Large-scale combinatorial optical barcoding of cells with laser particles

Abstract The identification of individual cells is crucial for advancements in single-cell analysis. Optically readable barcodes provide a means to distinguish and track cells through repeated, non-destructive measurements. Traditional fluorophore-based methods are limited by the finite number of unique barcodes they can produce. Laser particles (LPs), which emit narrowband peaks over a wide spectral range, have emerged as a promising technology for single-cell barcoding. Here, we demonstrate the use of multiple LPs to generate combinatorial barcodes, enabling the identification of a vast number of live cells. We introduce a theoretical framework for estimating the number of LPs required for unique barcodes and the expected identification error rate. Additionally, we present an improved LP-tagging method that is highly effective across a variety of cell types and evaluate its biocompatibility. Our experimental results show successful barcoding of several million cells, closely matching our theoretical predictions. This research marks a significant step forward in the scalability of LP technology for single-cell tracking and analysis.