Rat Eye | Rattus

The movie shows a 3D visualization of a tomographic scan of the eye of a 5 week old Wistar rat. The eye was instilled with µAngiofil and scanned on a SkyScan 1272 with a source voltage of 60 kV, a source current of 166 µA with camera and geometry settings leading to an isotropic voxel size of 1.25 µm. The diameter of the eye is approximately 5 mm.

The data set was visualized in 3D Slicer, where we exported the rotation as a set of single images. This set of images was then converted to a movie with

cat *.png | avconv -f image2pipe -framerate 24 -i - -c:v h264 -b:v 5000k -preset veryslow -pix_fmt yuv420p -vf scale=-2:1080 output.mp4

The output.mp4 movie was then converted to an auto-playing gif file with this small bash script.