Professor Osamu Shimomura discovered the protein aequorin and green fluorescent protein in the jellyfish Aequorea victoria in 1961. He isolated those proteins at the Friday Harbor Laboratories (see Fig. 1) of the University of Washington to answer the curious question, “Why do jellyfish emit light?” This discovery has been combined with genetic engineering and has brought us an invaluable tool for biological research. Based on his discovery, Prof. Shimomura was awarded the 2008 Nobel Prize in Chemistry for the discovery and development of the green fluorescent protein (GFP).

Fig. 1

A group of scientists who were working on fluorescent protein gathered for a symposium on Calcium‐Regulated Photoproteins and Green Fluorescent Proteins held at Friday Harbor, Washington, in 2004. This group includes Prof. Shimomura and several of the guest editors.

In many scenes in current biology, fluorescent proteins have been utilized to visualize target proteins and structures in live cells and tissues. The usage of fluorescent proteins is not limited to labeling, but they can also be used as reporters of intracellular environments, such as ions and adenosine triphosphate concentrations, pH, and temperature. In combination with FRET or FRAP techniques, fluorescent proteins even allow us to trace the molecular‐level dynamics of protein structures in live cells. The switchable capability of fluorescence emission has allowed us to realize superresolution microscopy techniques, research that was awarded the 2014 Nobel Prize in Chemistry. Recently, chemiluminescence, which was Professor Shimomura’s main research interest, became available to image intracellular targets even without light illumination. The discovery of fluorescent protein thus initiated the idea of using light‐protein interactions for biological research. For example, optogenetics can manipulate cell and animal activities by light‐induced conformational change of rhodopsin.

In honor of Prof. Osamu Shimomura’s ground‐breaking contribution to biomedical photonics, we organized a special section on Protein Photonics for Imaging, Sensing, and Manipulation: Honoring Prof. Osamu Shimomura, a Pioneer of Photonics for Biomedical Research. In this special section, we accepted five contributed papers that utilize fluorescent proteins for cutting‐edge research, ranging from the development of optical techniques to biological applications. Although the papers published in this section cannot cover all the examples of experiments using fluorescent proteins, they surely describe how the discovery of fluorescent protein continues to contribute to the development of new techniques and inspires scientists to create new experiments that can tackle biological problems. The guest editors are grateful to the editor‐in‐chief, Lihong Wang, for giving us opportunity, and also to the contributors and the JBO staff for their great efforts to realize this special section.