Although research and new technologies have introduced different ways of observing microorganisms, including scanning and electron microscopy, these methods are expensive and require equipment that is typically not found in a middle school classroom. The transmission-through-dye technique (TTD; Gregg et al., 2010), a new optical microscopy method that can be used with current basic light microscopes, relies on the fairly simple mechanism of filtered light passing through a dyed medium to produce an image that reflects cell thickness. With this technique, living microorganisms look bright red against a dark background, and movement can be seen easily among dead microorganisms and debris that show up black. Since the technique is low-cost and easy to implement, it addresses the needs of practitioners and is appropriate for a wide array of school contexts. We describe a three-week, hands-on, inquiry-based unit on TTD microscopy for middle and high school students.