The resolution and dimensionality with which biologists can characterize cell types have expanded dramatically in recent years, and intersectional consideration of such features (e.g., multiple gene expression and anatomical parameters) is increasingly understood to be essential. At the same time, genetically targeted technology for writing in and reading out activity patterns for cells in living organisms has enabled causal investigation in physiology and behavior; however, cell-type-specific delivery of these tools (including microbial opsins for optogenetics and genetically encoded Ca2+ indicators) has thus far fallen short of versatile targeting to cells jointly defined by many individually selected features. Here, we develop a comprehensive intersectional targeting toolbox including 39 novel vectors for joint-feature-targeted delivery of 13 molecular payloads (including opsins, indicators, and fluorophores), systematic approaches for development and optimization of new intersectional tools, hardware for in vivo monitoring of expression dynamics, and the first versatile single-virus tools (Triplesect) that enable targeting of triply defined cell types. Display omitted •Multiple recombinase-dependent expression of 15 new molecular payloads in single AAVs•Intersectional Ca2+ imaging, cell labeling, and optogenetic inhibition or excitation•Creation and in vivo validation of triple-feature-dependent viruses (Triplesect)•Design of a widely adaptable in vivo quantitative expression tracking system Fenno et al. enable versatile functional access to cell types defined by the presence of multiple (2 or 3) features, creating diverse expression-control logic contained in single viruses. This result is a comprehensive toolset enabling multiple-feature-dependent optogenetic inhibition and excitation and structure- or activity-based fluorescence imaging with diverse new indicators.