Optical profiling of autonomous Ca2+ nanodomains generated by lysosomal TPC2 and TRPML1

•TPC2-G-GECO1.2 is the optimal reporter for monitoring Ca2+ nanodomains selectively.•Lysosomal Ca2+ nanodomains are ∼100-fold larger than the global [Ca2+].•At phagocytosis TPC2 produces discrete Ca2+ hot-spots around the lysosomal surface.•On the same vesicle TPC2 and TRPML1 evoke separate non-overlapping Ca2+ nanodomains.•Each lysosomal Ca2+-channel family couples to a unique downstream physiology.