4D Surface Reconstructions to Study Microscale Structures and Functions in Soil Biogeochemistry

Abstract

The development of high-resolution microscopy and spectroscopy techniques has allowed the analysis of microscopic 3D objects in fields like nanotechnology and life and soil sciences. Soils have the ability to incorporate and store large amounts of organic carbon. To study this organic matter (OM) sequestration, it is essential to analyze its association with soil minerals at the relevant microaggregate scale. This has been previously studied in 2D. However, 3D surface representations would allow a variable angle and magnification analysis, providing detailed insight on their architecture. Here we illustrate a 4D surface reconstruction workflow able to locate preferential sites for OM deposition with respect to microaggregate topography. We used Helium Ion Microscopy to acquire overlapping Secondary Electron (SE) images to reconstruct the soil topography in 3D. Then we used nanoscale Secondary Ion Mass Spectrometry imaging to chemically differentiate between the OM and mineral constituents forming the microaggregates. This image was projected onto the 3D SE model to create a 4D surface reconstruction. Our results show that organo-mineral associations mainly form at medium curvatures while flat and highly curved surfaces are avoided. This method presents an important step forward to survey the 3D physical structure and chemical composition of microscale biogeochemical systems correlatively.

An Analytical TOOLBOX for the Characterization of Chalks and Other Fine-Grained Rock Types within Enhanced Oil Recovery Research and Its Application—A Guideline

“…Methods that can be applied routinely because they have been tested and sample preparation has been developed for the noted issue of resolution and high-resolution imaging at the same time are TEM-EDS (transmission electron microscopy coupled with energy dispersive X-ray spectroscopy) and MLA (mineral liberation analyser) if the phases are not smaller than 1 micron. In the near future, further developed applications like HIM-SIMS (helium ion microscopy coupled with secondary ion mass spectrometry; [16,17] and RAMAN-SEM (Raman spectroscopy coupled with scanning electron microscopy) will be able to match the same objective [18,19].…”

SIMS Performed on Focused Ion Beam Instruments : In-situ Correlative Structural and Chemical Imaging

“…This allows to go beyond traditional data acquisition workflows and processing methods. To this end, complete acquisition workflows and multimodal image processing approaches were then specifically developed for the afore-mentioned FIB platforms [6,7].…”

4D Reconstructions from Microscale Photogrammetry: Correlation of 3D Surface Representations with SIMS to Link Microstructural Topography and Chemical Information

“…Combining EM structural images with chemical maps from SIMS allows to better visualize complementary information and provides a deeper understanding about the sample. While correlating microscopy and spectroscopy has been mostly done with 2D images so far [2], this methodology has been extended recently to 3 + 1 dimensions [3,4], i.e. by creating first a topographic 3D surface model of a region of interest (ROI) and then by overlaying it with chemical images acquired on the same area.…”