3D-print a tomographic scan of a spider

We obtained a 3D data set of a spider and wanted to make a gift for an arachnophobic friend. Since we have access to a Form 2 3D printer we wanted to make a 3D print of the data set.

To do so, we did the following steps:

  • The size of the data set was reduced by binning it 2-fold with Fiji (e.g. half the image size in each of the x, y and z directions).
  • We binarized the data set to extract the spider from the background, smoothed the binarized image and binarized again to get rid of small noise present in the image. After this, we had a 141 MB big TIFF stack with the size of 612x612x395 pixels.
  • By using the 3D Objects Counter (also in Fiji) we extracted the biggest object in the data set, which corresponds to only the spider, discarding noise objects still present in the data set.
  • We then viewed the data set as surface in the 3D Viewer of Fiji, which gave us the result shown in the first picture below.
  • The 3D Viewer of Fiji can then be used to save the thresholded spider as STL file ready for printing with a 3D printer (File > Export surfaces > STL (binary)). This gave us a 74 MB big STL file (which is quite huge compared to the other STL files we usually print).
  • This STL file was then printed in 3D and spray painted to result in the gift shown in the second image below (ball point pen shown in the background for scale).

3D Viewer Final result

Friendly Neighborhood Spider-Man | Araneae

Spider

This friendly spider was bothering our secretary. After a nice long bath in 70% Ethanol (scented with Iodine) it was scanned on our SkyScan 1272 with a source voltage of 50 kV, a source current of 200 µA with camera and geometry settings leading to an isotropic voxel size of 21.7 µm. The body of the spider is approximately 1.2 cm long.

The visualization was made in 3D Slicer. To simulate a shadow, we added a MIP-image (inverted, binarized and heavily blurred) of the spider to the visualization in addition to the 3D stack.

Rat Eye | Rattus

rat eye movie

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

Adult zebrafish

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

zebrafish-embryo

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.