Production of 3D printed scale models from microscope volume datasets for use in STEM education

Understanding the three-dimensional morphology of a biological sample at the microscopic level is a prerequisite to a functional understanding of cell biology, tissue development and growth. Images of microscopic samples obtained by compound light microscopy are customarily recorded and represented in two dimensions from a single orientation making it difficult to extrapolate 3D context from the 2D information. The commercialisation of fast, laser-based microscope systems (e.g. confocal, multi-photon or lightsheet microscopy) capable of generating volume datasets of microscopic samples through optical sectioning, coupled with advances in computer technology allowing accurate volume rendering of these datasets, have facilitated significant improvement in our 3D understanding of the microscopic world in virtual space. The advent of affordable 3D printing technology now offers the prospect of generating morphologically accurate, physical models from these microscope volume datasets for use in science education, outreach and engagement. 3D printed scale replicas will provide improved sensory perception, offering tactile as well as visual interaction, leading to improved understanding of structure function relationships. Here we present a technique to reliably generate detailed, physical 3D models from Z-stacks of optical sections from confocal and lightsheet microscopes using affordable, entry-level 3D printing technology. We use the technique to generate 3D printed models of a variety of different biological samples at a range of scales including pollen grains from two species of plant; blood cells from both human and earthworm species, a section of plant root; the compound eye of an ant; and a developing Zebrafish larva; all of which have been used in our teaching, engagement and outreach activities. Our methods can, in principle, be used to generate 3D printed models from microscope volume datasets of any small fluorescent or reflective samples.