Quantitative mapping and spectroscopic characterization of particulate organic matter fractions in soil profiles with imaging VisNIR spectroscopy.

Organic matter is an important constituent of soils that controls many soil functions and is of vital importance for ecosystem services like climate regulation and food security. Soil organic matter (SOM consists of a wide spectrum of different organic substances that are highly heterogeneous in terms of chemical composition, stability against microbial decomposition and turnover time. SOM is heterogeneously distributed in the soil profile impeding its fast assessment. A technique to accurately measure SOM quality and quantity with a high spatial resolution in the soil profile is presently lacking. Imaging visible light and near infrared spectroscopy (imVisIR) is a promising technique for the fast and spatially resolved assessment of SOM quality and quantity. In this study, we evaluate the potential of imVisIR to quantitatively map the labile particulate organic matter fraction in undisturbed cores from mineral soils.

Hyperspectral imaging as a diagnostic tool to differentiate between amalgam tattoos and other dark pigmented intraoral lesions.

The goal of this project is to identify any in-depth benefits and drawbacks in the diagnosis of amalgam tattoos and other pigmented intraoral lesions using hyperspectral imagery collected from amalgam tattoos, benign, and malignant melanocytic neoplasms. Software solutions capable of classifying pigmented lesions of the skin already exist, but conventional red, green and blue images may be reaching an upper limit in their performance. Emerging technologies, such as hyperspectral imaging (HSI) utilize more than a hundred, continuous data channels, while also collecting data in the infrared. A total of 18 paraffin-embedded human tissue specimens of dark pigmented intraoral lesions (including the lip) were analyzed using visible and near-infrared (VIS-NIR) hyperspectral imagery obtained from HE-stained histopathological slides. Transmittance data were collected between 450 and 900 nm using a snapshot camera mounted to a microscope with a halogen light source. VIS-NIR spectra collected from different specimens, such as melanocytic cells and other tissues (eg, epithelium), produced distinct and diagnostic spectra that were used to identify these materials in several regions of interest, making it possible to distinguish between intraoral amalgam tattoos (intramucosal metallic foreign bodies) and melanocytic lesions of the intraoral mucosa and the lip (each with P < .01 using the independent t test). HSI is presented as a diagnostic tool for the rapidly growing field of digital pathology. In this preliminary study, amalgam tattoos were reliably differentiated from melanocytic lesions of the oral cavity and the lip.

Visible and near-infrared hyperspectral imaging techniques allow the reliable quantification of prognostic markers in lymphomas: A pilot study using the Ki67 proliferation index as an example.

In this study, we examined the suitability of visible and infrared (Vis-NIR) hyperspectral imaging (HSI) for the quantification of prognostic markers in non-Hodgkin lymphoma on the example of the Ki67 proliferation index. Ki67 quantification was done on six follicular lymphomas (FLs) and 12 diffuse large B-cell lymphomas (DLBCLs) by applying classic immunohistochemistry. The Ki67 index was comparatively assessed visually, using HSI-based quantification and a digital imaging analysis (DIA) platform. There was no significant difference between visual assessment (VA), DIA, and HSI in FLs. For DLBCLs, VA resulted in significantly higher Ki67 values than HSI (p = 0.023) and DIA (p = 0.006). No such difference was seen comparing analysis by HSI and DIA (p = 0.724). Cohen's κ revealed a "substantial correlation" of Ki67 values for HSI and DIA in FLs and DLBCLs (κ = 0.667 and 0.657). Here we provide the first evidence that, comparably to traditional DIA, HSI can be used reliably to quantify protein expression, as exemplified by the Ki67 proliferation index. By covering the near-infrared spectrum, HSI might offer additional information on the biochemical composition of pathological specimens, although our study could not show that HSI is clearly superior to conventional DIA. However, the analysis of multiplex immunohistochemistry might benefit from such an approach, especially if overlapping immunohistochemical reactions were possible. Further studies are needed to explore the impact of this method on the analysis and quantification of multiple marker expression in pathological specimens.

Small-scale distribution of copper in a Technosol horizon studied by nano-scale secondary ion mass spectrometry.

RATIONALE: In contaminated soil, copper (Cu) is commonly distributed among various very small particles. To enlighten the qualitative distribution of Cu in a contaminated Technosol (a soil developed from deposited technogenic material) on the sub-micron scale, we used nano-scale secondary ion mass spectrometry (NanoSIMS). METHODS: We studied seven areas (up to 40 µm × 40 µm) on a thin section of a soil horizon by NanoSIMS, measuring 12 C- , 18 O- , 32 S- , 63 Cu- and 56 Fe16 O- . We evaluated the NanoSIMS measurements with a novel digital image processing tool to enlighten the composition of measured areas and thus the distribution of Cu at the sub-micron scale. Image processing comprised spatial and spectral smoothing, normalization, endmember extraction and supervised classification. RESULTS: Copper was present in all areas studied on the thin section in hotspots. 63 Cu- was never the ion with the highest number of mean-normalized counts (MNCs). In classes indicating Cu accumulation, Fe or S had the highest MNCs with mostly small values for O, pointing to the presence of Cu in sulfides. Copper adsorbed on Fe oxides was also indicated. Direct interaction of Cu with organic matter was less important. Copper-containing minerals were rather adjacent to or surrounded by an organic matrix. CONCLUSIONS: The combination of NanoSIMS analyses with digital image processing gave us new insights into the distribution of Cu in contaminated soil. We suggest this combination as a new powerful tool for the identification of ionic contaminants in soil and other solid phases in the environment.

Identification of Distinct Functional Microstructural Domains Controlling C Storage in Soil.

The physical, chemical, and biological processes forming the backbone of important soil functions (e.g., carbon sequestration, nutrient and contaminant storage, and water transport) take place at reactive interfaces of soil particles and pores. The accessibility of these interfaces is determined by the spatial arrangement of the solid mineral and organic soil components, and the resulting pore system. Despite the development and application of novel imaging techniques operating at the micrometer and even nanometer scale, the microstructure of soils is still considered as a random arrangement of mineral and organic components. Using nanoscale secondary ion mass spectroscopy (NanoSIMS) and a novel digital image processing routine adapted from remote sensing (consisting of image preprocessing, endmember extraction, and a supervised classification), we extensively analyzed the spatial distribution of secondary ions that are characteristic of mineral and organic soil components on the submicrometer scale in an intact soil aggregate (40 measurements, each covering an area of 30 µm × 30 µm with a lateral resolution of 100 nm × 100 nm). We were surprised that the 40 spatially independent measurements clustered in just two complementary types of micrometer-sized domains. Each domain is characterized by a microarchitecture built of a definite mineral assemblage with various organic matter forms and a specific pore system, each fulfilling different functions in soil. Our results demonstrate that these microarchitectures form due to self-organization of the manifold mineral and organic soil components to distinct mineral assemblages, which are in turn stabilized by biophysical feedback mechanisms acting through pore characteristics and microbial accessibility. These microdomains are the smallest units in soil that fulfill specific functionalities.