Extended Data Fig. 1: HaloTag ligand dyes are cleared from the brain within hours.

a, Experimental procedure to measure dye-ligand clearance. The rise in fluorescence is not captured, as the animal is not imaged during the injection. b, Example images for a JF₆₆₉-HTL injection. The blue circle represents the region for which fluorescence was quantified in (c). Scale, 2 mm. c, Linear (left) and log (right) fluorescence (peak normalized and baseline subtracted) as JF₆₆₉-HTL is cleared from the brain. Double exponential fit in red; τ₁ and τ₂ are in minutes. d, Similar data for 12 experiments with 3 dyes (JF₅₂₅-HTL in green, JF₅₅₂-HTL in red, and JF₆₆₉-HTL in magenta). The black trace is a binned average, with standard error for all 12 experiments. The numbers in (d) represent the mean ± standard error of double exponential fits for the 12 experiments.