Imaging and reconstruction of developing neurons require cells that are labeled in a way that distinguishes them from their neighbors. This can be achieved with ballistic labeling, which refers to the delivery of a cell label by means of carrier particles (tungsten or gold) propelled from a pressurized gun. Ballistic delivery can reach many dispersed cells in one shot and can deploy a wide variety of cell markers to neurons in diverse preparations. The three most commonly used types of ballistic labels are carbocyanine dyes, dextran-conjugated fluorescent markers, and DNA plasmids. This article describes a protocol for using a Helios Gene Gun (Bio-Rad Laboratories) to inject coated particles into cells located near the surface of a tissue preparation. Shooting particles coated with carbocyanine dyes or dextran-conjugated fluorescent markers requires that a filter be placed between the gene gun and the target tissue. The filter prevents unbound dye clumps from reaching the tissue and attenuates the pressure wave reaching the tissue. DNA-coated particles can be shot without a filter if the target cells are located near enough to the surface (<20 μm deep) for the particles to penetrate using low helium pressures (35-40 psi).