Algorithms for the selection of fluorescent reporters

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve with ad hoc methods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through. Vaidyanathan et al. present a heuristic algorithm for the selection of fluorescent reporters in the context of single-cell analysis. They present a tool to enable biologists to design multi-colour fluorophore panels based on specific equipment's configurations. The authors demonstrate the efficacy of their algorithm by comparing computational predictions with experimental observations.

Automated summary

Molecular biologists rely on fluorescent probes for measurements, and selecting an ideal set of fluorophores is a multidimensional problem with suboptimal choices leading to unreliable results. Vaidyanathan et al. present an algorithm to design optimized multi-color fluorophore panels for biologists, demonstrating its efficacy through computational predictions and experimental observations.