Fluorescence detection offers a valuable means to identify specific molecular species within an intact sample, boasting a high signal-to-noise ratio. Its applicability to living cells enables the continuous monitoring of their abundance and localization over time. In recent years, significant strides have been made in these detection modalities, including super-resolution microscopy, high-throughput imaging, and multi-color flow cytometry. These advancements have subsequently led to a surge in research papers detailing the utilization of these cutting-edge platforms. This Methods Collection centers its focus on the labeling approaches upstream of detection. A comprehensive understanding of the intricacies involved in labeling protocols ensures the accuracy and reproducibility of results derived from these robust methodologies. Examples of protocols under consideration for this collection encompass live-cell labeling (e.g., Calcium imaging, endocytosis), addressable labeling using genetically encoded markers (e.g., SNAP/HaLo tag, GFP), labeling for phenotypic assays (e.g., Cell Painting, immunophenotyping), labeling of complex 3-dimensional samples (e.g., organoids, zebrafish), and super-resolution microscopy (e.g., SMLM approaches, STED, SIM).