Open Source Human Anatomy

3D Printing Aortic Bifurcation
3D Printed Aortic Bifurcation

I first saw a MakerBot Thing-O-Matic in action at the 2011 Bay Area Maker Faire, and it was truly a thing of beauty. I’ve used rapid prototyping machines and services since the mid 90’s, but here was something that you could build yourself, and have on your own desk! Wow. Later in the year, I happened to have a free day in New York during the NYC Maker Faire, so I was drawn to revisit this hacker dreamscape. There, I met @ErikDeBruijn, one of the developers of the Ultimaker: an elegant build-it-yourself 3D printing machine capable of relatively high speeds, stunning resolution, and a comparatively large print volume. I became immediately obsessed with visions of 3D printed anatomical structures, and medical device prototypes. I asked Erik if the Ultimaker was being used commercially, and he knew of a few customers that were using it in schools, and at least one other that was offering a service making 3D prints by the hour. Medical device development, not so much. That only made me more interested.

Later that day, I saw a great talk by Bre Pettis (@Bre) of MakerBot fame (30 minute video on An icon of the open source hardware movement, Bre gave lots of examples of digitized “things” that are freely shared on sites like Thingiverse, where users can upload, download, share, modify, and combine digital objects. And now print them out, too, effectively “teleporting” physical objects among like minded citizens of the internets. Digital “mashups” of Yodas, Gantstas, and Rabbits delighted the maker-faithful in attendance, while evoking dismissive comments from the guy sitting behind me: “What’s the point?” Dismissive guy, and many like him, see a toy. Which it is. But its more than a toy.

A few quotes from Bre’s talk resonated with me:

If you’re not sharing, you’re doing it wrong!

If you’re at a company, and keeping things secret… Stop it!

Publish those things (even if they’re not done, or done done)… Just share them, because so much of the future depends on it.

These are the noble words of an open source evangelist, and the principles upon which Linux, Firefox, Wikipedia, Arduino, and countless other open source projects depend. And then there’s my professional universe of medical device design and development. An industry that relies upon proprietary designs, trade secrets, secure patents, guarded intellectual property. The opposite of open. And yet, everything that we do in my industry is directed at improving the human condition, which is very much in the common interest of all humans. Is there a way to be “open” in a “closed” industry?

It isn’t easy. I wrote about the opportunity and challenges in Open Medsystems a few of years ago.  Medical device development is expensive, and it generally isn’t going to get funded unless the investors have some confidence that they can profit from their investment. So NDA’s will be signed, secrets will be kept, patents will be filed, and knowledge will be sequestered. Brilliant engineers and designers will face the same challenges, each alone in their own respective proprietary silos, not knowing of their kinship, not benefiting from each other’s ideas or mistakes. In the end perhaps one will win, or both will lose.

But there is hope. I’ve tried to do my part by publishing Open Stent Design on, releasing Stent Calculator on Google Code. But I think there’s a bigger “open source” opportunity for the medical device community, and I’m not alone. 3D medical imaging technologies, like CT scans and MRI’s, have made amazing advances in the last decade. These increasingly ubiquitous machines create torrents of 3D data sets, each a unique atlas of human anatomy, and each an exquisite three dimensional map of  a diseased system, organ, or tissue. These medical imaging data sets hold secrets waiting to be discovered -they describe the environment in which medical devices must do their healing work. 3D imaging data, usually in DICOM format, is easily anonymized, and easily rendered and manipulated with open source software such as the excellent OsiriX []. Translating medical imaging data sets into useful 3D geometry for analysis or simulation is messy work (see segmentation [Wikipedia]). But it is important, and at least one group is working on developing a Cardiovascular and Pulmonary Model Repository [] to do just that. Sponsored by NIH, this effort will collect medical imaging data sets for several body systems, perform segmentation, and make the raw data and analysis available to the public.

Freely available 3D anatomical data + open source 3D printers = freely available (plastic) body parts! Rapid prototyping of proprietary 3D data is nothing new in the medical device development world… but 3D printing of freely available anatomical models derived from freely available anonymized medical imaging data is all kinds of awesome! 3D printed blood vessels, organs, and bones can be used to mold or cast realistic benchtop models, which can be used to test and challenge medical device concepts in a realistic environment… Or better yet, many realistic environments, reflecting the many individual humans they are designed to help. And that is some true open-source mojo at work in a closed industry, to be benefit of all.

So after honing my Ultimaker skillz on snakes, whistles, cars, and alien eggs (“What’s the point?”), I have turned my attention to the beloved OsiriX DICOM Sample Library [], and tackled the aortic bifurcation of the AMNESIX model. After some quality time with OsiriX, I had a rough export of the aorta and iliac bifurcation, which I then cleaned up in MeshLab [], sliced using Netfabb [], then printed using ReplicatorG []. And though it isn’t final, done, or done done, it is now shared as Thing:15942 on Thingiverse!


5 replies on “Open Source Human Anatomy”

  1. Hi!

    I’ve read your bifurcation project with growing interest! Currently i’m involved in a project trying to reveal the hemodynamic differences between several aorta bifurcation stent configurations. Therefore we are building a in vitro set up, the incorperation of a human derived bifurcation model would really contribute to the project. I’m going to look into the steps you took with more detail.

    Furthermore on you posted a link to however I need a password to enter and use the data posted. Though I can’t work out how to gain acces. Maybe you can be of any help?

    Lasty I greatly appreciate your thoughts about sharing knowledge. Guys like me can really learn from this!

    With kind regards

    Erik Groot jebbink,
    student technical medicine
    University of Twente, Netherlands

  2. Hello Craig,

    Long time no see. I thought about you after the Devils won game 5 last night. Have you been watching the playoffs this year…amazing battles in the East and West…but mostly in the East. If the Devils make it to the Cup Final, then I hope to find a way to get to “The Rock” next week to see them. I wonder what a ticket would cost?

    Coincidently, I was shopping for 3D printers online yesterday. They have come down in price remarkably. It won’t be long before they proliferate to many American home as a hobby. This would be a cultural breakthrough since most people do not make things on their computers…most people dwell in the virtual realm of video games unfortunately. I hope 3D printers inspire kids to create…MAKE things!

    I have been using 3D printers for prototyping quite extensively the past 5 years or so. FDM parts made from ABS have supplanted many machined parts in my projects…I love them…I would love to have one as part of my consulting services. I have already paid for my friends machine with the work that I have sent his way.

    Craig, I would love to catch up. Send me an email.

    Brian (Beckey)

  3. I wanted to modify your statement (attributed to Bre’s talk) that, “If you’re not sharing, you’re doing it wrong!”. In plain truth, ,

    if you’re not sharing, you’re stealing.

    You are stealing from everyone who has ever talked with you given you ideas or shown you something interesting. You are stealing from everyone who has ever fed you, protected you or soothed you when you were feeling sad. You are stealing from all the past thinkers, makers and dooers who have helped build the world we live in. In short, you stealing from everyone. We are not alone, we are a society and we depend on many others to help make our world, from the old Mexican farm worker who just died while you were reading this to the CEO of Bechtel. I do not believe in the lone hero.

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