Methods and systems for purifying one or more microbial cells and/or viruses from a biological sample are provided. The biological sample is added to a well disposed in a medium. A potential is applied across the medium to cause the contaminants to enter one or more walls of the well, and retain the microbial cells and/or viruses in the well. The microbial cells and/or viruses can be removed from the well, and optionally adhered or fixed to a surface, or detected. In one embodiment, the microbial cells and/or viruses are retained in the well by embedding in the medium. The medium including the embedded microbial cells and/or viruses may be excised or otherwise removed and transferred to a glass slide or other solid surface. In some examples, a biological sample containing contaminants and one or more microbial cells is introduced to a well disposed in a porous filter medium, wherein the porous filter medium includes pores smaller than the one or more microbial cells, thereby preventing the one or more microbial cells from entering the porous filter medium.