Pike (Esox lucius) fry fixed in formalin and stained with IKI. Volume renderings and virtual sections made from the concatenated stacks of reconstructed slices from two microCT scans made with the sample on the same rotation axis (i.e. translated only in the anterior-posterior direction), one scan of the fish’s head and the other of the pectoral region. This procedure allowed higher-resolution scanning of both body regions (at the expense of extra scanning time). Left: External views of an overall volume rendering, with the transparency adjusted to reveal some internal structures. Top right: Midsagittal cutaway of the same volume rendering. Center right: Single-voxel horizontal virtual section through the volume image. Bottom right: Coronal sections through the same volume image stack. One shows layers in the brain, sections through the jaw adductor muscles, and gill-arch cartilages; the other shows retinal layers, connections with the optic nerves, and the lenses, which tend to stain very heavily. Horizontal bar = 500 μm. Voxel size 4.0 μm. Additional File 3 is a QuickTime movie of the a volume reconstruction from these scans.