Welcome to Embodi3D! Embodi3D is the web's first online community dedicated to biomedical 3-D printing. Learn about the uses and potential of 3-D printing in biomedical sciences by reading the blogs or downloading a printable file. Contribute to the discussion by posting a comment in the blogs or forums. Upload your 3-D printing creations to the File Vault. If you have a lot to say, start your own blog. Help the world to realize the awesome potential of biomedical 3-D printing. Welcome to the community! Register now and join us!
Image: A human lumbar vertebral body, from digital representation to physical object created with 3D printing.
Researchers in Germany have successfully re-created dinosaur bones using 3-D printing from original bones still embedded in rock. As reported in the March 2014 issue of the journal Radiology, a fossil of a vertebral body of a Plateosaurus still embedded in the rock was found and was scanned using a CT scanner. The digital dinosaur vertebra was then digitally removed from its rocky surrounding shell. The dinosaur bone was then 3-D printed using a selective laser sintering machine to create an exact duplicate. The 3-D printed model can then be handled and used for research, while the original remains undisturbed and safe within its original rocky matrix.
What does this advance mean for the field of paleontology? Can delicate objects now be studied without having to disturb them? Can rare bones, previously paid away a museum vaults, now be digitally shared with the world? Please leave your comments.
The journal article is available here http://pubs.rsna.org/doi/abs/10.1148/radiol.13130666
A Plateosaurus skeleton
Researchers from Vanderbilt University Medical Center and Dartmouth-Hitchcock Medical Center recently reported use of 3-D printing techniques to create a vascular model of an intracranial aneurysm. I have also used 3-D printing to create vascular models. In the journal Surgical Neurology International, the authors described their technique. They used digital subtraction with a fluoro-CT system to capture the anatomic image and create a surface model. Mesh editing was then performed with MeshLab. The model was printed on a Stratasys Objet 500 printer using the Tango Plus material. Such models may be useful in patient education or determining the best surgical approach.
The authors state they used stereolithographic techniques to create the model, but the Objet 500 printer uses PolyJet technology. Stereolithography involves multiple layers of UV curing of a liquid resin and the material is usually quite rigid. I've used stereolithography to create vascular models (to be described in an upcoming paper) and I know it works. There is a spec sheet for the printer here, and a description of different 3-D printing techniques here. Nonetheless, this is interesting and impressive work. One problem that I have had with the Tango Plus material is the minimum wall thickness, and I wonder if this was an issue. A nice thing about Tango Plus is the quite rubbery and compliant feel.
What do you think about the potential of 3-D printing for vascular applications? Please leave a comment!
The complete text of the article can be found here. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942610/
The digital model of the aneurysm
The physical model of the aneurysm
The Tango Plus material, showing its flexibility
Deniz Karasahin recently won a A'Design award for a 3-D printed medical cast that allows for improved ventilation and patient comfort when compared to traditional plaster or fiberglass casts. The organic 3-D printed structure has multiple ventilation holes which do not, presumably, compromise the mechanical integrity or strength of the cast.
The cast is created after scanning the patients target body area and importing the data into CAD software. The cast is printed with ABS plastic using a FDM process. Additionally, the inventor claims that Low Intensity Pulse Ultrasound (LIPUS) bone stimulators can be embedded into the cast material to improve healing. This promises to reduce the healing process by 38% and increase the here rate up to 80% in nonunion fractures.
This is very interesting. Of course, the cast itself looks very cool and I would definitely prefer a cast like this over a conventional plaster or fiberglass cast, as it seems like it would be much more comfortable.
I do have some questions about the LIPUS ultrasound treatment. A quick search of PubMed reveals that this technology has shown to help with tibial and radial fractures. Other studies show that it does not work for all bony fractures, for instance clavicle fractures. So it seems like the research is still out about exactly where this device might be used. Additionally, I can see practical problems with performing a 3-D surface scan on a swollen, mangled extremity in the ED, designing it using CAD software, and 3-D printing a cast on the spot. Right now there are barriers or practical implementation. Perhaps the cast could be more practically used as a replacement after a conventional cast has been placed in the acute setting. Should these casts become widely adopted, maybe someone will invent a 3-D printed cast of vending machine which will scan, design, and print your cast on the spot.
Read the design proposal here.
Researchers at the University of Leicester and Loughborough University have successfully 3D printed the skull of Richard III, the last Plantagenet King of England. For those of you rusty in your English history (as I am), Richard III was killed in battle at the Battle of Bosworth Field in 1485. This was the final major battle of the Wars of the Roses. The victor, Henry Tudor, went on to become King of England and founded the Tudor dynasty.
Richard III was buried in a nearby friary shortly after the battle, but the location of the friary was lost to antiquity. In 2012 the friary was discovered underneath a parking lot in Leicester, England and the subsequent excavation revealed the skeletal remains of the English King. The skeleton bore evidence of multiple traumatic injuries, especially to the skull, where there were multiple puncture and cleaving injuries. Additionally, there was significant scoliotic deformity of the spine, which is consistent with the famed hunchback appearance of the King. (Technically hunchbacks have kyphosis, not scoliosis, but close enough.)
To better illustrate the battle injuries and spinal deformities, and preserve the original bones, researchers performed CT scans of the bones and re-created them using 3D printing. They used the Mimics Innovation Suite from Materialise and printed the bones using laser sintering.
The Smithsonian Channel did a fascinating documentary about the excavation, including how they confirmed the identity of the skeleton using mitochondrial DNA via an unbroken line of maternal descendents (mitochondrial DNA is only passed from mother to child) to a Canadian furniture maker whose mitochondrial DNA exactly matched that extracted from the skeleton. Check out the Smithsonian Channel website for some additional details.
Thumbnail photo credit: Andrew Weekes Photography
The base of the skull is one of the most complex and difficult parts of the body for doctors in training to master. And one of the most important. It is comprised of multiple bones (the ethmoid, sphenoid, occipital, frontal, parietal, and temporal, to be exact) and has numerous foramina (holes) through which arteries, veins, and the vital cranial nerves and spinal cord exit the skull on their way to and from the body.
These structures, although very small, are critically important clinically. Compromise of a tiny foramen (hole) can lead to deafness, blindness, paralysis, or even stroke or death. Because of the importance of this small space, medical students around the world struggle to learn the complexities and subtleties of skull base anatomy.
Unfortunately, pictures in an anatomy book just don't cut it. Real human skulls can demonstrate this anatomy well, but these are expensive and the skull has to be cut and opened in order to display the relevant anatomy. This is why I created a 3D printed skull base from real CT scan data.
Available in full size and half-size models, the skull base exhibits exquisite anatomical detail. Digital files of the skull base are available for free download in full size (STL, COLLADA) and half-size (STL, COLLADA) versions.
Very high resolution prints are available for a fee at Shapeways in both full-size and half-size. The half-size model is quite inexpensive so you don't have to worry if it is damaged by rough handling of multiple students.
In the near future I will be posting more anatomical digital models.
For updates on news and new blog entries, follow us on Twitter at @Embodi3D
Researchers at the Children's National Medical Center in Washington DC have used 3D printed heart models to aid repair of congenital heart defects. In the International Journal of Cardiology, the researchers report the case of a patient with transposition of the great arteries, a congenital heart defect in which the pulmonary artery and aorta are switched. Without treatment this condition is fatal in infancy. The man apparently had surgical treatment as a child, but as an adult began to have problems when the surgical conduit allowing his heart to function properly began to close.
A 3D printed replica of the heart was created with Mimics software from the Materialise. The heart was then printed using an Objet Polyjet printer. The investigators tested a variety of catheters and planned the procedure using the model before attempting the actual procedure on the patient. The investigators even deployed a stent within the model for practice. With the benefit of testing on the 3D model, the procedure went as planned. The narrowing was opened with a stent and the heart function returned to normal.
3D printed vascular models have been used recently to assist in planning complex and unusual procedures. They've been used for treating abdominal aortic aneurysms, and now for treating postoperative congenital heart disease. I have personally created a 3D model to help with treatment of a rare vascular anomaly (publication pending, stay tuned). When will 3D models be used for bread-and-butter procedures? What are the barriers to this happening? Please leave a comment.
For updates on news and new blog entries, follow us on Twitter at @Embodi3D
Image source: International Journal of Cardiology
This is the second in a series of articles about skull models created from CT scan data and designed to provide a low-cost means of anatomy teaching. To see my past article about the skull base model, click here.
Learning detailed anatomy is a grueling process that doctors, nurses, and other health science students must go through. Traditionally, learning anatomy involved detailed study of textbooks, but learning 3D structures from 2D pages just doesn't work well. Dissecting cadavers is the traditional means of teaching doctors, but this process is tedious, messy, very expensive, and only available in select educational institutions (i.e. med schools). Most students of anatomy do not have access to these resources.
3D printing is putting the power of real 3D anatomy within reach of ordinary students at very low cost. These models are created from highly detailed CT scan data from real human bodies, not an artist's conceptualization. This half skull and cervical spine has been cut along median sagittal plane. This clearly shows the external bony anatomy (zygomatic arch, orbit, etc.) as well as intracranial anatomy (skull base formina, paranasal sinuses, etc.). Bony details of the cervical spine are also clearly shown.
You can 3D print your own model by downloading the free files. These files are available on this website in STL or COLLADA format, in full size and half-size versions. You can get them here: full size (STL, COLLADA), half-size (STL, COLLADA). Check out more downloadable files in the File Vault.
If you would rather have a high quality model made for you, you can buy one from Shapeways here (full-size, half-size).
Feel free to modify the files as you would like, just please don't use them for commercial purposes. If you create something cool, please give back to the community by sharing it on the Embodi3d website in the File Vault.
For updates on news and new blog entries, follow us on Twitter at @Embodi3D
I apologize for being slow with the posting recently. I was at a conference last week and this week I have been working on creating a 3D printable cardiac and arterial model (see image). More interesting blog articles will be coming shortly.
In the meantime, I encourage you to check out the blog of my friend, neuroradiologist, and 3D printing enthusiast Jenny Chen, MD., at Radbuz.com. You can follow her on twitter at @radbuzzz.
Thanks to 3D printing understanding of the complex neural pathways of the human brain became a little bit easier. The Philadelphia-based Franklin Institute's new exhibit, Your Brain, features a striking 3D printed model of the white matter tracts of the human brain. White matter tracts are the pathways that nerve cells use to connect to each other inside the brain, and are incredibly complex.
Dr. Jayatri Das, chief bioscientist at The Franklin Institute, incorporated the displays in a new expansion. The model was built from an MRI scan of a real brain and was then printed using the SLS print method from 3D Systems. It shows approximately 2000 tracts. Printing such a delicate structure proved to be quite a challenge and the project was turned down by several 3D printing bureaus before it was accepted by an outfit in Oklahoma. The model was printed in 10 separate parts and then assembled.
This is truly an amazing advance in anatomic visualization. It's truly beautiful - a piece of art.
For updates on news and new blog entries, follow us on Twitter at @Embodi3D.
Source and images: 3D Systems
There has been a lot of hype recently about 3D printed organs. There have been several instances in recent memory where somebody holds up a kidney or liver shaped 3D printed blob of jello-like cells and the press goes wild, as if the jello blob, because it is shaped like an organ, must be an organ and is ready to go directly into a patient. As someone who works with transplant patients all the time I can tell you it's not that simple. Real organs are incredibly complex.
Take the liver for example. On the microscopic level there is a meshwork of cells comprised of reticuloendothelial cells. Hepatocytes live within this meshwork. Endothelial cells line small spaces called sinusoids. All these structures are connected to microscopic bile ducts, arterioles, and veins. The picture below demonstrates the microscopic architecture. The point is that an organ is more than a mass of cells. There is very, very complex microscopic and macroscopic architecture.
That's why a recent research paper by a multinational team of investigators is so interesting. Reported in the journal Lab on a Chip, researchers from Australia, Italy, Korea, Saudi Arabia, and American teams at Harvard, Stanford, and MIT, report being able to 3D print capillaries. Additionally, they were able to grow "endothelial monolayers," which basically means a layer of cells that comprise the normal lining of capillaries in the body. An endothelium is important, because without it the blood within the capillaries will clot, leading to tissue death from lack of blood flow.
In theory this advance means that artificial organs with complex microscopic architecture, which is essential for a real organ to function, can be 3D printed. If the artificial organ is also manufactured using cells from the patient, this will eliminate the two greatest problems with modern organ transplantation. These are 1) insufficient number of transplantable organs (in the US they need to be harvested from recently deceased individuals who donate them, and there just aren't enough), and 2) immune rejection of the organ when the body inevitably realizes that the organ is from a different person.
External video demonstrating advances in 3D Printing and bioprinting
This reminds me of an episode of Star Trek when Captain Picard is impaled through the heart and the laughs when he sees the dagger protruding from his chest. He is saved by a heart transplant. Perhaps he is laughing because in the Star Trek future an artificial heart with accurate microarchitecture is probably as close as the nearest replicator. Given this latest research, maybe someday soon we will all feel comfortable about rumbling with a gang of Nausicaans, knowing we can get spare organs whenever we need them.
For updates on news and new blog entries, follow us on Twitter at @Embodi3D.
E-Nabling the Future is a volunteer organization dedicated to creating inexpensive 3D printable prosthetic hands and arms for children around the globe who are missing limbs. The movement has grown from an informal collaboration to a veritable movement, and they are now producing functional and inexpensive prosthetic limbs. Traditionally designed arm and hand prostheses can cost up to $40,000. According to 3Dprint.com, it is now possible to create an entire functional my electric arm for $350. Their most recent innovation uses electrical impulses from the bicep muscle to open and close the hand. This enabled a six-year-old boy named Alex who is missing his right arm to give his mother a big hug.
The picture of Alex's myoelectric prosthetic right hand gave me a sense of déjà vu -- I swear I had seen something like this before. Then it hit me. The prosthetic is eerily similar to Luke's prosthetic hand in The Empire Strikes Back. Thanks to the volunteers at E-Nabling the Future, science fiction is becoming science fact, and children are the beneficiaries of this amazing movement.
Please check out the E-Nabling the Future website, and if you are so inclined give a donation to this worthy cause.
For updates on news and new blog entries, follow us on Twitter at @Embodi3D.
Select images by Kt Crabb Photography
Community member Mike Kessler has successfully printed a half skull available for download in the File Vault using a filament printer. He made the skull to help a family member who is learning skull anatomy in medical school. The skull looks great. Fantastic job Mike! Check out Mike's complete album here.
If you have had success with printing one of the 3D anatomic models available for download on the site, please let us know how things went. If you are creating your own medical 3D models, please share them with the community in the File Vault.
I've been working on ways to artistically expand on 3D printed anatomic models beyond an exact replica of the anatomy. My first project is this Lace Skull. The skull is based on an anatomically accurate skull generated from a CT scan. I have made several of the earlier skull models available for download on the Embodi3D website here and here. Using a variety of methods, I have transformed the skull and given it a unique lace-like appearance. The overall surface contours are still anatomically accurate. The lace-like texture gives the model its unique aesthetic but also cuts down on printing material while maintaining mechanical strength.
I have made the STL files available for FREE download in the File Vault section of the Embodi3D website. You can find the STL files here (HALF-SIZE | FULL-SIZE). If you 3D print this file, please report back regarding your outcome. I printed a half-size model using the "White, Strong & Flexible" nylon material on Shapeways.
If you would rather have Shapeways print the model and ship it to you for a fee, you can go Shapeways to directly order the models here (HALF-SIZE | FULL-SIZE).
I hope you enjoy this 3D printable model. Please report back on your experiences with printing the model. Also, please share your own 3D printable creations with the community in the File Vault section of the website.
Lately I've been working on creating a 3D printed human heart from a CT scan. Printing cardiovascular structures like the heart is more difficult than bony structures since the blood vessels are usually not well visualized without a CT scan that uses intravenous contrast. Furthermore, the heart is always moving, and special techniques need to be performed during the scan to generate high-quality images that are free from motion artifact.
This is one of several models I've been working on. I haven't yet tried 3D print this model, but I thought I would share it with the community to see what people think. The STL file can be downloaded here.
If you 3D print this model, please share your results with the community. Post an update or upload pictures of your printed model. If you are creating your own 3D printable models, please consider sharing them with the community in the File Vault.
On another note, I am considering putting together some video tutorials on how to create 3D printed anatomic models from CT scans using freeware. If you are interested in seeing tutorials like this, please leave a comment. Happy printing!
Dr. Marco Vettorello is an anesthesiologist and intensive care physician in Italy. On the side he has been creating high quality anatomical models that are of great value for medical education. He has agreed to share his models with the Embodi3D community. All are available for free download. The models that he has shared include:
Thanks very much Dr. Vettorello! We appreciate you sharing with the Embodi3D community!
There is tremendous beauty and diversity in nature that goes unnoticed by humans because it is simply too small for us to see and appreciate. Embodi3D member Michael Holland hopes to change that. Via his eponymous company Michael Holland Productions, he has created a fascinating traveling museum exhibit called MacroMicro that reveals the striking complexity and beauty of the microscopic world through high-resolution micro-CT scanning and 3D printing.
On the remote island of Iriomote-jima, part of the Okinawa Islands of southern Japan, beautiful white sand beaches can be found. Closer inspection of the sand reveals that each grain has a star-shaped appearance. These white sand grains are primarily the skeletons of Baculogypsina sphaerulata, tiny marine organisms that produce an intricately detailed star-shaped calcium carbonate shell. These beautifully complex structures go completely unnoticed by the average beachgoer. But through use of high-definition microscopic CT scanning and 3D printing, these sand-like shells, when enlarged as big as a dinner plate, come alive.
The Humboldt squid, also known as jumbo squid, is a large squid with a mantle length that reaches up to 1.5 meters in length. Living in the eastern Pacific Ocean off the coasts of North and South America, these predatory invertebrates entrap their prey with tentacles that bear up to 200 suckers each. These predators have a devious secret. Within each sucker is a ring filled with serrated dagger-like spines. Once enveloped by the tentacles, hundreds of suckers attach to the helpless prey, and thousands of these tiny dagger-like structures penetrate it, ensuring that even the slipperiest of prey meets its inevitable doom. Enlarged to the size of a basketball and 3D printed (lead image, shown above), once can see how nasty this adaptation truly is.
Everything we hear -- beautiful music, the rustling of leaves, a loved one's laughter -- is made possible by the incus, malleus, and stapes. These three tiny bones are the smallest in the human body and form the basis of the middle ear, without which human hearing would not be possible. Noise around us causes our tympanic membrane, or eardrum, to vibrate. But how are these vibrations transmitted to our brains where we process sound information? This is where the incus, malleus, and stapes come in. Attached to the inner surface of the eardrum, these bones form a chain that transmits the vibratory motion to the inner ear. There, tiny hairs are disturbed, which sends an impulse through the auditory nerve to the brain, which we interpret as sound. Everything we hear is transmitted as vibrations through these three tiny bones, called the auditory ossicles. In Latin, the malleus, incus, and stapes mean the hammer, anvil, and stirrup, respectively. When enlarged to the size of a real hammer through 3D printing, you can see how these tiny bones got their names.
auditory ossicles of the ear
The innocuous Townsend's mole, Scapanus townsendii, is commonly found in the moist soils of the Northwestern North American coastline. It's short and stubby arms are perfectly designed for digging, a fortunate thing as it spends most of its time searching for earthworms and other food in shallow burrows. However, when its small size is accounted for, the mole's arms are massively powerful. Click on the video link below to hear Michael talk about this small furry Hercules and how its secrets are revealed through 3D printing.
The Townsend's mole
Through his MacroMicro exhibit and 3D printing, Michael is bringing the striking beauty of the microscopic world to us. Look for his MacroMicro exhibit in a museum near you beginning in 2016.
The MacroMicro exhibit
Researchers from Nagoya University in Japan are now using customized 3D printed liver models created from patient Computer Tomography (CT) scans for guidance during liver surgery, as reported at the 2014 Radiological Society of North America meeting. The human liver is a complex organ. Liver cells, called hepatocytes, do the work of cleaning the blood of toxins and waste -- the primary function of the liver. Hepatocytes are dependent on a complex network of vascular structures, including bile ducts, hepatic arteries, hepatic veins, and portal veins, which are organized into a complex branching network. This network is in turn organized into self contained units, each with its own bile ducts, arteries, and hepatic and portal veins, called segments, of which there are eight in the typical human liver.
When liver surgeons resect, or cut out, cancer from the liver, they remove the entire segment or segments that are involved, working hard to avoid any damage to segments that are uninvolved. The procedure is delicate, and there is no room for error. Cut out too little and there may be tumor left in the liver which can subsequently spread. Cut too much and a host of complications can arise, including bleeding, bile leak, liver failure, and potentially death. Furthermore, the surgeon must work under conditions where the tumor and vital structures may be poorly visualized or obscured by blood in the operative field.
This is where the 3D printed models come in. The Japanese researchers took CT scan data from the patient undergoing the liver cancer surgery and created a 3D printed model of the entire liver using a transparent material. They left the vascular structures hollow, and subsequently filled them with a colored material to color-code each type of vessel. The model was then vacuum sealed in a sterile pouch and brought unto the operating room during the surgery. The surgeon could handle the 3D model during the operation. Before making each cut, the surgeon could refer to the model and confirm where the tumor and each vital vessel was located, thus avoiding mistakes and reducing operating time.
Creating 3D printed models prior to surgery for preoperative planning and intraoperative guidance is something that I have done personally for endovascular procedures (a publication on my experience is forthcoming). I can tell you that the certainty of knowing what you are getting into, and avoiding nasty and unexpected surprises in the OR, is invaluable. Once surgeons experience the comfort of having an anatomically accurate intraoperative 3D printed reference model they will never want to go back. 3D printing in medicine is here to stay.
3D printed liver model showing the tumor to be resected.
3D printed liver model
I will be publishing more blog articles about 3D printing at the 2014 RSNA meeting. Follow this blog or follow on Twitter @Embodi3D.
3D printing is a hot topic at this year's Radiological Society of North America (RSNA) meeting in Chicago. I've been involved in medical 3D printing for the past two years, and every month there seems to be more interest. At this year's RSNA meeting, the level of interest is higher than I have ever seen before. There are literally dozens of sessions related to 3D printing in radiology, and they all seem to be very well attended. The Sunday session on "Fundamentals of 3D Printing" had a line out the door and down the hall as shown by the picture below. So many people were standing in the room that they had to close the session due to fire safety limits.
Perhaps one of the biggest draws is the vast array of striking 3D printed models on display from a variety of vendors that offer 3D printing and consulting services. 3D printer manufacturers have been working hard on new and exciting 3D printing materials. As a result, there is now a large selection of materials to choose from, each with a unique set of properties. When the right anatomy, materials, and printers are combined effectively, the models can truly become things of beauty.
While you can't get your hands on the individual models shown here, Embodi3D does maintain a growing library of 3D printable models for you to download and 3D print yourself. I will put links to some of my favorite downloadable files at the end of this article.
Long lines were seen outside of most 3D printing sessions, including this one on Sunday morning.
In this hands-on session which teaches 3D printing software, each of 50 workstations was occupied. There was standing room only in the back of the room.
3D printed model of a kidney with a tumor and blood vessels (pink). This model uses two colors to highlight anatomy. 3D Systems Medical Modeling
3D printed model using colored gypsum powder shows the various structures of the heart. 3D Systems Medical Modeling
A human brain. 3D Systems Medical Modeling
3D model of a spine with severe deformity. 3D Systems Medical Modeling
Multicolor 3D model of the skull, with cut away that shows the cerebral arteries (red) and veins (blue). 3D Systems Medical Modeling
Hollow model of an abdominal aortic aneurysm using two colors. The atherosclerotic calcium is shown in pink. 3D Systems Medical Modeling
This large model of a skull and mandible was designed to demonstrate jaw alignment. 3D Systems Medical Modeling
This transparent brain shows various white matter fiber tracks in different colors, an amazing property of newer 3D printing materials. Stratasys.
Multicolor 3D print of a heart. Stratasys
3D print of heart with detailed pulmonary arteries and veins. Stratasys
3D print of a skull using transparent material. Materialise
Example of 3D printed orthopedic surgery cutting guides used for knee replacement surgery. Materialise
Glass-like 3D print of a pediatric heart. Materialise.
Select 3D Printable files available for free download on Embodi3D.com.
Must register to download. Registration is free and only takes a minute.
Human heart #1
Human heart #2
Half skull, sagittal cut
3D printing is revolutionizing the treatment of aortic stenosis, as reported by researchers from St. Joseph's Hospital in Phoenix, Arizona and presented at the 2014 Radiological Society of North American (RSNA) meeting. Aortic stenosis is a deadly condition where the valve that connects the heart to the aorta does not open properly. The aortic valve, as it is called, is designed to open freely to allow blood pumped from the heart to move in a forward direction into the aorta, the main artery of the body. At the end of a heart contraction, the valve closes to prevent the blood from flowing backwards. In patients with aortic stenosis, the valve fails to open during contraction, thus preventing blood from flowing forward during cardiac contraction (systole). The heart compensates by squeezing harder and harder to maintain adequate forward flow. Eventually, the heart becomes too strained and a variety of severe complications can ensure, including heart attack, heart failure, syncope (fainting), and sudden death. In patients with severe aortic stenosis there is a 50% chance of dying within two years if untreated.
Traditional treatment of aortic stenosis involved open heart surgery to replace the valve. This is a major operation and involves sawing through the breast bone to open the chest and gain access to the heart. As one can imagine, the procedure is risky and recovery takes a long time. Many patients who are too ill or weak and are not eligible for the surgery.
Fortunately, there is a new procedure where a prosthetic aortic valve can be implanted by navigating a plastic tube, or catheter, to the heart through a puncture in the artery of the hip or sometimes via a direct puncture through the apex of the heart. This procedure, called a Transcatheter Aortic Valve Replacement, or TAVR, promises to make aortic valve replacement minimally invasive, that is doable through a small hole instead of requiring open surgery. Recovery time is significantly less and patients who are ineligible for conventional surgery can often get TAVR.
The major problem with TAVR is that it can be very difficult to accurately place the prosthetic valve through the catheter, and poor placement can result in devastating consequences. Unlike open surgery, where the surgeon has direct access to the diseased heart valve, with TAVR the physician must work through the catheter. The valve is loaded on a collapsed metal mesh called a stent. The stent is then inched forward through the catheter into the proper position. The position is checked with x-ray and then the stent is expanded -- hopefully in the correct position relative to the diseased aortic valve, pushing it aside and replacing it with the new prosthetic valve. Once the prosthetic valve is expanded it cannot be retrieved or repositioned, and millimeters matter. Valves come in different sizes. If the valve is the wrong size or malpositioned by even a few millimeters it can cover the coronary arteries and lead to heart attack, cause blood clots to form leading to stroke, or even come free and cause tearing of the aorta.
Different sized TAVR aortic valves
This is where 3D printing comes in. The Arizona researchers used contrast enhanced computed tomography (CT) scans to gather precise data on the anatomical structure of the heart, aorta, and aortic valve from three patients with severe aortic stenosis, and manufactured precise 3D printed replicas of the aortas. Then they tested various valve sizes and position to see what had the best anatomic fit. They then did CT scans of the prosthetic valves within the 3D models and compared those to postoperative CT scans of the actual patients after TAVR, and found that the pre-surgical test fitting in the 3D printed models accurately predicted how the valves would perform in real patients. Use of the 3D printed models helped the surgeons choose the correct size valve and positioning prior to the surgery, thus reducing the risk of he TAVR procedure.
Digital rendering of the aorta
Testing the implantable valve in the 3D printed model by deploying it through a catheter (blue)
I have personally used customized 3D printed models I designed to test wires and catheters prior to complex mesenteric artery aneurysm treatments (publication forthcoming), and I can tell you that knowing your wires and catheters will work before the procedure is far better than figuring it out with trial and error during the procedure. Presurgical testing with 3D printed models is here to stay.
If you are interested in learning more about applications of 3D printing in medicine or how to make your own 3D models, please register as a member (it's free and only takes a minute!) and join the community of medical professionals who are all trying to build the future of 3D printing in medicine. Ask a question, start a discussion, or download free 3D printable models to make on your own. I will put some links to a few of the free downloadable models related to this article below.
FREE 3D PRINTABLE DOWNLOADS
Heart and pulmonary artery tree
Human heart #2
Summary: This is an advanced tutorial and assumes that you already know how to create STL files from CT scans. If you do not yet know how to do this, stay tuned, as a series of tutorials is planned on this website. Here we will use a free, open-source software package Blender to repair and correct a bony pelvis and lumbar spine model generated from a CT scan. If you would like to follow along with this tutorial, you can download the relevant Blender and STL files here, and follow along.
>>DOWNLOAD THE TUTORIAL FILES AND FOLLOW ALONG.<<
UPDATE: If you have very extensive mesh errors in your model, you can read my other medical 3D printing tutorial on how to repair mesh errors quickly using Blender.
You can watch the YouTube video for a high-yield introduction, but also read this page for additional details.
Background on the Problem
Before we dive in, let's take a moment to discuss what the medullary cavity of a bone is and why it's a problem if you're trying to 3D print bone models made from a CT scan. Bones are not solid, even though they may appear to be so. Most bones have a very hard, very dense outer layer comprised of cortical bone. This tough outer part of the bone is very hard and is what gives bones their strength. The inner core of most bones contains fatty bone marrow, and is made of much softer bone that is less dense, called spongy bone. On a CT scan you can see these two different types of bone. Take this CT scan of the pelvis, for example.
In the CT scan image shown in Figure 1, the hard, dense cortical bone is seen as a bright white outer surface of these pelvic bones. The white color indicates that it is very dense. The spongy bone, which is less dense and contains fatty bone marrow, can be seen in the center of the iliac bones and sacrum on this image. This type of bone is not white, but is a grayish color on a CT scan image. In some areas it is approaching black in color, which means is not very dense at all. Outside the bone we can see muscle represented by this light gray color, and intra-abdominal fat which is represented by this dark gray color.
If we measure the density of these bones in Hounsfield units, which is the unit of density that is measured on a CT scan, we can see that the dense cortical part of the iliac bone in this image measures 768 Hounsfield units, and is shown in the rightmost red circle (Figure 2). The less dense medullary bone within the sacrum measures 1.7 Hounsfield units, as shown within the red circle in the middle. If we measure the muscle in the gluteus maximus area, this measures 51 Hounsfield units, as shown in the red circle on the left. So in this case the medullary bone is actually less dense then muscle around it. How can bone be less dense than muscle? Because it is filled with fatty bone marrow. Remember, fat floats on water, and is thus less dense than water. (What also floats on water? A duck. But that is another story...) In Figure 2, the green circles represent the area of interest that is being measured. The text and red circles represent the measurements for the those areas of interest.
The fact that medullary bone and bone marrow is not dense causes a problem when we are trying to convert CT scan data into a digital model that is 3D printable. This is because algorithms designed to select the bone from all the other stuff in the body, such as fat, muscle, air, etc), use density as a means to identify the bones. Here's an example of the 3D model of the pelvis and lumbar spine created from the CT scan we were just looking at. If you look closely at Figure 3 you can see there's a lot of internal geometry within the bones that is not desired (red circles). This extra geometry can cause problems when the file is sent to 3D printer or 3D printing service. The model may be rejected because of characteristics of this internal medullary space, for example there may be thin walls and automated quality checkers may flag the model as unprintable. Furthermore, if you try to perform certain manipulations on the mesh, such as Boolean operators, this unwanted mesh may cause these operations to fail. If we want to 3D print our bone models, it is best to get rid of extraneous and unwanted mesh.
Getting started on cleaning your mesh in preparation for 3D printing.
1) Start by importing your STL file into Blender. If you don't have Blender, it is available for free at http://www.blender.org. Blender is available in Windows, Macintosh, and Linux versions. Be forewarned. Although Blender is powerful, it takes a little bit of time to get used to it. Be patient. Open Blender and select File -> Import -> Stl (stl) as shown in Figure 4. If you are following along with this tutorial using the tutorial files, select the "Pelvis and Lumbar spine, uncleaned.stl" file.
You will find that the mesh appears quite large. This is because Blender uses an arbitrary unit of measure for distance called a Blender Unit. The way that STL files are interpreted, one Blender unit is equivalent to 1 mm, thus the model appears quite large. Use the scroll wheel on your mouse to zoom out. If you want, you can re-size your mesh by hitting the S key.
You may also find that your mesh appears clipped, as shown in Figure 5. This is because by default Blender uses a clipping distance of 1000 by default for the view, clipping any objects in the scene too far from the camera. This is easily fixed. View the Properties bar by clicking the "+" in the upper right corner, as shown by the red circle in Figure 5. Or, you can type N to show the Properties panel. Then under View, type 100,000 in the Clip: End field, as shown in Figure 6.
2) To identify where you have extraneous mesh, you must first go to Edit mode. Before doing this, make sure you have selected your model by right clicking it. The model should be surrounded by a yellow halo, which indicates that it is selected, as shown in Figure 7.
Enter Edit mode by hitting the Tab key, or by selecting Edit mode from the Mode button, located on the bottom left toolbar, as shown in Figure 8. Use the Z key to toggle between types of viewport shading. You can also use the viewport shading button in the bottom toolbar as shown in Figure 9. Select Wireframe viewport shading.
3) Use the scroll wheel to zoom in and out, and the middle button to pan about. Zoom into the L3 vertebral body (3rd lumbar vertebral body. If you need a refresher on lumbar anatomy, check out Wikipedia). As was shown in Figure 3, there is excessive mesh in the medullary cavity of the bone that is persistent within the model. We want to remove it.
How this extra mesh got here has to do with the original CT scan and how the surface STL model is generated from CT scan data. If you look at the original CT scan of this vertebral body, as shown in Figure 10, you can see very small perforating holes within the posterior part of the vertebral body, as shown by the red arrows. These are nutrient foramina. They are tiny holes in the bone that allow arteries to penetrate through the thick outer cortex and into the medullary cavity, supplying blood to the bone marrow. When the surface generating algorithm creates the STL file from the CT scan, it finds its way from the surface into the nutrient foramina and maps the internal medullary cavity of the bone. Essentially, the algorithm determines that the bone is hollow, and has a connecting tunnel between the surface and the hollow interior, as shown in Figure 11. This is actually true, but for the purposes of 3D printing we are not interested in extremely complex geometries within the medullary cavities of the bone. For practical purposes of 3D printing we wish the bones to be solid, even though in nature they are not.
4) The easiest way to delete the medullary mesh is to identify where the mesh is connected to the surface via these nutrient foramina. To do this, inspect the mesh carefully using Wireframe viewport shading, which should give you an idea of where these connecting tunnels are located. Once you have identified the area, use the lasso tool by holding down the CTRL key and left clicking a loop around the area of interest, as shown in Figure 12. You must be in Wireframe viewport shading in order to make the selection. If you are in Solid viewport shading, you will only select the surface elements. Also, make sure you are in vertex selection mode. The three selection modes (Vertex, Edge, Face) are shown circled in red on the bottom toolbar in Figure 12.
5) Once you have selected the mesh elements of interest, you will hide the non-selected mesh elements. This simplifies your view and also reduces the processing time needed by the computer to display the image to you in real time. With large data sets, such as those collected by CT scans, even a powerful desktop system can become very sluggish when the entire mesh is displayed and manipulated at once during editing. Hiding temporarily unneeded mesh saves a lot of time.
6) With your mesh elements of interest selected in orange as shown in Figure 12, hold down the control key and hit the "I" button. This inverts the selection, as shown in Figure 13. Next, hide the selected mesh by hitting the "H" key. You should now have a very limited amount of mesh displayed, as shown in Figure 14.
Rotate the mesh to a different orientation and then select your target mesh, invert the selection, and hide the inverted selection again. At this point you should have a very small amount of mesh that you are focusing on, such as that shown in Figure 15.
7) Now that your visible mesh is small enough to work with, switch back to Solid viewport shading using the viewport shading box in the lower toolbar, or by hitting the "Z" key. Zoom in and identify where the nutrient foramina are present on the surface of the bone. Go to face selection mode using the face selection button on the bottom mouth bar or by hitting CTRL-TAB-3. Using the right mouse button to select a face near the opening of the nutrient foramen. Using the CTRL key and right mouse button, select a loop of face is completely around the foramen, as shown in Figure 16. Make sure you select an entire loop of faces around the hole. You want to complete cut it away from the surface.
Now delete this selection. Hit the delete key, and select Faces (or hit the delete key followed by the F key). You should now have a hole in your mesh, and the tunnel between the surface and the medullary mesh has been cut completely. Double check to make sure there are no stray edges or face still connecting the two parts.
😎 Now we are going to close the hole. Go to Edge the selection mode using the button in the lower toolbar or by hitting CTRL-TAB-2. Holding down the ALT key, right-click on one of the edges abutting the hole. Blender should select the entire circumference of the hole, as shown in Figure 17. Next, fill in a face using the F key. A face should appear. Convert this face to triangles by hitting CTRL-T. if you want to smooth out the mesh, you can take an extra step and apply local smoothing by hitting W followed by O. Your hole should be filled in and smoothed, as shown in Figure 18.
Repeat steps 6 through 8 for each nutrient foramen tunnel connecting the surface to the medullary cavity.
9) When you have finished making all the edits to your viewable mesh, it is time to unhide the hidden mesh that comprises the bulk of your model. Hit Alt-H to unhide all the hidden mesh. Most of it will be selected. Hit the A key to unselect all. The A key toggles between select all and select none.
10) Once you have determined that all tunnels between the surface and medullary cavity have been deleted and filled, it is time to delete the entire block of medullary mesh in one operation. Make sure you are in edit mode, with wireframe viewport shading. Using the right mouse button, select a vertex from the medullary block mesh, as shown in Figure 19.
We are now going to select every vertex that is connected to this single vertex. Because the entire medullary mesh is disconnected from the rest of the model, the remainder of the model should not be selected. Hit the CTRL-L key to select all contiguous vertices. You should find that only the unwanted medullary mesh is selected, as shown in Figure 20. Hit the delete key, followed by "V" for vertices, and the entire block of unwanted medullary mesh will be deleted at once. Wow! That was gratifying! After all that work you have probably deleted several thousand unwanted vertices in one swoop.
Your target bone, in this case L3 -- the third lumbar vertebra -- should now be free of unwanted medullary cavity mesh. You can repeat this process for each medullary cavity in your model. In the particular model that accompanies this tutorial, that would be L4, the bilateral iliac boness, sacrum, and a few other places. It can be a time-consuming process, but with practice even a complex model with tens of thousands, or millions of faces can be cleaned in a few hours.
I hope you found this tutorial helpful. If you have questions, please leave a comment below. If you are making 3D anatomic models from medical scan data, please consider sharing your creations with the Embodi3D community. Embodi3d is a community of biomedical 3D printing enthusiasts. We are all trying to help each other, and by sharing your models you can contribute greatly to the community.
Here are a few examples of 3D printable anatomic models Embodi3D members have shared for free. Please share too!
Human male skull
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Hello and welcome back. Once again, I am Dr. Mike, board-certified radiologist and 3D printing enthusiast. Today I'm going to show you how to correct severe mesh defects in a bone model generated from a CT scan. This will be in preparation for 3D printing. I'll be using the free software programs Blender and Meshmixer.
In my last medical 3d printing video tutorial, I showed you how to remove extraneous mesh within the medullary cavity of a bone. That technique is best used when mesh defects are limited. In instances where mesh defects in a bony model are severe and extensive, a different approach is needed. In this video, I'll show you how to correct extensive mesh errors in bony anatomical models using Blender and Meshmixer. This assumes that you know how to generate a basic STL file from a CT scan. There are a variety of commercial and freeware products that allow you to do this, on a variety of platforms. If you don't yet know how to do this, stay tuned, as I have a series of tutorials planned which will show you how to do this on a variety of operating systems and budgets.
If you wish to follow along with this tutorial, you can download the free tutorial file pack by clicking this link. This is highly recommended, as the files allow you to follow along with the tutorial, which will make learning easier. Included is the STL file used in this tutorial. Also, a powerful Blender script is included which will enable you to easily and efficiently prepare your own bone models for 3D printing. It's a real timesaver. If you haven't registered at Embodi3D.com, registration is free and only takes a moment.
DOWNLOAD THE ACCOMPANYING FILE PACK. CLICK HERE.
You can watch the video tutorial for a quick overview, or read this article for a detailed description.
Initial analysis using Meshmixer
Let's take a look at an STL file of a talus fracture in the ankle. This 3D model is from a real patient who suffered a fracture of the talus. The talus is the bone in the ankle that the tibia, or shinbone, sits on. This STL file is included in the file pack. Let's open this file in Meshmixer (Figure 1). Meshmixer is free software published by Autodesk, a leading maker of engineering software. If you don't have Meshmixer, you can go to Meshmixer.com and download it for free.
Once you have the file open in Meshmixer, click on the Analysis button and select Inspector. The inspector shows all the errors in this mesh. Blue parts represent holes in the mesh. Red parts show areas where the mesh is non-manifold. Magenta parts show disconnected components. As you can see, there are a lot of problems with this mesh, and it is not suitable for 3D printing in its current state (Figure 2).
Meshmixer has a feature to automatically repair these mesh defects. However, there are so many problems with this mesh that the auto repair function fails. Click on the Auto Repair All button. Meshmixer has tried to repair these mesh defects, and has successfully reduced the number of defects. However, it is also introduced gaping holes in the model. Entire bones are missing (Figure 3). This clearly isn't the desired outcome.
Opening the STL file in Blender
The solution to this problem can be found with Blender. Blender is a free, open-source software package that is primarily designed for animation. It is so feature-rich however, that it can be used for a variety of different purposes, and increasingly is being used for tasks related to 3D printing. If you don't have Blender, you can download it from blender.org. At the time of this writing, the current version is 2.73 a.
Open up Blender. Go ahead and delete the default cube shown in the middle of the screen (Figure 4) by right clicking it and hitting the "X" key followed by the "D" key. If you are new to Blender, you'll soon learn that much of what you can do with Blender can be done with keyboard shortcuts. This can be daunting to learn for beginners, but makes use of Blender very efficient for heavy users.
Next open the STL file in Blender. Go to the File menu in the upper left, select Import, and select "Stl (.stl)." Then, navigate to the folder for the tutorial files and select the "ankle - talus fracture.stl" file. You probably don't see anything, as is shown in Figure 5. To understand how this happens, you need to know a little bit about how Blender measures distances. Blender uses an arbitrary measure of distance called a "blender unit." One blender unit is equivalent to one of the little squares seen in the viewport. However, in real life distances are measured in real units, such as feet, inches, centimeters, and millimeters. Most STL files that are generated from medical imaging data have default unit of measurement of millimeters. When Blender imports the file it converts the millimeter units to blender units. Since our imported model is the size of human foot, measuring 240 mm or so, the model will be 240 blender units, or 240 of those little squares, in length. We can't see it because the model is too big! Our viewport is zoomed into much! Zoom out using the mouse wheel way, way back until you can see the model as shown in Figure 6.
Figure 5: Where is the model?
Figure 6: There it is!
Correcting the Object Origin
You will notice that the origin of the ankle object, as shown by the red blue and green axes (Figure 6), is actually outside of object itself. Left uncorrected, this can be a really annoying issue. When you rotate or pan around the object, you will rotate or pan around these three axes, instead of the ankle object itself. Fortunately, correcting this takes only a moment. In the lower left-hand part of the window select the Object menu. Be sure that you have the ankle object selected first. Then choose Transform, Geometry to Origin. The ankle object is then moved to the red blue and green axes. With the object origin now in the center of the mesh, the mesh will be much easier to work with.
Figure 7: The ankle mesh and object origin are now aligned.
Inspect the ankle mesh
If you look closely at the ankle mesh you can see immediately that it has a lot of problems. In the solid shader mode, the bones look very faceted. The polygons are large, giving the bones a unnatural appearance (Figure 8). Don't worry, will fix this. If you turn on wireframe mode by hitting the "Z" key you can see that there is a lot of extraneous mesh within the bones that represents unwanted mesh from the medullary cavities of these bones (Figure 9). Furthermore, if you check for non-manifold mesh by holding control-shift-alt-M, you'll see that there are innumerable non-manifold mesh defects (Figure 10).
Figure 8: Note the very faceted appearance of the bones.
Figure 9: There is a significant amount of unneeded and extraneous mesh, particularly within the medullary cavities of the bones.
Figure 10: Non-manifold mesh defects.
If you are unfamiliar with the term "non-manifold," let me take a moment to explain. A mesh is simply a surface. It is infinitely thin. If the mesh is continuous and unbroken, and has a contained volume within it, then the mesh can be considered to represent something solid. In this case, the mesh surface represents the interface between the inside of the object and the outside of the object, such as the sphere shown in Figure 11. An object like this is considered to be "manifold," or watertight. It represents a solid that can really exist in the physical world, and can thus be 3D printed.
If however, I cut a hole in the sphere, as shown in Figure 12, then there is a gap in the mesh. A 3D printer won't know what to do with this. Is this supposed to be solid like a ball, or hollow like a cup? If it is supposed to be like a cup, how thick are the walls supposed to be? The walls in this mesh are infinitesimally thin, so what is the correct thickness? This mesh is not watertight - that is, should water be placed in the structure it would leak out. The mesh is non-manifold. It cannot be 3D printed. If we use the control-shift-alt-M sequence to highlight non-manifold mesh, as shown in Figure 13, we can see that Blender correctly identifies the edge of the hole as having non-manifold mesh.
Closing major holes manually in Blender
In this particular mesh, there are many, many small mesh errors and two very large ones. The distal tibia and fibula bones have been cut off by the CT scanner, leaving gaping holes in the mesh as shown in Figure 14. Fixing these manually will only take a moment and make things easier down the road, so let's take care of that now. Enter Edit mode by hitting the Tab key, or clicking it in the Mode menu. If you hit control-shift-alt-M to select non-manifold edges, you can clearly see that these bone cuts are a problem as shown in Figure 15.
Go to Vertex selection mode by clicking the vertex button or hitting control-tab-1 on the keyboard as shown in Figure 16. Select one of the vertices from the medullary portion of the tibia bone as shown in Figure 17. This mesh represents the medullary cavity of the tibia bone, and is not connected to the rest of the mesh. Hit control-L to select all contiguous vertices (Figure 18). All the unwanted medullary cavity mesh should now be highlighted. Delete this by hitting the "X" key followed by the "V" key, or by hitting the delete and selecting "vertices." There is another small bit of medullary cavity mesh at the edge of the tibia cut. Perform the same routine and delete this as well.
Next we will direct our attention to the unwanted medullary mesh of the thinner fibula bone. Click on a vertex in the fibula medullary mesh and hit control L. You will note that the entire mesh is highlighted as shown in Figure 19. This indicates that the medullary mesh is connected to the rest of the mesh in some way. We don't need to manually delete all of the medullary mesh. We just need to get it away from the edge where we will create a new face to close the bone edges. Go to Edge selection mode by hitting control-tab-2 or clicking the edge selection button as shown in Figure 20. Hit the "A" key to unselect everything. Then, click on a single edge along the unwanted medullary mesh, as shown in Figure 21.
Next we will by holding down the alt key and right clicking on the edge again. Blender should select the loop around the entire edge as shown in Figure 22. We will now expand the selection by holding down the control tab and hitting the plus key on the number pad. Hit the plus key three times. Your selection should now look like that in Figure 23. Delete the highlighted mesh by hitting the "X" and "V" keys, or hitting the delete key and selecting vertices.
Next we are going to close the holes by holding down the alt key and right clicking along the edge of the cut line of the fibula. An entire loop should be selected as shown in Figure 24. Create a face by hitting the "F" key. Convert to triangles by hitting Control-T. The end of the fibula should be closed, as shown in Figure 25. Repeat the same for the open edge of the tibia bone. Afterwards the mesh should look as it does and Figure 26.
Creating a Shell of the model using the Shrinkwrap and Remesh modifiers in Blender
So how will it ever be possible to correct the hundreds and hundreds of mesh errors in the ankle model? This is the million-dollar question. A mesh of this complexity often cannot be fixed using automated mesh correction software, as we saw with Meshmixer. Correcting this many errors manually is a time-consuming and tedious process. I've spent hundreds of hours correcting mesh errors like this one by one. But, after years of creating 3D printable anatomical models, I've developed a technique to fix these mesh errors in only a few minutes.
The secret is this: You don't fix the mesh errors. Leave them alone. You create a new mesh to replace them!
Let's start by creating a sphere. If you are in Edit mode, exit that by hitting the Tab key. If you are still in wireframe viewport mode, hit the "Z" key to return to solid viewport shading. In the lower left-hand side of the window, hit the Add menu. Select Mesh, UV sphere and add a sphere. An "Add UV Sphere" panel will show up on the left side of your screen as shown in Figure 27. We want the sphere to have lots of detail. Under Segments enter 256. Under Rings, enter 128. The default size of the sphere is only one blender unit (1 mm) in size. This is too small, we want the thing to be huge. Enter 1000 for size. At this point you should have a very large sphere surrounding your entire scene. Believe it or not, this sphere will eventually be your new ankle object. Let's go ahead and rename it "Ankle skin" as shown in Figure 29.
Figure 27: Add a UV sphere
Figure 28: Configure the sphere. Segments 256, rings 128, size 1000
Figure 29: Rename the sphere to "Ankle skin"
Applying the Shrinkwrap Modifier
Select the "Ankle skin" object. Click on the Modifiers tab, it looks like a small wrench (Figure 30). From the Ad Modifier drop-down menu, select the Shrinkwrap item. Specify the Ankle object as "the target. Set off set to 0.5. Check the" Keep Above Surface" box. Your sphere will have shrunken down to envelop the ankle, as shown in Figure 30. Apply the modifier by hitting the "Apply" button. At this point you're thinking that your Ankle skin object hardly looks like an ankle, and you're right. If you try to apply the shrinkwrap modifier again, you won't get any change in the mesh. Blender has shrunken the sphere as best it can given the limited geometry of the sphere. To go further we need to change the geometry a bit, which is where the Remesh modifier comes in.
Figure 30: The Shrinkwrap modifier
Applying the Remesh Modifier
Next go to Add Modifier again, and select Remesh. Set Mode to Smooth, Octree Depth = 8, and uncheck Remove Disconnected Pieces. By now you should have something that looks like Figure 31. Apply the modifier by clicking the Apply button.
Figure 31: The Remesh modifier
Apply the Shrinkwrap Modifier again
Apply the shrinkwrap modifier again, using the same parameters as before. Your Ankle skin object should look like Figure 32. Now we are getting somewhere! There is still a long way to go, but the mesh somewhat resembles the bones of the foot. By repeatedly applying the Shrinkwrap and Remesh modifiers the Ankle skin object, which was originally a sphere, will slowly approximate the surface of the error-filled original ankle mesh. Because of the original skin was a sphere, and hence manifold, as it is shrink-wrapped around the ankle mesh it will preserve (for the most part) it's mesh integrity. There will be no unnecessary internal geometry. Any holes or other defects in the original mesh will be covered. Unfortunately, repeatedly applying the shrinkwrap and remesh modifier again and again is somewhat tedious (although not as tedious as manually correcting all the errors in the original mesh). Fortunately, we can automate this process using Python scripting. This allows us to create a new mesh in a matter of minutes.
Automating the Shrinkwrap Process using Python Scripting
For those of you less familiar with Blender's more advanced features, you may be surprised to learn that it is fully scriptable. That means that you can program it to perform tasks repeatedly using a Python script. In this case we want to repeatedly execute shrinkwrap and remesh modifiers on our ankle skin object. With each iteration the skin will more closely approximate the surface of the original mesh. If you are familiar with Python scripting, you can write a script yourself to call the necessary modifiers and specify the necessary variables. To make things easier for you, I have written a Python script for you. It is included in the free tutorial file pack.
Change the bottom window to the text editor. View button in the bottom left-hand corner as shown in Figure 33. Select Text Editor. Click on the "Open" button and navigate to the folder with the tutorial file pack files as shown in Figure 34. Double-click on the "shrinkwrap loop.txt" file as shown in Figure 35.
Figure 33: Select the text editor
Figure 34: Click on the Open button
Figure 35: Open the "shrinkwrap loop.txt" file
The script file should now open in the text editor window. Adjust the target_object variable to be the target you want your skin wrapped around, in this case the "Ankle - Talus Fracture" object. Leave the shrinkwrap_offset variable at 0.5 for now. You can specify how many shrinkwrap-remesh iterations you want to run. For now leave it at 20. Click the "Run Script" button as shown in Figure 36. The script will now run, and it will apply the shrinkwrap-remesh modifiers 20 times. On my machine it takes about one minute for the script to execute.
At this point you'll notice that the ankle skin object very closely approximates the original ankle object, as shown in Figure 37. Run the script again using the same settings. At this point the mesh is really looking pretty good. Let's run the script a final time with the smaller offset to more closely approximate the real bones. Set the shrinkwrap_offset variable to 0.3 and run the script again reducing iterations to 10. After completion the mesh should appear as it does in Figure 38. If you compare our new skin mesh as shown in Figure 39 (left) to the original ankle object in Figure 39 (right) you can see that our new skin is actually much more realistic than the original mesh. The highly faceted appearance of the original mesh has been replaced by a smoothed appearance of our shrink-wrapped skin. Furthermore, whereas the original mesh actually had separate bones that were disconnected, the new, shrink-wrapped mesh is a single interconnected object. From a 3D printing standpoint this is much better as the ankle bones will print together as a single unit
Figure 39: Comparison of original plus new shrink-wrapped mesh.
Finalizing the Ankle Model for 3D printing using Meshmixer.
Select the new ankle object. Export the object to the STL file format. From the file menu select Export and then "Stl (.stl)." Let's call the file "ankle corrected.STL." Open the new STL file in Meshmixer. You will notice that Meshmixer immediately identifies some mesh errors as shown in Figure 40. This is because the Remesh modifier in Blender occasionally introduces non-manifold mesh defects. You will note however that the number of defect is significantly less than our original model which was shown in Figure 1. With this smaller number of errors, Meshmixer can fix them automatically. Go to the Analysis button and select Inspector. Meshmixer will highlight the individual mesh defects, as shown in Figure 41. Click on the "Auto Repair All" button. Meshmixer will then automatically repair the mesh defects. The result is shown in Figure 42.
Figure 41: Meshmixer inspector
Figure 42: Corrected mesh
The mesh looks great, and is ready for 3D printing! Export the STL file by going to the File menu in Meshmixer and selecting Export. Save the file as "ankle final result.STL".
Please share with the community.
If you have found this tutorial helpful and are actively creating 3D printable anatomic models, please consider sharing your work with the Embodi3D community. You can share your models in the File Vault. If you have comments or advice, you can share your expertise in the Forums. If you are interested in blogging about your adventures in medical 3D printing, contact me or one of the administrators and we can set up blogging on your Embodi3D user account. If you wish to hire someone to help you with your anatomical 3D printing project, you can place an ad for free in the Services Needed Forum, If you are doing your own anatomical 3D printing and are willing to help others, list your services for free in the Services Offered Forum.
This is a community. We are all helping each other. Please consider giving back if you can.
Have fun 3D printing!
A lot of great 3D printable anatomic files have been shared on Embodi3D in the past few years. One of the most popular categories is skulls. There are many files available, and they are organized under Skull and Head STLs in the file Downloads area of the site. You can download any of these files by registering an account and in most cases the files are free to download.
Below I created a list of my favorite skull files for your learning and enjoyment.
These 3D printable skull models are a fantastic resource for education and show both normal anatomy and disease and injury. Thanks to the generosity of our contributors, all of these models are available for free download and 3D printing.
This a diverse set of files ready for 3D bioprinting. These STL skull files come from CT scans and demonstrate some of the pathology physicians encounter. Several different cuts and individual bones make much of the anatomy easily accessible which is great for education.
I hope you enjoy this collection. If you are using these skull files for an interesting project, please share your experiences with the community by posting a comment.
3D printable skull 1 - front tooth out, from Dr. Gobbato
3D printable skull 2 - Male skull
3D printable skull 3 - from Dr. Marco Vettorello
Skull fracture 1 - fracture of frontal bone
Skull fracture 2 - fracture of mandible (jaw bone)
Skull after craniotomy surgery (with surgical hole drilled into it)
Half skull (sagittal cut) great for education
skull base, showing foramina, for medical education
Full and half size "Lace" skulls. A unique item for your desk.
Frontal bone of skull (forehead bone)
Mandible (jaw bone)
I have received several requests for spine STL files from CT scans and these files have been added to the file vault over time as more people are 3D printing vertebrae for medical moldeling. There was a really good response to my last article about the wonderful 3D printable skull models available for free download on the embodi3D.com website. So, I've decided to do another article about spine models.
Embodi3D.com contains a large collection of spine STL files within the Spine and Pelvis category of the Downloads area. These 3D printable files are available for download by registering an account. The vast majority of files are available for free download.
The spine is a very complicated anatomic structure. Some spinal bones, or vertebrae, are designed for flexibility, as in the cervical spine in the neck. Others are designed to support ribs, as in the thoracic spine in the chest. The lumbar spine, in the low back, has large, hearty vertebra that are designed to bear weight. The spine is the focus of many maladies, and a good anatomic understanding of the spine is needed before disease processes and their treatments can be fully understood.
I personally do many procedures on the spine. A few include lumbar punctures, epidural steroid injections, selective nerve root blocks, vertebroplasty, kyphoplasty, myelograms, lumbar drain placements, chemotherapy infusions, and biopsies of all kinds. Anatomy can be learned with books or pictures, but there is nothing quite like holding a 3D printed medical model in your hands to make that anatomy "click." 3D printed spine models can help teach spinal anatomy to all levels of students, from grade school to med school. To help others find the best medical models, I have put together a collection of the best 3D printable spine models available for free download on Embodi3D. I hope you find this collection useful and interesting.
Lumbar Spine STL Files from CT Scans
Whole lumbar spine and sacrum
L3 Lumbar vertebra
Another L3 Lumbar vertebra
L4 Lumbar vertebra
Lumbar spine wedge compression fracture
Thoracic Spine STL Files For 3D Printing
Whole thoracic spine
Cervical Spine STL Files For Medical Models
Whole cervical spine
Whole cervical spine with skull base
C1 (atlas) vertebra
Hello, it's Dr. Mike here again with another tutorial on medical 3D printing. In this tutorial we are going to learn what types of medical imaging scans can be used for 3D printing. We will also explore the characteristics those scans must have to ensure a high quality 3D print. This is one of a series of 3D printing tutorials that will teach you how to create 3D printed anatomical and medical models yourself. Open source and commercial software are covered in the tutorials along with 3D printer selection and setup. This tutorial is followed by a tutorial on Creating 3D Printable Medical Models in 30 minutes using free software: Osirix, Blender, and MeshMixer.
Introduction to Selecting a Medical Scan for 3D Printing
If you listen to the hype in the press, it sounds like any medical imaging scan can be easily converted into a high quality 3D printed anatomic model, and any structure of interest can be shown clearly and beautifully. This is simply not true. In fact, most conventional medical imaging scans are not suitable for 3D printing. Those few that are suitable will probably only produce high-quality 3D prints of a few anatomic structures. In this tutorial I will go over the basic elements that make a medical scan suitable for 3D printing. I will briefly discuss different imaging modalities such as CT, MRI, and ultrasound. By the end of this tutorial you should be able to recognize whether a medical scan is suitable for 3D printing. If you are planning on having a medical scan done with the intention of 3D printing from the scan, you will be able to protocol the scan appropriately to enable a high quality 3D print.
I'd first like to take a moment to discuss the standard imaging planes used in medical scans. When a medical scan is performed, images of the body are usually captured and displayed in one of three standard imaging planes. These are the transverse plane (also called axial plane), the coronal plane, and the sagittal plane. Figure 1 demonstrates these planes. In layman's terms, the axial plane divides the body into top and bottom, the coronal plane front and back, and the sagittal plane right and left. CT and MRI scans are typically comprised of several series of images. Each series is comprised of a stack of images in the same plane spaced out evenly. When a medical scan is converted into a format suitable for 3D printing, such as an STL file, the computer takes this stack of images and extrapolates the volume of an object. A surface is then calculated around that volume. That surface is what becomes the 3D printed model.
Figure 1: Standard imaging planes used in medical scans. Source: National Cancer Institute
Imaging Modality: CT versus MRI versus ultrasound
In order to understand what scans are best used for 3D printing, a very basic understanding of the types, or modalities, of medical scans is needed. The medical physics behind how these scans work can literally fill volumes. Radiology residents are required to take board examinations on the physics and engineering of medical scanners as part of their training. I will attempt to summarize only the most critical information about medical scans into a few short paragraphs to get you up and 3D printing as quickly as possible.
Computed Tomography, or CT scans, are created when an x-ray beam is rotated around the patient. An x-ray detector on the opposite side of the emitter records the strength of the beam that emerges from the other side of the patient. Knowing the angle and position of the x-ray emitter and the strength of the beam emerging from the other side of the patient, a computer can calculate the x-ray appearance of the body in three dimensions. An x-ray beam is generally absorbed or deflected by electrons in matter. Since the density of electrons in matter is more or less the same as the actual physical density of matter, a CT scan can be considered to be a density map of the patient. Things that are dense, such as bone or metal, will appear white. Things that are not dense, such as air, appear black. Figure 2 shows how the different densities of tissue appear on a standard CT scan. When intravenous contrast is given, which contains an iodine-containing chemical that is very dense, it appears white. Fat is not very dense and floats on water, thus it has a blackish appearance.
What else floats on water? Choices: bread, apples, very small rocks, cider, gravy, cherries, mud, churches, lead, a duck. (This is a joke. If you get the reference, please leave a comment and give yourself a star).
Figure 2: Effect of tissue density on CT scan appearance. This CT scan image of the head at the eyes shows fat in the temporal fossa as black (red arrow), intermediate density brain tissue as gray (green arrow) and dense calcium-laden bone in the skull as white (blue arrow).
Magnetic Residence Imaging, or MRI, is a type of imaging that uses very strong magnetic fields to generate an image. The hydrogen atoms that are part of almost all biological structures (water, fat, muscle, protein, etc.) align with the magnetic field. Radio waves can be sent into the scanner causing the hydrogen atoms to flip orientation. When the radio waves are turned off, the hydrogen atoms flip back and emit their own faint radio signal. Based on analysis of these faint radio emissions and by varying the magnetic field strength and timing of the radio wave pulses, a variety of images can be generated. These different pulse sequences can be used to highlight different types of tissue.
Take Figure 3 for example. Four different pulse sequences are shown of the same slice of brain: T1, T2, FLAIR, and T1 with gadolinium contrast. On the T1 image tissues with fat are a bright white, as shown by the fat in the skin (white arrow). The hard, calcium-filled tissue of the skull is black, with the exception of a small amount of bone marrow which is gray in color and sandwiched between the inner and outer skull plate (yellow arrow). The watery cerebral spinal fluid in the lateral ventricles are black (red arrow). However, on the T2 image the watery cerebral spinal fluid is bright white (red arrow). T2 images show water very well. In addition to the water in the ventricles, swelling of the brain tissue due to an adjacent brain tumor can be seen as a white appearance (blue arrow). FLAIR images are similar to T2 images except pure water has been subtracted from the image. Thus tissue swelling (blue arrow) is still clearly visible but the cerebral spinal fluid in the ventricle (red arrow) now appears black. Finally, in the T1 images with gadolinium IV contrast small blood vessels are visible. Additionally, you can actually see the brain tumor and meninges turning white from contrast enhancement (purple arrows).
Figure 3: MRI of the brain at the same level using four different pulse sequences. The patient has a left frontal lobe brain tumor.
When 3D printing from an MRI scan, it is important to select images from a pulse sequence that will highlight the structure you wish to visualize. Arteries, tumors, body fluid, bones, and general tissue are all best seen on different sequences. If you choose the wrong imaging sequence to generate your 3D model from, you will encounter only frustration.
Ultrasound images are generated when soundwaves are sent into the body by an ultrasound emitter. The waves then bounce off various structures and are detected by a receiver, typically built into the emitter. The concept is similar to sonar that is used on ships and submarines. Based on the strength and depth of the soundwave return, an image can be created. Ultrasound images can be used for 3D printing, however it is very difficult to do so because individual images are not registered in a fixed place in space. The images are acquired by sliding the ultrasound transducer on the skin. The exact location in space and angle of the transducer at the time of image acquisition is not known, which makes generation of a 3D volume difficult or impossible. In general, ultrasound is not recommended as a source of imaging data for 3D printing for the beginner.
Key features of medical imaging scans used in 3D printing
There are certain features common to all scan modalities that can help you to create a good 3D print. When considering making a 3D medical or anatomic model you must first decide what you want the model to show. Should it show bones, arteries, or organs? Having a model with unnecessary structures included not only makes it more difficult to manufacture, but it also diverts attention away from the important parts of the model. Give this careful thought. Once you have decided what you want to show, evaluate the medical scan you want to create your model from carefully. If the scan doesn't have the proper characteristics, you can exponentially increase the difficulty of getting a 3D printable model from it.
1. Presence of Intravenous contrast
Take a look at these two axial (transverse) images from CT scans of the upper abdomen (Figure 4). Both images show slices of the upper abdomen at the level of the tops of the kidneys and liver. What is the difference between the two? You'll notice that on the rightmost scan the aorta is white, whereas on the left scan the aorta is gray. Figure 5 is a zoomed image of this region and shows this in more detail. This is because the rightmost scan was performed with intravenous contrast and that contrast is causing the aorta and other vessels to turn a bright white color.
Figure 4: The effect of intravenous contrast.
Figure 5: Close-up view of the abdominal aorta with (right) and without (left) intravenous contrast.
Take a closer look at the kidneys. Figure 6 shows a zoomed-in image. The outer part of both kidneys on the contrast-enhanced scan on the right are a light shade of color. This is due to blood mixed with contrast going into the outer cortex of the kidney. With the contrast-enhanced scan you can clearly see the edge of the kidney, even where it touches the liver. On the noncontrast scan the border of the kidney is only discernible where it is adjacent to the darker colored fat. Where it touches the liver it is difficult to see where the kidney ends and the liver begins. If you want to make a print of the kidney, it will be very difficult to discern the edge of the kidney without IV contrast.
Figure 6: Close-up view of the right kidney with (right) and without (left) intravenous contrast.
If you are trying to create a 3D printed model of a bone, it is best to create it from a scan without IV contrast. This is because the bone is the only thing that will be a white color in the scan. This allows your software to easily separate the bones from other tissues. The presence of intravenous contrast may trick the software into thinking that blood vessels or organ tissue is actually bone, and it may improperly include these structures in the 3D printable surface model. These unwanted structures can be manually removed, but this can be an incredibly time-consuming and laborious exercise. It is best to avoid this problem in the first place.
On the other hand, if you are trying to 3D print a blood vessel, tumor, or organ, then intravenous contrast is absolutely necessary. Vessels and tumors will light up, or enhance, with IV contrast, turning white on a CT scan. Which will make separation of these structures from background tissue more easy to perform.
2. Timing of intravenous contrast
If you are creating a 3D printed model of a blood vessel, tumor, or organ, merely having intravenous contrast in your scan is not sufficient. You also must have the proper contrast timing. Contrast injected into a vein before a medical scan is not static. It is a very dynamic entity, and flows through the blood vessels and tissues of the body at different times before being excreted by the kidneys.
Intravenous contrast is injected through an IV catheter, typically in the arm immediately before initiation of scanning. The contrast flows with the blood into the superior vena cava, the large vein in the chest, and then into the heart where it is then pumped into the pulmonary arteries. It is at this point, typically about 15 to 20 seconds, that is the best time to perform a scan to clearly visualize the pulmonary arteries. The contrast-filled blood then flows out of the lungs back to the heart where it is pumped into the aorta and its branches. This may be about 30 seconds after contrast injection, and is the best time to see the arteries. The contrast-filled blood then percolates into the capillaries of the tissues throughout the body. This is the point of maximal tissue enhancement, and is usually the best time to see tumors and organs. The blood then leaves the tissues and drains back into the veins, which is the best time to look at the veins. Finally, after about five minutes or so, the contrast begins to be excreted by the kidneys into the urine, and can be seen within the collecting system of the kidneys, the ureters, and the bladder.
Take a look at Figure 7. When the scan was performed in the arterial phase (left) you can clearly see the aorta, arteries of the intestine, and outer rim (cortex) of the kidneys have turned white with contrast-enhanced blood (green arrows). After about five minutes the scan was repeated (right), and on these delayed phase images only a small amount of contrast is left within the aorta and blood vessels. However, contrast can be seen concentrated within the central portions of the kidney (red arrow). This is urine mixed with contrast collecting in the renal pelvis and ureter.
Figure 7: Transverse (axial) images from a contrast-enhanced CT scan from a patient with intravenous contrast in the arterial (left) phase and delayed urographic (right) phase.
The point I'm trying to make here is that merely having intravenous contrast is not good enough. When the scan was taken relative to the contrast injection, in other words the timing of the contrast, is critically important to visualizing the target structure.
3. Oral contrast
In addition to intravenous contrast it is very common for oral contrast to be given prior to CT scans of the abdomen or pelvis. This is that nasty stuff that you are asked to drink about two hours before your scan. Oral contrast is designed to stay within the intestines so they can be clearly seen and evaluated. Take a look at Figure 8. In this CT scan of the abdomen intravenous contrast has clearly been given as the right kidney is white and enhancing (red arrows). Oral contrast has also been given, as several loops of small intestine can be seen filled with a substance that appears white on the CT scan (green arrows).
Unless you are trying to 3D print the intestines, for the most part oral contrast is something you do not want in your source imaging scans. If you are trying to separate out bones, organs, or blood vessels for printing, the presence of oral contrast will increase the likelihood that intestines will be accidentally included in your 3D printable model.
Figure 8: The effects of oral contrast on a CT scan of the abdomen.
4. Slice thickness
Take a look at these two CT scans of the chest (Figure 9). What is the difference between them? Both of them have IV contrast and both of them are showing the heart. Obviously, the scan on the right is of higher quality than that on the left, but why? The reason has to do with the thickness of the image slices. When CT scans are performed they are reconstructed into slices in the axial (transverse) plane. The axial plane is the plane that is parallel to the ground if you are standing upright. When the axial slices are stacked on top of each other the data can be used to create images in a different plane, such as when viewed from the front (the coronal plane), as in these example images. The axial slices that were used to create the coronal image on the left were 5 mm thick, whereas the axial slices used to create the image on the right were only 1 mm thick. You can see that the thick slices in the leftmost image generate structures with a very coarse appearance. If you try to 3D print an anatomic model from a scan with thick slices, your model will have a similar rough appearance. It is very important to use scans with thin slices, preferably less than 1.25 mm in thickness, when creating a model for 3D printing.
Figure 9: The effect of slice thickness on three-dimensional reconstructions.
5. Imaging artifact
Finally, take a look at these two CT scans of the face (Figure 10). What is the difference between them? The scan on the left clearly shows the teeth of the upper jaw as well as the bones of the upper cervical spine. The scan on the right however has white and black lines crisscrossing the mouth and obscuring the teeth. This type of artifact, called a beam hardening artifact, was created by metallic fillings in the teeth. When the CT scan was performed, the x-ray beam could not penetrate the metal fillings in the teeth to reach the detector. Subsequently, the scanner has no information about the x-ray appearance of the tissues along that x-ray path. When it generates an image from the x-ray data, the x-ray path with the missing information is shown as a white or a black line. The same phenomenon can be seen with any metallic object within the body, such as an artificial hip or spine fixation rods. If the scan on the right were converted to an STL file for 3D printing, the white lines would be 3D printed as well and the print would look as if sharp spikes were coming out of the mouth. Metallic objects also cause imaging artifact in MRIs. Metal on MRIs typically looks like a big black blob that obscures everything around it.
Figure 10: Two CT scans through the face and jaw. What is the difference between the two?
6. Reconstruction kernel
Take a closer look at the two CT scans of the face (Figure 10). In particular, look closely at the muscle and fat tissue of the neck. The scan on the left shows the muscle and fat tissue as being somewhat noisy. It has a granular type of appearance. On the rightmost scan however, the muscle and fat tissues appear rather smooth. This is because the two scans use a different type of reconstruction kernel. Think of the reconstruction kernel as equivalent to a sharpening or blurring function in Photoshop. The sharper kernel on the left shows the edges of the bones very clearly at the expense of causing a speckled appearance of the muscles and fat. The softer kernel on the right shows the muscle and fat more accurately, at the expense of causing the bones to have a more indistinct edge. Sharp kernels are used to make it easier to find hairline fractures and other difficult to detect abnormalities in the bones. However, for 3D printing smoother reconstruction kernels are generally best. Reconstruction kernel is primarily a factor only in CT scans.
Figure 11: Zoomed image from Figure 10 of the angle of the jaw. Note how the sharp kernel has much more clearly defined bone edges, but also has a speckled, noisy appearance to the soft tissues. Final thoughts
So there you have it. In this tutorial we have gone over the main types of imaging modalities used for 3D printing (CT, and MRI), as well as six very important factors to consider with any type of imaging scan you are thinking about using for 3D printing. There is a saying when it comes to medical 3D printing: "garbage in, garbage out." No matter what your skill level or amount of available free time, if you start the 3D printing process with a problem-laden medical scan, you will encounter nothing but frustration and probably end up with a bad 3D model assuming you can make the model at all. Do yourself a favor and carefully evaluate your medical scan prior to sinking the time and energy into creating a 3D model from it.
I hope you enjoyed this tutorial and found it helpful. If you liked this article please look see my next to tutorial on Creating a 3D Printable Medical Model in 30 Minutes Using Free Software: Osirix, Blender, and MeshMixer. Additionally, you may wish to check out the Tutorials section of the website.
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Below are a few 3D models to download. If you wish to follow the latest medical 3D printing news, you can follow Embodi3D on various social media platforms.
Thank you very much and happy 3D printing!
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A Collection of Free Downloadable STL Skulls for you to 3D print yourself.
3D printable human heart in stackable slices, shows amazing internal anatomy.
A Collection of Spine STL files to download and 3D print.