Abstract.SignificanceFluorescence head-mounted microscopes, i.e., miniscopes, have emerged as powerful tools to analyzein-vivoneural populations but exhibit a limited depth-of-field (DoF) due to the use of high numerical aperture (NA) gradient refractive index (GRIN) objective lenses.AimWe present extended depth-of-field (EDoF) miniscope, which integrates an optimized thin and lightweight binary diffractive optical element (DOE) onto the GRIN lens of a miniscope to extend the DoF by2.8×between twin foci in fixed scattering samples.ApproachWe use a genetic algorithm that considers the GRIN lens’ aberration and intensity loss from scattering in a Fourier optics-forward model to optimize a DOE and manufacture the DOE through single-step photolithography. We integrate the DOE into EDoF-Miniscope with a lateral accuracy of70μmto produce high-contrast signals without compromising the speed, spatial resolution, size, or weight.ResultsWe characterize the performance of EDoF-Miniscope across 5- and10-μmfluorescent beads embedded in scattering phantoms and demonstrate that EDoF-Miniscope facilitates deeper interrogations of neuronal populations in a100-μm-thick mouse brain sample and vessels in a whole mouse brain sample.ConclusionsBuilt from off-the-shelf components and augmented by a customizable DOE, we expect that this low-cost EDoF-Miniscope may find utility in a wide range of neural recording applications.