Mouse skull (from micro-CT)

by MarkU, published

Mouse skull (from micro-CT) by MarkU Mar 28, 2012

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The data for this STL is taken from a micro-CT scan of a mouse skull, processed in ImageJ - rsb.info.nih.gov/ij/ . The original data was provided by Mark Henkelman of the Mouse Imaging Centre (MICe) mouseimaging.ca

Files include the whole skull, and then a left half-skull sliced just to the left of the midline. I made this one as I was interested in the structure of the turbinate bones in the nasal passages, and it can be tricky to visualize complex 3D structures like this on a computer screen, even with 3D rendering.

Note that this is downsampled from the original micro-CT image as ImageJ was not able to cope with converting the full file to an STL on my computer. I will also try to upload the 160 Mb 3D TIFF file containing the full scan. The internal detail visible in this file is amazing (sequential images scan from the tip of the nose through the back of the head).

Photos show the half skull printed on a Stratasys FDM machine (black) and an Objet 24 (white). The FDM print is scaled up by an additional factor of two due to resolution limitations.

UPDATE 2012.10.15: Uploaded a demo print of the model done on the Zcorp ZPrinter 450 (same size as the black ABS one). The colour is arbitrary, I put it in to test the printer's colour capabilities.

UPDATE 2013.04.06: Uploaded a demo print of the model done on the Replicator2 (red, same size as the black ABS one). Quality on surfaces where I had to remove support / raft is only marginally inferior (if anything) to the Stratasys machine using soluble support, surfaces that did not require support are equivalent.

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Nice, thanks for the low sketch option.

Looks like I can export the surface as a wavefront (.obj) from imageJ and use Meshlab to convert it to a .stl easily enough.

This is much faster (and cheaper without matlab) than the way I was previously doing it.


for a less sketchy-looking URL

It's been a while since I did the conversion but I think I used this:

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ted on Mar 30, 2012 said:

How do you convert your dicom data to .stl using imageJ? I've been using Matlab to do surface rendering from CTs, but imageJ would be a nice (free) solution as well.

MarkU on Mar 30, 2012 said:

It's been a while since I did the conversion but I think I used this:

bre on Mar 29, 2012 said:

This is so cool. I want a Micro CT scanner now.

orderinentropy on Mar 30, 2012 said:

Until NYCR builds a Micro CT, you can still have some fun.

For viewing medical data:


orderinentropy on Mar 29, 2012 said:

...I don't think they exist.

Thanks! I had been wondering about converting medical scan data to usable models.

cymon on Mar 29, 2012 said:

That is the skull of a ROUS you've got in your hand there.

EvoGenius on Mar 29, 2012 said:

"Rodents Of Unusual Size? I don't think they exist."

*gets attacked by ROUS*