Such context can help with the interpretation of heterogeneity among a population of IMs as inherent to the IMs or in response to environmental heterogeneity (see below). The compatibility of Raman and Fourier-transform infrared imaging with other methods such as fluorescent in situ hybridization, stable-isotope probing, secondary ion mass spectrometry, and X-ray computed tomography makes it possible to extract local environmental context for the behavior or location of IMs. Harrison and Berry compare applications of vibrational microspectroscopy (a combination of spectroscopy and microscopy) for chemical imaging of microbial cells and their surroundings at high resolution and high throughput. describe a variation of flow cytometry called “mass cytometry” where fluorochromes are replaced with heavy metal ions and which allowed the researchers to establish a direct link between the uptake of (antibacterial) silver and cell viability at the single-cell level. While flow cytometry is a very useful high-throughput interrogation technique, it is incompatible with single-cell interrogation methods that are not fluorochromogenic. For wet approaches, much of the recently reported progress relates to increased compatibility with other methods that interrogate the same IM for multiple attributes or experiences, or at increasingly finer spatial or temporal resolution and/or with higher throughput. Techniques of importance to μIBE fall into one of two categories that we refer to here as “wet” and “dry.” Both types allow the observation and interrogation of IMs and their surroundings, but wet techniques do so of “real” IMs (i.e., bacteria, yeast, fungi, protists, etcetera) in a laboratory or field setting, while dry techniques involve virtual IMs (or “agents”) in computer-simulated environments ( Kreft et al.). We frame these articles in a narrative that explores the progress made on techniques that extract and process information from individual microbes (IMs) and their environment, how that information allows the discovery and prediction of novel single-cell behaviors, and how those discoveries might generate new ideas about the outcomes and impacts of microscopic activity at macroscopic levels. Embracing the idea that “progress in science depends on new techniques, new discoveries, and new ideas, probably in that order” (Brenner, 2002), we introduce here a collection of 14 articles authored by 65 leading experts on the topic of “The Individual Microbe” ( ). The collection and interpretation of data along these scales (from very small spatial dimensions to very large population sizes) remains a major challenge. The field of microbial individual-based ecology, or μIBE (Kreft et al., 2013), is grounded in the notion that to truly understand the interactions of microorganisms with their biotic and abiotic environment, one cannot ignore the scales at which such interactions occur.