Single-organelle localization-based super-resolution imaging for subcellular molecules micro-dynamics

•This review presents an in-depth analysis of the latest advancements in molecular probe design and super-resolution imaging techniques, offering insights into subcellular molecular dynamics.•This review outlines probe design strategies, emphasizing the crucial role of photostability, signal-to-noise ratio, and targeted binding in enhancing our understanding of single-organelle functionalities.•This review highlights the challenges associated with this rapidly developing field, providing a outlook for future research in single-organelle localization-based super-resolution imaging. Combining probes with advanced imaging techniques has enabled single-organelle localization-based super-resolution imaging, revolutionizing our ability to investigate subcellular molecules with unprecedented precision. This review presents an in-depth discussion on the design and applications of small-molecule probes for specific small and large molecules, alongside advancements in super-resolution imaging. This review discusses super-resolution imaging, emphasizing its operational principles, technological progress, and unique benefits. We also outline innovative probe design strategies that may enhance our understanding of subcellular molecular dynamics and their single-organelle localization. Probe design strategies for diverse intra-organelle molecules are also provided, stressing the need to consider elements such as photostability, signal-to-noise ratio, and targeted binding. Challenges associated with this field, potential solutions, and an outlook are also discussed in detail. By integrating probe design with state-of-the-art imaging technologies based on single-organelle localization, this review provides a path toward remarkable revelations in single-organelle functionalities at the most intricate level of molecular interactions.