A Novel Technique for Producing Three-Dimensional Data Using Serial Sectioning and Semi-Automatic Image Classification

Abstract

The three-dimensional characterization of internal features, via metrics such as orientation, porosity, and connectivity, is important to a wide variety of scientific questions. Many spatial and morphological metrics only can be measured accurately through direct in situ three-dimensional observations of large (i.e., big enough to be statistically representative) volumes. For samples that lack material contrast between phases, serial grinding and imaging—which relies solely on color and textural characteristics to differentiate features—is a viable option for extracting such information. Here, we present the Grinding, Imaging, Reconstruction Instrument (GIRI), which automatically serially grinds and photographs centimeter-scale samples at micron resolution. Although the technique is destructive, GIRI produces an archival digital image stack. This digital image stack is run through a supervised machine-learning-based image processing technique that quickly and accurately segments data into predefined classes. These classified data then can be loaded into three-dimensional visualization software for measurement. We share three case studies to illustrate how GIRI can address questions with a significant morphological component for which two-dimensional or small-volume three-dimensional measurements are inadequate. The analyzed metrics include: the morphologies of objects and pores in a granular material, the bulk mineralogy of polyminerallic solids, and measurements of the internal angles and symmetry of crystals.

Shell microstructures (disturbance lines) of Arctica islandica (Bivalvia): a potential proxy for severe oxygen depletion

“…As shown here, the relationship between DO and BMU size or elongation was statistically significant, but the explained variability was too small and the error too large to be used to reconstruct DO concentration from morphometric data of the BMUs (Figure 9). Perhaps, the surface roughness, size, shape, or other parameters reveal a closer relationship with DO concentration if studied in three dimensions (e.g., Howes et al, 2021;Mehra et al, 2022).…”