Processes for producing a microCT image for virtual histology using x-ray microscopic computed tomography are described along with processes for rapid and inexpensive high-throughput methods of high resolution imaging for screening an ex vivo embryo for phenotype using computed tomography imaging. Staining of particular components of specimens with one or more staining agents is described which contributes to high quality image generation and identification of anatomical structures as well as localization of molecular targets. Inventive animal and specimen holders are detailed which allow for reduced post-imaging processing of generated images. In particular, animal and specimen holders are provided which include a highly transparent bed or liner which separates the animal or specimen from a less transparent structure. A further animal holder is provided for placing and/or maintaining the animal in a desired position during an imaging procedure or multiple imaging procedures including a bed conforming to the animal's body.