This course will cover two main topics. First we give some guidance about best practices and common pitfalls in state of the art imaging techniques of soil samples, rocks and sediments from scales of nm to cm. This includes typical samples sizes, quality of information, limits of detection, important sample preparation steps, common image artifacts, as well as practical considerations like accessibility and costs. We will demonstrate possible combined analyses to integrate physical and biogeochemical processes and properties in natural porous media. We will especially emphasize μCT imaging, fluorescence microscopy (including FISH approaches) and nano-scale secondary ion mass spectrometry (NanoSIMS).
Second we provide a short overview of fundamental image processing steps like image enhancement, image segmentation and image analysis. A few case studies are demonstrated with the popular, freely available Fiji/ImageJ software. There will be enough time for Q&A’s at the end to help the participants with the own work related to image analysis.