Amira 6 3d software package

Quail, duck, and quck mandibles were collected at HH37 and cut into 10 µm coronal sections (i.e., in the horizontal plane of the mandible). Adjacent sections stained for either osteoid or TRAP at 80 µm intervals were imaged and merged using Adobe Photoshop. Images were imported into the Amira 6 3D Software package (FEI, Hillsboro, OR) and aligned manually using anatomical landmarks including Meckel’s cartilage and the epithelium along the oral cavity. After image slices were aligned for each specimen, then the areas of interest (osteoid, TRAP, and Meckel’s cartilage) were manually segmented into data objects (image voxels) using a range of segmentation tools. Once all areas of interest were labeled for each specimen, 3D models were generated and volumetric data for TRAP and osteoid were extracted. For each quail and duck specimen, the data were represented as the average volume of the left and right sides of the mandible. For quck specimens, data from the donor and host sides were extracted separately.