Comparative analysis of tissue reconstruction algorithms for 3D histology.

Motivation: Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking. Results: We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches. Availability and implementation: Code: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702. Supplementary information: Supplementary data are available at Bioinformatics online.

Carbon coated TiO2 nanoparticles prepared by pulsed laser ablation in liquid, gaseous and supercritical CO2.

We report on the synthesis of TiO2 nanoparticles using nanosecond pulse laser ablation of titanium in liquid, gaseous and supercritical CO2. The produced particles were observed to be mainly anatase-TiO2 with some rutile-TiO2. In addition, the particles were covered by a carbon layer. Raman and x-ray diffraction data suggested that the rutile content increases with CO2 pressure. The nanoparticle size decreased and size distribution became narrower with the increase in CO2 pressure and temperature, however the variation trend was different for CO2 pressure compared to temperature. Pulsed laser ablation in pressurized CO2 is demonstrated as a single step method for making anatase-TiO2/carbon nanoparticles throughout the pressure and temperature ranges 5-40 MPa and 30 °C-50 °C, respectively.

Reactive laser interference patterning on titanium and zinc in high pressure CO2.

Direct laser interference patterning (DLIP) is a versatile technique for surface patterning that enables formation of micro-nano sized periodic structures on top of the target material. In this study, DLIP in high pressure, supercritical and liquid CO2 by 4-beam DLIP was used to pattern titanium and zinc targets. Field emission scanning electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy was used to characterize the patterned surfaces. Field emission SEM analysis showed presence of ordered uniform donut ring pattern with hollow centers for both titanium and zinc with a period slightly under 3 µm while topographical images from atomic force microscopy revealed donut rings protruding outwards typically around 200 nm from target surface and consisted of a crevice at the center with a depth typically around 300 nm and 250 nm for titanium and zinc target, respectively. Based on X-ray photoelectron spectroscopic analysis, this is the first study to report formation of TiO2, TiC, ZnCO3, and zinc hydroxy carbonate on the pattern by DLIP in supercritical and liquid CO2 for titanium and zinc targets. Pressurized CO2 is demonstrated as a promising environment with mirror-based DLIP system for reactive patterning. Due to the superior transport properties and solvent power of supercritical CO2, the current study opens possibilities for reactive patterning in environments that may not have been previously possible.

Pulsed Laser Ablation-Induced Green Synthesis of TiO2 Nanoparticles and Application of Novel Small Angle X-Ray Scattering Technique for Nanoparticle Size and Size Distribution Analysis.

This paper aims to introduce small angle X-ray scattering (SAXS) as a promising technique for measuring size and size distribution of TiO2 nanoparticles. In this manuscript, pulsed laser ablation in liquids (PLAL) has been demonstrated as a quick and simple technique for synthesizing TiO2 nanoparticles directly into deionized water as a suspension from titanium targets. Spherical TiO2 nanoparticles with diameters in the range 4-35 nm were observed with transmission electron microscopy (TEM). X-ray diffraction (XRD) showed highly crystalline nanoparticles that comprised of two main photoactive phases of TiO2: anatase and rutile. However, presence of minor amounts of brookite was also reported. The traditional methods for nanoparticle size and size distribution analysis such as electron microscopy-based methods are time-consuming. In this study, we have proposed and validated SAXS as a promising method for characterization of laser-ablated TiO2 nanoparticles for their size and size distribution by comparing SAXS- and TEM-measured nanoparticle size and size distribution. SAXS- and TEM-measured size distributions closely followed each other for each sample, and size distributions in both showed maxima at the same nanoparticle size. The SAXS-measured nanoparticle diameters were slightly larger than the respective diameters measured by TEM. This was because SAXS measures an agglomerate consisting of several particles as one big particle which slightly increased the mean diameter. TEM- and SAXS-measured mean diameters when plotted together showed similar trend in the variation in the size as the laser power was changed which along with extremely similar size distributions for TEM and SAXS validated the application of SAXS for size distribution measurement of the synthesized TiO2 nanoparticles.