Disclaimer: these examples are mostly taken from my pre-Eikomagos career
The aim of the study is to gain insight into the (co-)location of yeast and bacteria in the scalp afflicted by dandruff, particularly down hair follicles.
A scalp biopsy was embedded and imaged using a Gatan 3View system. The latter is a Field Emission Scanning Electron Microscope (FESEM) with an integrated ultramicrotome. The top face of the embedded sample is imaged and then the top 100nm layer is removed using the microtome. The next layer is imaged. We thus obtain:
As there were a few samples only, segmentation was performed by manual tracing the features of interest. In what follows we consider the top 100μm of a sample containing a hair follicle. The image on the left shows four slices (total slices 1000) through this sample in correct spatial relation to each other.
Identified in this volume were: the hair shaft, the oily sebum, substance, bacteria and yeast cells.
The image and video below show a 3D visualisation of the segmented volume. Both the bacteria and the yeast are associated with the sebum. The yeast cells can be found in the top 50μm, whereas the bacteria can be found throughout the entire 100μm volume and are in fact found down to 200μm (second volume from 100-200μm not shown).