Using large area imaging to integrate biogeochemical data across spatial scales

Abstract:

Large Area Imaging (LAI) systems such as the Carl Zeiss "Atlas" module allow acquisition of SEM images on the scale of millimeters to centimeters with an image resolution ranging from nanometers to micrometers. This provides researchers with the powerful capability to investigate large areas of up to tens of millimeters in scale and expand anywhere within these areas to see details on the micrometer to nanometer scale while retaining full contextual information regarding the areas under investigation.

Biogeochemical processes operate on multiple scales and evidence of these phenomena can be difficult to observe across scales. For example, microbial etching of glass occurs on a nanometer scale as organic acids locally lower pH and destabilize Si-O bonds. However, interpreting a pattern of glass etching as abiotic or biogenic depends on observations at the micrometer to centimeter scale to assess evidence for microbial populations and/or biological behavior, assess fluid flow, changes in elemental composition and mineralogy. LAI is particularly suited to the investigation of multi-scale, interdisciplinary biogeochemical datasets.

Using LAI we have generated contiguous image data at resolutions as high as 100 nm (pixel size) for areas approaching 25 cm², using backscattered and secondary electrons in both traditional high vacuum and variable pressure SEM modes. Image stitching produces seamless mosaics composed of multiple image tiles; mosaic acquisition times can be as little as a few hours of fully automated operation.

Using this primary information, additional micrometer-scale data sets such as EDX spectroscopy, millimeter-scale datasets such as transmitted light photomicrographs, and nanometer-scale information such as synchrotron-based spectroscopy, can be registered and fused with the LAI SEM images. LAI and data fusion facilitates critical connections across spatial scales to test hypotheses that cross the threshold of traditional microscopy methods.