Reveal the mechanism of brain function with fluorescence microscopy at single-cell resolution: from neural decoding to encoding.

As a key pathway for understanding behavior, cognition, and emotion, neural decoding and encoding provide effective tools to bridge the gap between neural mechanisms and imaging recordings, especially at single-cell resolution. While neural decoding aims to establish an interpretable theory of how complex biological behaviors are represented in neural activities, neural encoding focuses on manipulating behaviors through the stimulation of specific neurons. We thoroughly analyze the application of fluorescence imaging techniques, particularly two-photon fluorescence imaging, in decoding neural activities, showcasing the theoretical analysis and technological advancements from imaging recording to behavioral manipulation. For decoding models, we compared linear and nonlinear methods, including independent component analysis, random forests, and support vector machines, highlighting their capabilities to reveal the intricate mapping between neural activity and behavior. By employing synthetic stimuli via optogenetics, fundamental principles of neural encoding are further explored. We elucidate various encoding types based on different stimulus paradigms-quantity encoding, spatial encoding, temporal encoding, and frequency encoding-enhancing our understanding of how the brain represents and processes information. We believe that fluorescence imaging-based neural decoding and encoding techniques have deepened our understanding of the brain, and hold great potential in paving the way for future neuroscience research and clinical applications.