. Nevertheless, Iodixanol supplementation is a simple and affordable technique to improve image quality in any live imaging application without having to resort to more expensive and highly specialized microscopes.

DOI:http://dx.doi.org/10.7554/eLife.27240.002

Films Consisting of Innumerable Tapered Nanopillars of Mesoporous Silica for Universal Antireflection Coatings

Films with a fine structure consisting of innumerable nanopillars of mesoporous silica (MPS) are formed by a reactive ion etching process with a fluorine-containing gas. Each nanopillar has a tapered shape with a uniform height, which effectively suppresses reflection by the formation of an ideal graded refractive index structure. The nanopillars are spontaneously formed under low-pressure conditions, wherein locally deposited Al-F compounds, originating from an alumina plate in the etching chamber, work as a fine etching mask. The high etching rate of the MPS film allows a very high aspect ratio of the nanopillars. The refractive index of the MPS nanopillars can be universally tuned by a controlled incorporation of TiO2 into the mesopores, which results in effective reduction of reflectance on a given substrate. The outstanding antireflection performance is experimentally demonstrated for glass substrates with a wide refractive index range.

Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analog. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyze bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance toward the discovery of the mechanisms of microbial colonisation of the rhizosphere.

Deep tissue fluorescent imaging in scattering specimens using confocal microscopy

In scattering specimens, multiphoton excitation and nondescanned detection improve imaging depth by a factor of 2 or more over confocal microscopy; however, imaging depth is still limited by scattering. We applied the concept of clearing to deep tissue imaging of highly scattering specimens. Clearing is a remarkably effective approach to improving image quality at depth using either confocal or multiphoton microscopy. Tissue clearing appears to eliminate the need for multiphoton excitation for deep tissue imaging.

Flow cytometry with gold nanoparticles and their clusters as scattering contrast agents: FDTD simulation of light-cell interaction

The formulation of the finite-difference time-domain (FDTD) approach is presented in the framework of its potential applications to in-vivo flow cytometry based on light scattering. The consideration is focused on comparison of light scattering by a single biological cell alone in controlled refractive-index matching conditions and by cells labeled by gold nanoparticles. The optical schematics including phase contrast (OPCM) microscopy as a prospective modality for in-vivo flow cytometry is also analyzed. The validation of the FDTD approach for the simulation of flow cytometry may open up a new avenue in the development of advanced cytometric techniques based on scattering effects from nanoscale targets.