The embodiments of methods of preparing self-aligned isolation regions between two neighboring sensor elements on a substrate described above enable reducing cross-talk (or blooming) of neighboring. The methods use an oxide implant mask to form a deep doped region and also to form a shallow doped region. In some embodiments, the shallow doped regions are narrower and are formed by depositing a conformal dielectric layer over the oxide implant mask to narrow the openings for implantation.