$$\textsf {Fluo}$$: A Domain-Specific Language for Experiments in Fluorescence Microscopy (Application Paper)

Fluorescence microscopy is a true workhorse in the domain of life sciences, essential for unraveling the inner workings of cells and tissue. It is not only used from day to day in industry, also academia push boundaries in research using and doing fluorescence microscopy. It is in the latter context that software that is sufficiently modular in terms of experiments and hardware is desirable. Existing solutions are too closely tailored to their accompanying hardware setup or too limited in terms of expressivity. We present Fluo: a domain-specific language (DSL) in Haskell for setting up fluorescence microscopy experiments that can be combined and nested freely. It provides domain-specific features such as stage loops and time lapses, and is modular in terms of hardware connections. Fluo has been operational since 2015 at the Nanobiology Lab. It has not only improved researchers' efficiency, but has also given rise to novel research results. For example, performing simultaneous Forster Resonant Energy Transfer (FRET) measurements, a mechanism for tracking energy transfer between a donor-acceptor pair, uses advanced time-lapse experiments and serves as an example use case in the paper. We reflect on the choice of Haskell as a host language and the usability of the DSL.