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.

Adult zebrafish | Danio rerio

A 3D visualization of a tomographic scan of a zebrafish in native state (9 months old). The zebrafish was scanned with an isotropic voxel size of 10 µm. The total length of the zebrafish embryo is approximately 3 cm.

The data set was visualized using ClearVolume in Fiji.

Zebrafish embryo | Danio rerio

A 3D visualization of a tomographic scan of a stained zebrafish embryo (44h old).

The embryo was 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 3 µm. The total length of the zebrafish embryo is 2.7 mm.

The visualization was made with 3D Slicer.

Mouse skull | Mus

The image shows a 3D visualization of a tomographic scan of a skull of a mouse approximately five months old.

The visualization was made with 3D Slicer.

The mouse head was scanned on a SkyScan 1272 with a source voltage of 90 kV, a source current of 111 µA with camera and geometry settings leading to an isotropic voxel size of 11.25 µm. The whole head is approximately 27 mm long.

Stained zebrafish | Danio rerio

We scanned a fixed (4% PFA) and stained (1% Lugol solution) zebrafish. The fish was scanned on a SkyScan 1272 at 2.5 um pixel size.