From Recording to Intervention: Causal Lineage Tracing With Primed Conversion

Abstract—Predicting cell fate requires reconstructing a cell’s integrated history: its lineage, the signals it received, how its internal state evolved and its spatial context. Existing recording methods write this information into DNA and read it only at the experiment’s end, allowing reconstruction of what happened but not testing whether it was required. Closing this gap demands real-time observation with the capacity to intervene: perturbing specific cells based on what is observed, while sparing others as matched controls. Primed conversion, a dual-wavelength photoconversion method, confines activation to a single cell in three dimensions by requiring both blue and red light beams to intersect. The same photochemistry can release optogenetic actuators, so a single illumination both marks and edits a cell. Combined with oblique plane microscopy for continuous volumetric imaging, this architecture enables conditional intervention throughout development or tumour evolution, generating genetic mosaics with internal controls that turn lineage tracing from passive recording into an experimental test of which events were required for a given fate. In this perspective, an integrated optical platform is outlined that couples primed conversion, optogenetic actuators and oblique plane microscopy to achieve causal, real time intervention on defined cells.