Development & Art by Phil Gosch

Using Blenders 3D-printing tools for medical analysis

Hey Guys!

I’m currently working on my bachelors project in biomedical engineering at the technical university of Graz. My research topic is “Generation of cartilage thickness maps of arthrotic knee joints”. For those interested, the german description of the topic can be found here.

Basically what I’m doing is:  Take the MRT-scans of knees of patients who suffer from arthrotically damaged knee joints, then to extract the cartilage from this volume scan using custom written semi-automatic software. The software used for this step was written at the TU Graz as part of a diploma project I’m not directly affiliated with. Below you can see a picture of the segmented cartilage viewed in ITK-Snap, alonside the original MRT-data:


Viewing the segmented cartilage inside ITK-Snap

My main task is to generate thickness-maps using the segmented cartilage volume-data. I’m still researching what seems to be the best way to approach this, as there are several possible methods to do this and there seems not to be one “standard” that is used in most publications. The only thing my advisor and me are pretty sure of is that it’s not a trivial task… :)

But I know of one way to visualize a quick preview of cartilage thickness and that is Blenders 3D-Printing toolbox! One of the features of this toolbox is to run a thickness analysis on a given mesh and luckily for me, the ITK-Snap software is able to export the segmented data as a *.STL file, which is a common used file format and there’s a pretty capable Blender importer which comes with Blender by default!

So I exported a *.STL file and opened it inside Blender and after the usual resizing and repositioning you have to deal with most of the time when importing files from other (non dcc-)software I got a pretty good looking mesh to run the mesh-thickness analysis on:


The segmented knee cartilage analyzed by Blenders 3D print toolbox


Detail view

While I’m pretty sure I won’t make use of Blenders thickness analysis tool in my bachelor thesis, this is a great way to do some rapid prototyping and get a feeling for the thickness-distribution of my cartilage samples. Also it’s really easy to set up and to get a first impression of the thickness only takes a few minutes inside Blender. So thanks to whoever coded this useful feature and I hope it helps to see how thinking outside of the box can lead to nice results. :)

I’ll keep you updated about my thesis if anyones interested,

Happy Blending!


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  1. peter October 27, 2013

    Well why not use blender for it?
    I mean blender has good phyton support from which you have access to any point of your mesh. With python ypu can make also use of numpy too, and thats calculating faster then mathlab.

    Blender is also based on academic math itself.
    So perhaps you like to dive into this and expand the open source or just write some scripts for it

    • SaphireS October 27, 2013 — Post Author

      You’re right of course, and I’ll definitely look into it! But I have to talk to my advisor first, then I’ll see..

  2. joe July 11, 2014

    hi, can u please mail me the .stl file of articular cartilage. I have a analysis project going on and i just cannot find a suitable cartilage file to download.
    Thanks in advance :)

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