An imaging system may be formed from multiple stacked wafers. A first wafer may include backside illuminated photodiodes, floating diffusion regions, and charge transfer gate structures. The first wafer may be bonded to a second wafer that includes pixel trunk transistors such as reset transistors, source-follower transistors, row-select transistors and associated logic circuits. The pixel trunk transistors may be formed using bottom-gate thin-body transistors. The first and second wafers may share the same backend metallization layers. The second wafer may further be bonded to a third wafer that includes digital signal processing circuits. The digital signal processing circuits may also be implemented using bottom-gate thin-body transistors. Additional metallization layers may be formed over the third wafer. The first, second, and third wafers may be fabricated using the same or different technology nodes.