Dear Community Members,
After many months of work, we are happy to announce the addition of a feature that will allow you to sell medical models you have designed on Embodi3D.com. While we always have encouraged our members to consider allowing their medical STL files to be downloaded for free, we understand that when a ton of time is invested in creating a valuable and high-quality model, it is reasonable to ask for something in return. Now Embodi3D members have two options: 1) You can share your medical models for free, or 2) you can charge for them. We hope these two options encourage more sharing and file uploads. The more models available, the more it helps the medical 3D printing community.
For more details on how to sell your medical masterpieces on Embodi3D, go to the selling page.
Thanks, and happy 3D printing!
In this tutorial we will learn how to use the free medical imaging conversion service on embodi3D.com to create detailed anatomic muscle and skin 3D printable models in STL file format from medical CT scans. Muscle models show the detailed musculature by subtracting away the skin and fat. Even when created from a scan of an obese person, the model looks like it comes from a bodybuilder, Figure 1A. Skin models show an exact replica of the skin surface. The finest details are captured, including wrinkles and veins underneath the skin. Hair however is not captured in a CT scan and thus the model does not have any hair, Figure 1B.
Figure 1A (left): A muscle 3D printable model. Figure 1B (right): A skin 3D printable model
These models can be used for a variety of purposes such as medical and scientific education and research. Additionally, the skin models can be used to re-create a person's likeness in 3D from a medical scan. If you have had a CT scan of the head, you can create a lifelike replica of your head. You can create replicas of your friends, family, or even pets if they have had a medical CT scan. Alternatively, if you have a loved one who passed away but had a CT scan prior to death, you can use the scan to re-create an exact replica of their face. Even scans that are years old can be used for this purpose. Some people may consider this to be a little creepy, so if you are considering doing this think carefully first.
Before proceeding please register for an embodi3D.com account if you haven't already. You will need an account to use the service.
It is highly recommended that you download the associated file pack for this tutorial so that you can follow along with the exact same files that are used in this tutorial.
>> DOWNLOAD THE FREE FILE PACK BY CLICKING HERE <<
If you are interested in learning how to use the free embodi3D.com service, see my prior tutorials on creating bone models, processing multiple models simultaneously, and sharing and selling your models on the embodi3D.com website.
If you are interested in converting your own CT scan or that of a friend or family member, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figure 2 shows the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. If you have downloaded the file pack for this tutorial, example CT scans are included
Figure 2A, the Image Management (radiology) department at my hospital, where you can pick up a DVD of your CT scan as shown in Figure 2B (right). My hospital does this for free, but some may charge a trivial fee.
PART 1: Creating a Muscle STL model from NRRD File
Before we begin please bear in mind that this process only works for CT scan images. It will not work for MRI images. Before proceeding please check that the scan you wish to convert is a CT (CAT) scan!
Step 1: Convert Your CT scan to an Anonymized NRRD File with 3D Slicer
Open 3D Slicer. If you don't have the software program you can download it for free from slicer.org. Once Slicer has opened, take the folder from the download pack that is called STS_004. This folder contains anonymized DICOM images from a CT scan of the legs of a 24-year-old woman who had a muscle tumor. Drag and drop the entire folder onto the Slicer window, as shown in Figure 3. Slicer will ask you if you want to load the images into the DICOM database. Click OK. Slicer will also ask you if it should copy the images into the database, click Copy. Slicer will take about one minute to load the scanned.
Figure 3: Drag-and-drop the STS_004 DICOM folder from the file pack onto the Slicer window
Next, load the scan into the active wor king area in slicer. If the DICOM browser is not open, click on the Show DICOM browser button, as shown in Figure 4. Click on the STS_004 patient and series, and click the Load button, as shown in Figure 4. The leg CT scan will now load into the active seen within Slicer, as shown in Figure 5.
Figure 4: Open the DICOM browser and load the study into the active seen
Figure 5: The leg CT scan is shown in the active seen
Step 2: Trim the Scan so that only the Right Thigh is included.
Click on the Volume Rendering module from the Modules drop-down menu as shown in Figure 6. Turn on volume rendering by clicking on the eyeball button, as shown in Figure 7. Then, center the model in the 3D pane by clicking on the crosshairs button, Figure 7. If you don't have the same window layout as shown in Figure 7, you can correct this by clicking on the Four-Up window layout from the window layout drop-down menu, as shown in Figure 8.
Figure 6: Turn on the volume rendering module
Figure 7: Center the rendered volume.
Figure 8: Make sure you are in the Four-Up window layout
Next we are going to crop the volume so that we exclude everything other than the right knee and thigh. From the modules menu, select All Modules, Crop Volume, as shown in Figure 9. Turn on ROI visibility by clicking on the eyeball button, as shown in Figure 10. Then, move the region of interest box so that it only encapsulates the right thigh, as shown in Figure 10. You can adjust the size of the box by grabbing on the colored circular handles and moving the sides of the box as needed.
Figure 9: The Crop Volume module.
Figure 10: Turning on and adjusting the crop volume ROI (Region Of Interest)
Once the crop volume ROI is adjusted to the area that you want, perform the crop by clicking on the Crop button, Figure 11.
Figure 11: the Crop button.
The new, smaller volume that encompasses the right fight and knee has been assigned a cryptic name. The entire scan had a name of "2: CT IMAGES – RESEARCH," and the new thigh volume has a name "2: CT IMAGES-RESEARCH-subvolume-scale_1." That's a mouthful and I want to rename it to something more descriptive. I'm going to select the Volumes module, and then select the "2: CT IMAGES-RESEARCH-subvolume-scale_1" from the Active Volume drop-down menu. Then, from the same drop-down menu I'm going to select "Rename Current Volume". Type in whatever name you want. In this case I'm choosing "right thigh."
Figure 12: Renaming the newly cropped volume.
Step 3: Save the right thigh volume as an anonymized NRRD file.
Click on the Save button in the upper left-hand corner. The save window is then shown. All the checkboxes on the left except for the one that corresponds to the right by. Make sure the file format for this line says NRRD (.nrrd). Make sure you specify the proper directory you want the file to be saved as. When you are satisfied click on save. This is demonstrated in Figure 13. In the specified directory you should see a called right thigh.nrrd.
Figure 13: The save file options.
Step 4: Upload the NRRD file to embodi3D.com
Make sure you are logged into your embodi3D.com account. Click on Imag3D from the nav bar, Launch App. Then drag-and-drop your NRRD file onto the upload pain, as shown in Figure 14.
Figure 14: Uploading the NRRD file to embodi3D.com.
Figure 15: File processing options.
Step 5: Download your new STL file after processing is completed.
In about 5 to 15 minutes you should receive an email that says your file has finished processing and is ready to download. Follow the link in the email or access the new file via your profile on the embodi3D.com website. Your newly created STL file should have several rendered thumbnails associated with it on its download page. If you want to download the file click on the Download button, as shown in Figure 16.
Figure 16: the download page for your new muscle STL file
I opened the file in AutoDesk MeshMixer to have another look at it, and it looks terrific, as shown in Figure 17. This file is ready to 3D print!
Figure 17: The final 3D printable muscle model.
PART 2: Creating a Skin Model STL File Ready for 3D Printing
Creating a skin model is essentially identical to creating the muscle model, except instead of choosing the CT NRRD to Muscle STL on the embodi3D.com service, we choose CT NRRD to Skin STL.
Step 1: Load DICOM image set into Slicer
Launch Slicer. From the tutorial file pack drag and drop the MANIX folder onto the Slicer window to load this head and neck CT scan data set. This is shown in Figure 18.
Figure 18: Loading the head and neck CT scan into Slicer. It may take a minute or two to load. From the DICOM browser, click on the ANGIO CT series as shown in Figure 19.
Figure 19: Loading the ANGIO CT series from the MANIX data set
Step 2: Skip the trimming and crop volume operations
In this case we don't need to trim and crop a volume as we did with the muscle file above. We can skip Step 2.
Step 3: Save the CT scan in NRRD format.
Just as with the muscle file above, save the volume in NRRD format. Click on the save button, make sure that the checkbox for the nrrd file is selected and all other checkboxes are deselected. Specify the correct directory you want the file to be saved in, and click Save.
Step 4: Upload your NRRD file of the head to the embodi3D website.
Just as with the muscle file process as shown above, upload the head NRRD file to the embodi3D.com website. Enter in the required fields. In this case, however, under Operation choose the CT NRRD to Skin STL operation, as shown in Figure 20.
Figure 20: Selecting the CT NRRD to Skin STL file operation
Step 5: Download your new Skin STL file
After about 5 to 15 minutes, you should receive an email that says your file processing has been completed. Follow the link in the email or look for your file in the list the files you own in your profile. You should see that your skin STL file has been completed, with several rendered images, as shown in Figure 21. Go ahead and download your file. You can then check the quality of your file in Meshmixer as shown in Figure 22. In this instance everything looks great and the file is error free and ready for 3D printing.
Figure 21: The download page for your newly created 3D printable skin STL file.
Figure 22: Opening the file in Meshmixer for quality control checks. The file is error free and incredibly lifelike. It is ready for 3D printing.
Thank you very much! I hope you enjoyed this tutorial. If you use this service to create 3D printable models, please consider sharing your models with the embodi3D community. Here is a detailed tutorial that I wrote on exactly how to do this. This community is built on medical 3D makers helping each other. Please share the models that you create!
Please note the democratiz3D service was previously named "Imag3D"
In this tutorial you will learn how to quickly and easily make 3D printable bone models from medical CT scans using the free online service democratiz3D®. The method described here requires no prior knowledge of medical imaging or 3D printing software. Creation of your first model can be completed in as little as 10 minutes.
You can download the files used in this tutorial by clicking on this link. You must have a free Embodi3D member account to do so. If you don't have an account, registration is free and takes a minute. It is worth the time to register so you can follow along with the tutorial and use the democratiz3D service.
>> DOWNLOAD TUTORIAL FILES AND FOLLOW ALONG <<
Both video and written tutorials are included in this page.
Before we start you'll need to have a copy of a CT scan. If you are interested in 3D printing your own CT scan, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figures 1 and 2 show the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available.
Figure 1: The radiology department window at my hospital.
Figure 2: An example of what a DVD containing a CT scan looks like. This looks like a standard CD or DVD.
Step 1: Register for an Embodi3D account
If you haven't already done so, you'll need to register for an embodi3d account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download.
Step 2: Create an NRRD file with Slicer
If you haven't already done so, go to slicer.org and download Slicer for your operating system. Slicer is a free software program for medical imaging research. It also has the ability to save medical imaging scans in a variety of formats, which is what we will use it for in this tutorial.
Next, launch Slicer. Insert your CD or DVD containing the CT scan into your computer and open the CD with File Explorer or equivalent file browsing application for your operating system. You should find a folder that contains numerous DICOM files in it, as shown in Figure 3. Drag-and-drop the entire DICOM folder onto the Slicer welcome page, as shown in Figure 4. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory.
Figure 3: A typical DICOM data set contains numerous individual DICOM files.
Figure 4: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan.
Once Slicer has finished loading the study, click the save icon in the upper left-hand corner as shown in Figure 5. One of the files in the list will be of type NRRD. make sure that this file is checked and all other files are unchecked. click on the directory button for the NRRD file and select an appropriate directory to save the file. then click Save, as shown in Figure 6.
Figure 5: The Save button
Figure 6: The Save File box
The NRRD file is much better for uploading then DICOM. Instead of having multiple files in a DICOM data set, the NRRD file encapsulates the entire study in a single file. Also, identifiable patient information is removed from the NRRD file. The file is thus anonymized. This is important when sending information over the Internet because we do not want identifiable patient information transmitted.
Step 3: Upload the NRRD file to Embodi3D
Now go to www.embodi3d.com, click on the democratiz3D navigation menu and select Launch App, as shown in Figure 7. Drag and drop your NRRD file where indicated. While NRRD file is uploading, fill in the "File Name" and "About This File" fields, as shown in Figure 8.
Figure 7: Launching the democratiz3D application
Figure 8: Uploading the NRRD file and entering basic information
Figure 9: Basic information fields about your uploaded NRRD file
Next, turn on democratiz3D Processing by selecting the slider under democratiz3D Processing. Make sure the operation CT NRRD to Bone STL is selected. Leave the default threshold of 150 in place. Choose an appropriate quality. Low quality produces small files quickly but the output resolution is low. Medium quality is good for most applications and produces a relatively good file that is not too large. High quality takes the longest to process and produces large output files. Bear in mind that if you upload a low quality NRRD file don't expect the high quality setting to produce a stellar bone model. Medium quality is good enough for most applications.
If you wish, you have the option to specify whether you want your output file to be Private or Shared. If you're not sure, click Private. You can always change the visibility of the file later. If you're happy with your settings, click Save & Submit Files. This is shown in Figure 10.
Figure 10: Entering the democratiz3D Processing parameters.
Step 4: Review Your Completed Bone Model
After about 10 to 20 minutes you should receive an email informing you that your file is ready for download. The actual processing time may vary depending on the size and complexity of the file and the load on the processing servers. Click on the link within the email. If you are already on the embodied site, you can access your file by going to your profile. Click your account in the upper right-hand corner and select Profile, as shown in Figure 11.
Figure 11: Finding your profile.
Your processed file will have the same name as the uploaded NRRD file, except it will end in "– processed". Renders of your new 3D model will be automatically generated within about 6 to 10 minutes. From your new model page you can click "Download this file" to download. If you wish to share your file with the community, you can toggle the privacy setting by clicking Privacy in the lower right-hand corner. You can edit your file or move it from one category to another under the File Actions button on the lower left. These are shown in Figure 12.
Figure 12: Downloading, sharing, and editing your new 3D printable model.
If you wish to sell your new file, you can change your selling settings under File Actions, Edit Details. Set the file type to be Paid, and specify a price. Please note that your file must be shared in order for other people to see it. This is shown in Figure 13. If you are going to sell your file, be sure you select General Paid File License from the License Type field, or specify your own customized license. For more information about selling files, click here.
Figure 13: Making your new file available for sale on the Embodi3D marketplace.
That's it! Now you can create your own 3D printable bone models in minutes for free and share or sell them with the click of a button.If you want to download the STL file created in this tutorial, you can download it here. Happy 3D printing!
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
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.
Last year as part of my tests for creating bony anatomic models, I created a model of a lumbar vertebral body from a CT scan. The process was somewhat time-consuming as manual mesh editing was required to separate the vertebral body from its adjacent bony structures. I used Blender for this. Nonetheless, the end result looks good and accurately demonstrates the bony anatomy of a lumbar vertebra.
I've created a YouTube video which briefly summarizes the steps of creation.
Also, I've made the COLLADA file available for download for free to registered users, so you can 3D print it yourself. http://www.embodi3d.com/files/file/16-lumbar-vertebra/
If you wish to have the file printed and shipped to you, Shapeways can do it for a fee here: http://shpws.me/s5dU
Please share your thoughts and comments. Has anybody else had experience with creating bony models of this sort? Register and leave a comment or download the file.
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
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
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.
Medical researchers have taken 3D bioprinting into another level as they have replicated DNA structures that can be used as “inks” in 3D designs to aid in the research of different yet new areas in medical diagnostics and the creation of nanomaterials. What is exciting about this development is that DNA can be programmed by changing the sequence of its amino acids, plus it is a stable structure.
According to MIT associate professor and proponent of the study Mark Bathe, his team created computer-modeled DNA structures using DNA “scaffolds” in 2005. The structures were created first in 2D and then were later created into 3D structures when 3D medical printers became available.
At first, the researchers were able to develop only limited shapes with the program. However, after streamlining the research, they were able to generate 3D DNA structures that are as complex as biological DNA structures. Researchers were able to create rings, spheres, discs as well as other complex shapes like tetrahedron, octahedron and dodecahedrons from the synthetic DNA structures. Because of the ability to cut the synthetic DNA structures, researchers from MIT has seen the potential of these structures for diverse applications. Potential applications of the synthetic DNA include the study of bacterial toxins and drug therapy delivery.
Currently, the algorithm is still unable for public use. However, the MIT researchers have noted that they are still currently improving the technology so that it can be used to create more medical and scientific nanostructures for varied applications.