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A Ridiculously Easy Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes
By Dr. Mike
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 To complete basic information about your NRRD file. Do you want it to be private or do you want to share it with the community? Click on the Private File button if the former. If you are planning on sharing it, do you want it to be a free or a paid (licensed) file? Click the appropriate setting. Also select the License Type. If you are keeping the file private, these settings don't matter as the file will remain private. Make sure you accepted the Terms of Use, as shown in Figure 9. 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!- 3 comments
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Selling Your Medical Model Files on Embodi3D.com
By embodi3d
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!- 0 comments
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Easily Create 3D Printable Muscle and Skin STL Files from Medical CT Scans
By Dr. Mike
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. While the file is uploading, fill in the required fields, including the name of the uploaded file, a brief description, file privacy, and license type. Except the terms of use. next, turn on Imag3D processing. Under operation, select "CT NRRD to Muscle STL." Leave the threshold value unchanged. Under quality, select medium or high. Specify your privacy preference for your output STL file. If you are going to share this file, you can choose to share it for free or sell it. Please see my separate tutorial on how to share and sell your files on the embodi3D.com website for additional details. When you're happy with your choices, save the file, as shown in Figure 15: 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!
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Our community blogs
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This week we would like to share the most downloaded 3D models and resources from our site. These may be good resources for educational purposes as they demonstrate the detailed anatomy of the human body. We have a list of the top human heart STL files and another list of free human anatomy STL files.
The 1st place is for Dr. Mike’s tutorial on how to create 3D printable bone models. 3D printing is an evolving technology that enables the creation of unique organic and inorganic structures with high precision. In medicine, this technology has demonstrated potential uses for both patient treatment and education as well as in clinical practice. Learning how to create 3D models and taking this technology as a great advantage for medical education and practice is important for all of us as physicians and this tutorial makes it easy to learn.
The list also includes other great 3D models, like skull and heart. Let’s then take a look into this ten awesome models. Don’t forget to register in order to download the models, you can do it by clicking here.
1. 2.952 Downloads An improved tutorial that shows you how to create 3D printable bone models even more easily and for free on any operating system. Try it! https://www.embodi3d.com/files/file/115-file-pack-for-3d-printing-with-osirix-tutorial/
2. 913 Downloads 3D printable model of a human heart was generated from a contrast enhanced CT scan. https://www.embodi3d.com/files/file/64-3d-printable-human-heart-model-with-stackable-slices/
3. 893 Downloads 3D printable brain is from an MRI scan of a 24 year old human female.
https://www.embodi3d.com/files/file/30-human-brain-from-mri-scan/
4. 714 Downloads This full-size skull with web-like texture was created from a real CT scan.
https://www.embodi3d.com/files/file/26-3d-printable-lace-skull-full-size/
5. 648 Downloads 3D printable model of stroke.
6. 609 Downloads Skull with web-like texture was created from a real CT scan.
https://www.embodi3d.com/files/file/25-3d-printable-lace-skull-half-size/
7. 422 Downloads Anatomically accurate heart and pulmonary artery tree was extracted from a CT angiogram.
https://www.embodi3d.com/files/file/59-heart-and-pulmonary-artery-tree-from-ct-angiogram/
8. 396 Downloads Tutorial: "3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer”
https://www.embodi3d.com/files/file/89-tutorial-file-pack/
9. 392 Downloads Tutorial A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes
https://www.embodi3d.com/files/file/6441-imag3d-tutorial-support-files-dicom-and-nrrd/
10. 373 Downloads Bony anatomy and skin surface of the L and R feet.
https://www.embodi3d.com/files/file/52-feet-from-ct-scan/
References
1. Colaco, M., Igel, D. A., & Atala, A. (2018). The potential of 3D printing in urological research and patient care. Nature Reviews Urology.
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Intellectual property protection
The protection of the intellectual property of the 3D models can be a serious issue for every 3D modeler. It sucks when your model is posted for selling at a webside without your consent with a juicy price and you're gaining NOTHING from it. Some 3D artists are adding watermarks to their models, which can be easily removed by an amateur with a free surface modelling program (Meshmixer, Meshlab etc.). But there is an easy solution for this injustice - an invisible watermark. On Watermark3D you can add such watermark, incorporated into the mesh of your 3D model itself, which is hard for removing and can be checked on the same website during an intellectual property dispute. For the removing of the watermark you have to remesh the whole model, which will decrease the overall quality of the model substantially. I hope that I'll spare you the pain, which I experienced recently. Enjoy
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Latest Entry
Need of advancements for 3D printing from MRI data
Hello the Biomedical 3D Printing community, it's Devarsh Vyas here writing after a really long time!
This time i'd like to share my personal experience and challenges faced with respect to medical 3D Printing from the MRI data. This can be a knowledge sharing and a debatable topic and I am looking forward to hear and know what other experts here think of this as well with utmost respect.
In the Just recently concluded RSNA conference at Chicago had a wave of technology advancements like AI and 3D Printing in radiology. Apart from that the shift of radiologists using more and more MR studies for investigations and the advancements with the MRI technology have forced radiologists and radiology centers (Private or Hospitals) to rely heavily on MRI studies.
We are seeing medical 3D Printing becoming mainstream and gaining traction and excitement in the entire medical fraternity, for designers who use the dicom to 3D softwares, whether opensource or FDA approved software know that designing from CT is fairly automated because of the segmentation based on the CT hounsifield units however seldom we see the community discuss designing from MRI, Automation of segmentation from MRI data, Protocols for MRI scan for 3D Printing, Segmentation of soft tissues or organs from MRI data or working on an MRI scan for accurate 3D modeling.
Currently designing from MRI is feasible, but implementation is challenging and time consuming. We should also note reading a MRI scan is a lot different than reading a CT scan, MRI requires high level of anatomical knowledge and expertise to be able to read, differentiate and understand the ROI to be 3D Printed. MRI shows a lot more detailed data which maybe unwanted in the model that we design. Although few MRI studies like the contrast MRI of the brain, Heart and MRI angiograms can be automatically segmented but scans like MRI of the spine or MRI of the liver, Kidney or MRI of knee for example would involve a lot of efforts, expertise and manual work to be done in order to reconstruct and 3D Print it just like how the surgeon would want it.
Another challenge MRI 3D printing faces is the scan protocols, In CT the demand of high quality thin slices are met quite easily but in MRI if we go for protocols for T1 & T2 weighted isotropic data with equal matrix size and less than 1mm cuts, it would increase the scan time drastically which the patient has to bear in the gantry and the efficiency of the radiology department or center is affected.
There is a lot of excitement to create 3D printed anatomical models from the ultrasound data as well and a lot of research is already being carried out in that direction, What i strongly believe is the community also need advancements in terms of MRI segmentation for 3D printing. MRI, in particular, holds great potential for 3D printing, given its excellent tissue characterization and lack of ionizing radiation but model accuracy, manual efforts in segmentation, scan protocols and expertise in reading and understanding the data for engineers have come up as a challenge the biomedical 3D printing community needs to address.
These are all my personal views and experiences I've had with 3D Printing from MRI data. I'm open to and welcome any tips, discussions and knowledge sharing from all the other members, experts or enthusiasts who read this.
Thank you very much!
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Hello everybody it's Dr. Mike here again with another medical 3D printing tutorial. In this tutorial we are going to be going over freeware and open-source software options for medical 3D printing. This tutorial is based on a workshop I am giving at the 2017 Radiological Society of North America (RSNA) Annual Meeting in Chicago Illinois, November 2017. In this tutorial we will be going over desktop software that can be used to create 3D printable anatomic models from medical scans, as well as a free online automated conversion service. At the end of this tutorial you should be able to make high-quality 3D printable models from a medical imaging scan using free software or services.
Do I need to use FDA-approved software for Medical 3D Printing?
Before I dive into the tutorial I'd like to take a minute to talk to learners from the United States about the US Food and Drug Administration (FDA) and how this federal agency impacts medical 3D printing. Many healthcare professionals are confused and concerned about the ability to use non-FDA-approved software for medical 3D printing. Software vendors sell software that has been FDA-approved, but the software is usually quite expensive, to the tune of many thousands of dollars per year in license fees. There has been a lot of confusion about whether non-FDA-approved free software can be used for medical applications.
In August 2017 a meeting was held at the main FDA campus between FDA staff and representatives from RSNA. During this meeting the FDA clarified its stance on the issue (Figure 1). Basically the FDA indicated that if a doctor needs a 3D printed model for patient care, the doctor does NOT need to use FDA-approved software, as this is a medical decision and the FDA does not regulate the practice of medicine. FDA-approved software is not required even if the doctor is using the model for diagnostic use (Figure 2). If a company or other organization is marketing or designing software for diagnostic use, then that company or organization is required to seek FDA approval for that product. Basically if you are a physician or working on behalf of the physician and require a model, FDA-approved software is not required as long as you are not running a commercial service or company. Despite this leeway granted by the FDA's interpretation, I encourage anyone considering using freeware to create models for diagnostic use to use common sense and double check your findings before making any critical decision that could impact patient care. I also encourage you to look at the slides from the FDA presentation directly at the link below. Of course, none of this applies if you are not creating models for medical use.
https://www.fda.gov/downloads/MedicalDevices/NewsEvents/WorkshopsConferences/UCM575723.pdf
Figure 1: Title slide from the FDA presentation
Figure 2: The relevant slide from the FDA presentation. Doctors creating 3D printable models for clinical and diagnostic use do not need to use FDA-approved software as this is considered practice of medicine, which the FDA does not regulate.
Medical 3D Printing Overview
In this tutorial we're going to go over two different ways to use free and open-source software to convert a medical imaging scan to a 3D printable model. This can be done using free desktop software or a free online service. The desktop software requires more steps and more of a learning curve, but also allows more control for customized models. The online service is fast, easy, and automated. However, if you want to design customized elements into your model, you'll not be able to. The overall workflow of the session is shown in Figure 3.
Figure 3: Workflow overview
Part 1: Free online service – embodi3D.com
Step 1: Download the scan
Please download the scan for this tutorial from the embodi3D.com website at the link below. You have to have a free embodi3D.com account in order to download. If you don't have an account go ahead and register by clicking on the "Sign Up" button on the upper right-hand portion of the page. Registration is easy and only takes about one minute. You will have to confirm your email address before your account is active, so make sure you have access to your email.
Step 2: Inspect the scan
If you don't already have it, download and install the desktop software program 3D Slicer from slicer.org (http://www.slicer.org/). Slicer is a free medical image viewing and research software application. We are going to use Slicer to view our scan. Once Slicer is installed, open the application. Drag-and-drop the file "CTA Head.nrrd" onto the Slicer window. Slicer will ask if you want to add the file, click OK. The scan should now show in Figure 4. If your window doesn't look this then select the Four Up layout from the Layouts drop-down menu.
Figure 4: The 4 panel view and Slicer
You can navigate and manipulate the images with Slicer using the various mouse buttons. Your left mouse button to adjust the window/level settings as shown in Figure 5.
Figure 5: Use the left mouse button to adjust window/level.
The right mouse button allows you to zoom into a specific panel, as shown in Figure 6.
Figure 6: The right mouse button controls zoom.
The scroll wheel allows you to move through the various slices of the scan, as shown in Figure 7.
Figure 7: The mouse wheel controls scrolling
Step 3: Upload the scan to embodi3D.com
Now that we have an idea about what's in the scan, you can upload it to embodi3D.com for automatic processing into a 3D printable model. Go to https://www.embodi3d.com/. If you don't yet have a free embodi3D.com user account, you will need one now. Go ahead and register. The process only takes a minute. Under the democratiz3D menu, click Launch App, as shown in Figure 8.
Figure 8: Launching the democratiz3D medical scan to 3D printable model automated conversion service.
Drag and drop the file "CTA Head.nrrd" onto the upload panel, as shown in Figure 9. The NRRD file format is an anonymized file format so this transfer is HIPAA compliant. If you want to know more about how to create an NRRD file from a DICOM data set, please see my tutorial on the topic here.
Figure 9: Drag-and-drop the scan file "CTA Head.nrrd" onto the highlighted upload panel
A submission form will open up. The first part of the form will ask you questions about the source file you're uploading. The second part will ask about the new model being generated. Start with the first part of the form, as shown in Figure 10, and fill in information about your uploaded scan file, including a filename, short description, any tags you wish to use to help people identify your file, whether you wish to share the file with the community or keep it private, and whether you want to make the file free for download or for sale. Obviously if you keep the file private this last setting doesn't matter as nobody will be able to see the file except you.
Figure 10: The first part of the form relates to information about your uploaded scan file. Make sure you fill in at least the required elements.
In the second part of the form fill in information about your model file that will be generated, as shown in Figure 11. First of all, make sure democratized processing is turned on. The slider should be green in color, as shown in Figure 11. This is very important because if processing is turned off, you will not generate an output model file!
Specify what operation you would like to perform on the scan, and whether you would like to generate a bone, muscle, or skin model. Also, specify the desired quality of the output model (low, medium, high, etc.) and whether you want the output model to be shared with the community (recommended) or private. If your file is going to be shared, choose a Creative Commons license that people can use it under. When you're satisfied with your parameters, click the Submit button.
Figure 11: The second part of the form relates to information about your 3D printable model to be generated. Choose an operation, quality level, as well as privacy settings.
Step 4: Download your finished 3D printable model.
After anywhere between 5 to 20 minutes you should receive an email saying that your model processing is complete. The exact time depends on a variety of factors including the complexity of your model, the quality that you've chosen, as well as server load. Once you receive the email follow the link to the model download page. Alternatively you can find the model by clicking on your username at the upper right-hand corner of any embodi3D.com webpage and selecting My Files. Once you find your model page you can inspect the thumbnails to make sure the model meets your criteria, as shown in Figure 12. When you are ready click the download button, agree to the terms, and your model STL file will download to your computer.
Figure 12: Download your file after processing is complete.
That's it! Your 3D printable model is ready to send to a printer. The process takes about 2 to 3 minutes to enter the data, plus 5 to 15 minutes to wait for the processing to be done. The embodi3D.com service is batchable, so it is possible for you to upload multiple files simultaneously. The service will crank out models as fast as you can upload them.
Part 2: Free desktop software – 3D Slicer and Meshmixer
You can use the free software program 3D slicer and Meshmixer to generate 3D printable models. The benefit of using desktop software is that you have more control over the appearance of the model and which structures you want included and excluded. The downside of using desktop software is that software is complicated and somewhat time-consuming to learn. If you haven't already download 3D Slicer and Meshmixer from the links below. Be sure to choose the appropriate operating system for your computer.
http://www.slicer.org/
http://meshmixer.com/Step 1: Download the tutorial scan file and load into Slicer as described above in Part 1 Steps 1 and 2.
Step 2: Create a surface model from the scan data.
From within Slicer, open the Grayscale Model Maker module. In the Modules menu at the top now bar, select All Modules and choose the Grayscale Model Maker item, as shown in Figure 13.
Figure 13: Selecting the Grayscale Model Maker module.
You will now be taken to the Grayscale Model Maker module, which will convert the volumetric data in the CT scan to a surface model that can be used to create a STL file for 3D printing. In the parameters panel on the left side of the screen, make sure that the parameter set value is set to "Grayscale Model Maker", and the Input Volume is set to "CTA Head." Under Output Geometry, choose Create a New Model, since we wish to create a new output model. These parameters are shown in Figure 14.
Figure 14: Input parameters for the Grayscale Model Maker module
Set the Threshold value to 150 Hounsfield units. Also, set the Decimate value to 0.8 and make sure the Split Normals checkbox is unchecked. These are shown in Figure 15. When you're happy with your parameters, check Apply, and the grayscale model maker will work for a minute or so to create your surface model.
Figure 15: Additional input parameters for the Grayscale Model Maker module
Step 3: Save the surface model to an STL file.
Now that you have generated a surface model, you are ready to export it to an STL file. Click on the Save button on the upper left-hand corner of the 3D Slicer window. A Save dialog box will pop up, as shown in Figure 16. Find the row that contains the item "Output Geometry.vtk." Make sure that the checkbox next to this item is checked. All other rows should be unchecked. In the File Format column, make sure that the file shows as STL. Finally, make sure that the directory specified in the third column is the one you wish to save the file to. When everything is correct go ahead and click Save. Your surface model will now be exported and STL file saved in the directory specified.
Figure 16: The Save dialog box
Step 4: Repair the model in Meshmixer
The model is in STL format, but it has multiple errors in it which need to be corrected prior to 3D printing. We will do this in the freeware software program Meshmixer. Open Meshmixer, and drag-and-drop the just-created STL file "Output Geometry.stl" onto the Meshmixer window. The model will now open in Meshmixer. You will notice that the model is quite large, having about 300,000 polygons, as shown in Figure 17.
Figure 17: Open the model in Meshmixer
Navigating in Meshmixer is quite intuitive. The left mouse button uses tools and selects structures. The right mouse button is used to rotate the model. The scroll wheel is used to zoom in and out, as shown in Figure 18.
Figure 18: Navigating in Meshmixer
Run an initial repair on the model using the Inspector tool
We will be able to get rid of most (but not all) errors using the automated Inspector tool. Click on the Analysis button on the left navigation pane and choose the Inspector tool. Inspector will run and highlight all of the problems with the model, as shown in Figure 19. As you can see there are many hundreds of errors. Click on the Auto Repair All button to automatically attempt to fix these. At least one error will remain after the end of the process, but don't worry we will fix that later. Click on the Done button.
Figure 19: The Inspector tool shows errors in the mesh
Remesh the model
The Remesh operation recalculates all the polygons in the model, adjusting their size, and giving the model in more natural and less faceted look. Remesh and can also help to fix lingering mesh errors. First, select all the polygons in the model by hitting control-A. The entire model should turn orange, as shown in Figure 20.
Figure 20: Selecting all the polygons in the model.
Next, run the Remesh operation. Hit the R key, or choose Select-> Edit-> Remesh. The Remesh operation will now run, and will take approximately 1.5 to 2 minutes, depending on the power of your computer. This is shown in Figure 21.
Figure 21: The Remesh operation.
At the end of the Remesh operation, your model should have a much smoother and more natural appearance. You can adjust some of the Remesh parameters in the visualized pane, and the operation will recalculate. When you're happy with the result, click on the Accept button. This is shown in Figure 22.
Figure 22: The model after the Remesh operation.
Repeat the Inspector tool operation
Now that we have re-mashed the model, we can rerun the Inspector tool to clean up any residual errors. Click on Analysis and then the Inspector menu item. Click Auto Repair All, and inspector should repair any problems that still remain. When you're finished, click the Done button, as shown in Figure 23.
Figure 23: Running the Inspector tool a second time
Expose the cerebral vessels.
We are now going to take an extra step and make a cut through the crowd of the skull to expose the cerebral vessels. This can be easily achieved in about one minute. First, make sure to select all the vertices in the model by hitting control-A or using the menus Select-> Modify-> Select all, as shown in Figure 24. The entire model should turn orange to indicate that it is selected.
Figure 24: Selecting all the polygons in the model prior to performing a cut.
Next, start a plane cut by choosing Select-> Edit-> Plane cut. The plane cut will show on the screen. The portion of the model that is transparent will be cut off. The portion of the model that is opaque will be left behind. Move the plane by using the purple and green arrow handles. Rotate the plane by using the red arc handle, as shown in Figure 25.
Figure 25: Move and rotate the plane cut using the arrow and arc handles.
In this case we wish to move the plane cut to the four head, and rotated 180° so that the transparent portion of the cut is at the top of the head, and the opaque portion encompasses the face, jaw, and lower part of the skull. After you have finished positioning the plane, your model should look similar to Figure 26. When you're happy with position, click Accept.
Figure 26: The best position of the plane cut tool
The crown of the skull will now be cut off, exposing the cerebral vessels within the brain. This includes the anterior, posterior, and middle cerebral arteries as well as the venous structures such as the straight sinus and sigmoid sinuses, as shown in Figure 27. As you can see, this is a highly detailed model and excellent for educational purposes and teaching neurovascular anatomy.
Figure 27: The final model
Conclusion
In this tutorial we learn how to create a 3D printable skull and vascular model utilizing the free online service from embodi3D.com, as well as free desktop software 3D Slicer and Meshmixer. Both methods have their advantages and disadvantages. Embodi3D.com has a very fast and easy to use service. The desktop software is more difficult to use and learn, but gives more flexibility in terms of customization. Alternatively, you can use a combination of the two techniques, for example generating your model on the embodi3D.com website and then performing custom modifications, such as the plane cut we did in this tutorial, utilizing Meshmixer.
I hope you found this tutorial helpful and entertaining. Please give the tutorial a like. If you are engaged in medical 3D printing, please consider sharing your work on the embodi3D.com website. Thank you very much and happy 3D printing!
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Segmentation of a foot MRI scan
So I have seen some questions here on embodi3D asking how to work with MRI data. I believe the main issue to be with attempting to segment the data using a threshold method. The democratiz3D feature of the website simplifies the segmentation process but as far as I can tell relies on thresholding which can work somewhat well for CT scans but for MRI is almost certain to fail. Using 3DSlicer I show the advantage of using a region growing method (FastGrowCut) vs threshold.
The scan I am using is of a middle aged woman's foot available here
The scan was optimized for segmenting bone and was performed on a 1.5T scanner. While a patient doesn't really have control of scan settings if you are a physician or researcher who does; picking the right settings is critical. Some of these different settings can be found on one of Dr. Mike's blog entries.
For comparison purposes I first showed the kind of results achievable when segmenting an MRI using thresholds.
With the goal of separating the bones out the result is obviously pretty worthless. To get the bones out of that resultant clump would take a ridiculous amount of effort in blender or similar software:
If you read a previous blog entry of mine on using a region growing method I really don't like using thresholding for segmenting anatomy. So once again using a region growing method (FastGrowCut in this case) allows decent results even from an MRI scan.
Now this was a relatively quick and rough segmentation of just the hindfoot but already it is much closer to having bones that could be printed. A further step of label map smoothing can further improve the rough results.
The above shows just the calcaneous volume smoothed with its associated surface generated. Now I had done a more proper segmentation of this foot in the past where I spent more time to get the below result
If the volume above is smoothed (in my case I used some of my matlab code) I can get the below result.
Which looks much better. Segmenting a CT scan will still give better results for bone as the cortical bone doesn't show up well in MRI's (why the metatarsals and phalanges get a bit skinny), but CT scans are not always an option.
So if you have been trying to segment an MRI scan and only get a messy clump I would encourage you to try a method a bit more modern than thresholding. However, keep in mind there are limits to what can be done with bad data. If the image is really noisy, has large voxels, or is optimized for the wrong type of anatomy there may be no way to get the results you want.
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Very few infectious diseases in recent years have commanded the kind of attention and concern that Zika Virus has. Although Zika outbreaks have been reported in Africa, Southeast Asia and other parts of the world since the 1952, recent announcement by the Center for Disease Control and Prevention (CDC) confirming its link with microcephaly has forced everyone to sit up and take notice. The CDC estimates that the current pandemic is widespread with at least 50 countries reporting active Zika transmissions at this time. Most people with Zika virus infection will not have any symptoms though some may experience mild fever, conjunctivitis, muscle and joint pain, and headaches.
The virus is primarily transmitted by the Aedes mosquito. However, pregnant women may pass the infection to their babies, which may lead to microcephaly, a neurological condition associated with an abnormally small brain in the infant. The condition can lead to birth defects ranging from hearing loss to poor vision and impaired growth. Prompt diagnosis and treatment of Zika virus infections in pregnant women can, nonetheless, lower the risk of microcephaly to a great extent. Researchers have, therefore, put in a lot of time, money and effort to find a solution, and as always, three-dimensional (3D) medical printing and bioprinting technologies are leading the way.
Understanding the Disease
To begin with, 3D printing has played a crucial role in conclusively establishing the link between Zika virus and microcephaly. Researchers at John Hopkins Medicine used 3D bioprinting technology to develop realistic models of brain that revealed how the virus infects specialized stem cells in the outer layers of the organ, also known as the cortex. The bioprinted models allowed researchers to study the effects of Zika exposure on fetal brain during different stages of pregnancy. The models are also helping the scientists with drug testing, which is the obvious next stage of their research.
Zika Test Kit
Engineers at Penn’s School of Engineering and Applied Science, under the leadership of Professor Changchun Liu and Professor Haim Bau, have developed a simple genetic testing device that helps detect Zika virus in saliva samples. It consists of an embedded genetic assay chip that identifies the virus and turns the color of the paper in the 3D printed lid of the device to blue. This can prompt healthcare professionals to send the patient for further testing and to initiate treatment. Unlike other Zika testing techniques, this screening method does not require complex lab equipment. Each device costs about $2, making Zika screening accessible to pregnant women from the poorest parts of the world.
Treating Microcephaly
The scientists at the Autonomous University of the State of Morelos (UAEM) in Mexico are relying on the additive printing technology to create a microvalve that may help treat microcephaly in infants. The valve reduces the impact of the neurological disease and slows its progression by draining out excessive cerebrospinal fluid associated with this disorder. It can be inserted into the infant brain through a small incision to relieve fluid pressure and provide space for normal development. Researchers estimate the device will be available for patient use by 2017. These examples clearly demonstrate the impact of 3D printing on every aspect of the fight against Zika virus from diagnosing the disease to treating it. The results have been extremely promising, and both researchers and healthcare professionals are immensely hopeful that additive printing technology will help them overcome the infection quickly and effectively.
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Harvard University researchers have 3D printed the first organ-on-a-chip with integrated sensors. This new technology could revolutionize the biomedical research field, which has relied on expensive and time-consuming animal studies and cell cultures for decades.
Organs-on-chips, or microphysiological systems (MPS), are microchips that recapitulate the microarchitecture and functions of living human organs in vitro. The Wyss Institute at Harvard University explains MPS as follows: “Each individual organ-on-chip is composed of a clear flexible polymer about the size of a computer memory stick that contains hollow microfluidic channels lined by living human cells interfaced with a human endothelial cell-lined artificial vasculature, and mechanical forces can be applied to mimic the physical microenvironment of living organs.” Typically, MPS are made in clean rooms using a complex, multi-step lithographic process. Collecting data requires microscopy or high-speed cameras.
What makes this new MPS different, is the simplified manufacturing process and the integrated sensors. Both improvements were accomplished with multi-material 3D printing. The researchers designed six “inks” that enable integration of sensors. The researchers successfully 3D printed a heart-on-a-chip with integrated sensors. They then used the heart-on-a-chip in various studies, including drug responses. The integrated sensors enable continuous data collection, allowing scientists to study gradual changes over longer periods of time.
Read the research published in Nature Materials or watch this video to learn more:
Photo and video credit: Wyss Institute for Biologically Inspired Engineering at Harvard University
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According to the US Department of Health and Human Services, 22 patients die each day in need of an organ transplant because the demand for organs far outpaces the supply. If the compelling idea of producing 3D printed organs is realized many lives could be saved.
A big challenge in this field is to produce printable material that can support cells and is also permeable to nutrients. A hydrogel is a type of synthetic cross-linked polymer that is highly water absorbent. Hydrogels are commonly used as tissue engineering scaffolds for cells because of their biocompatibility.
This is a hot topic in the field right now, and many people around the world are working on developing new bioprinting methods. A challenge to the development of these methods is how well the printed object corresponds to the plan.
A group of Chinese scientists did a study of how various printing parameters affected printing fidelity. They published their results last week in Scientific Reports, the premier scientific journal Nature brand’s open source online journal.
The printing material or bioink must be liquid before printing and gel after printing. To make their hydrogels, they used sodium alginate (the same material this group used to print vasculature), gelatin, and a solution of calcium chloride as a cross linker.
In order to develop a bioprinting process, they feel it is important to understand the impact of changing the printing parameters including air pressure, temperature, feed rate, and printing distance. Another parameter included the ratio of gelatin and alginate.
Using a lab-built 3D printer, they started out with printing 1D lines on a flat surface, connected at different angles. They moved on to lattice shapes as shown in the image above, looking at how well the lattice maintained its shape with different line spacings. The hydrogel tends to spread somewhat upon printing. The printing surface was cooled so that the gel formed. The experiments also determined the impact of gravity.
They used extrusion based printing as opposed to other types of printing because cells are sensitive to thermal and mechanical stress. They found that the 3D printing process did not damage or kill mouse fibroblast cells suspended in the hydrogel as it only had a slight impact on cell survival.
Finally, the looked at a 3D object with successive printed layers as shown in the figure below.
a- Digital model b- Outline of the first layer c- First layer with outline filled in d- Views of 3D structure with about 30 printed layers
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Here is a tutorial for the Grayscale Model Maker in the free program Slicer, specifically for modeling pubic bones since they are used in anthropology for age and sex estimation. The Grayscale Model Maker is very quick and easy!
And I can't stand the "flashing" in the Editor.
For this example, I am using a scan from TCIA, specifically from the CT Lymph Node collection.
Slicer Functions used:
- Load Data/Load DICOM
- Volume Rendering
- Crop Volume
- Grayscale Model Maker
- Save
Load a DICOM directory or .nrrd file.
Hit Ok.
Make sure your volume loads into the red, yellow, and green views. Select Volume Rendering from the drop-down.
Select a bone preset, such as CT-AAA. Then click on the eye next to "Volume."
...Give it a minute...
Use the centering button in the top left of the 3D window to center the volume if needed. Since we only want the pubic bones, we will use the ROI box and Crop Volume tools to isolate that area.
To crop the volume check the "Enable" box next to "Crop" and click on the eye next to "Display ROI" to open it. A box appears in all 4 windows. The spheres can be grabbed and dragged in any view to adjust the size of the box. The 3D view is pretty handy for this so you can rotate the model around to get the area you want.
The model itself doesn't have to be perfectly symmetrical because you can always edit it later. Once you like the ROI, we can crop the volume.
To crop the volume, go to the drop-down in the top toolbar, select "All Modules" and navigate to "Crop Volume."
Once the Crop Volume workspace opens, just hit the big Crop button and wait. You won't see a change in the 3D window, but you will see your slice views adjust to the cropped area. At this point, you can Save your subvolume that you worked so hard to isolate in case your software crashes! Select the Save button from the top left of the toolbar and select the .nrrd with "subvolume" in the file name to save.
Now we will use the All Modules dropdown to open the Grayscale Model Maker. If you want to clear the 3D window of the volume rendering and ROI box, you can just go back to Volume Rendering, uncheck the Enable box and close the eyes for the Volume and ROI.
When using the Grayscale Model Maker, the only tricky thing here is to select your "subvolume" from the "Input Volume" list, otherwise your original uncropped volume will be used.
Click on the "Output Geometry" box and select "Create a new Model as..." and type in a name for your model.
Now move down to "Grayscale Model Maker Parameters" in the workspace.
I like to enter the same name for my Output Geometry into the "Model Name" field.
Enter a threshold value: 200 works well for bone, but for lower density bone, you might need to adjust it down. Since the Grayscale Model Maker is so fast, I usually start with 200 and make additional models at lower values to see which works best for the current volume.
***Here is where I adjust settings for pubic bones in order to retain the irregular surfaces of the symphyseal faces.***The default values for the Smoothing and Decimate parameters work well for other bones, but for the pubic symphyses, they tend to smooth out all the relevant features, so I slide them both all the way down.
Then hit Apply and wait for the model to appear in the 3D window (it will be gray).
You can see from the image above that my model is gray, but still has the beige from the Volume Render on it since I didn't close the Volume Rendering.
If for some reason you don't see your model: 1) check your Input Volume to make sure your subvolume is selected, 2) click on that tiny centering button at the top left of your 3D window, or 3) go to the main dropdown and go to "Models." If the model actually generated, it will be there with the name you specified, but sometimes the eye will be closed so just open it to look at your model.
Now we an save your subvolume and model using the Save button in the top left of the main toolbar. You can uncheck all the other options and just save the subvolume .nrrd and adjust the file type of your model to .stl. Click on "Change Directory" to specify where you want to save your files and Save!
This model still needs some editing to be printable, so stay tuned for Pt. 2 where I will discuss functions in Meshlab and Meshmixer.
Thanks for reading and please comment if you have any issues with these steps!
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A neurosurgeon from Saskatoon in Canada has 3D printed a replica of a patient’s brain to help him plan a complex medical procedure.
Working with a team of engineers, Dr. Ivar Mendez created an accurate replica of the patient’s brain, which will allow him to practice surgery.
Dr. Mendez is the head of surgery at the University of Saskatchewan, and is already familiar with using advanced technologies to improve surgical results. He uses computers in the operating room, and has a medical engineer as part of his surgical team.
However, putting together a 3D brain was a more complicated task, but it would make it possible for him to practice working on some of the smallest components of a brain.
"You can imagine it as having a pea inside a sock or balloon," Mendez told CBC. "It is a complex system.”
What makes the model so valuable is that it’s an exact replica of the patient’s actual brain. If they have a tumor or other abnormality, Mendez and his team can create a replica that includes these unique features.
The patient in question was planned to undergo deep brain stimulation. Dr. Mendez needed to insert electrodes into the brain to help soothe overcharged neurons. He usually plans this kind of surgery using a computer model, but wasn’t successful in this case.His idea was to position one electrode to affect two target neurons, but the computer model wasn’t capable of this kind of surgical planning. Human brains are particularly complex, which makes it difficult for computers to predict how the tissue will react to certain tools.
“I wanted a way to really, before I did a surgery, to know exactly how this was going to reach the brain and the targets I wanted,” Mendez told The Star Phoenix.
That’s why Mendez decided to team up with the school of engineering at U Saskatchewan, as well as radiology technicians and a neuropsychology specialist. The team worked together to make the MRI data understandable to the 3D printer.
The 3D model took 7 months of planning before a prototype was created. It was printed using a transparent material similar to rubber, that allows surgeons to see all the internal structures of the brain as well. Mendez said it also feels fairly similar to an actual human brain."I'm a neurosurgeon but I'm also interested in art. To me, this was an object of beauty,” he said.
Dr. Mendez believes the development of the technology will bring new opportunities for surgical practice.
"I envision that in the future we may be able to do procedures that are very difficult or impossible today," he said. "I feel that in the next 20, maybe 25 years, we will be able to print biological materials. We may be able to print organs."
Image Credits:
CBC
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Bioprinting cancer to aid medical research
Much of the press for medical 3D bioprinting has revolved around recreating parts of the human body for medical transplants, implants, and reconstructive surgery. We often find these stories easy to relate to, with visuals that help us understand the benefits of each bioprinting solution.
However, another important aspect of bioprinting that may not be as obvious is its potential contribution to early-stage disease research. This type of research occurs in the laboratory, and focuses on how our cells (the tiny building blocks that make up every part of our body) function and interact during diseases. 3D bioprinting could present a step forward in how researchers construct experiments that help them understand disease.
Researching Cancer
One of the crucial steps to understanding each type of cancer is figuring out how it communicates with other cells, and what it is saying. Cells in a tumor may talk to cells from within the same tumor, or surrounding healthy cells, and all of this communication could be important for cancerous cells to grow and spread. Thus understanding how cells interact is an important step towards blocking this communication using medical treatments.
To easily set up experiments in the lab, researchers use cancer cell lines - cells which have been taken from tumors and trained to grow in the lab. These cell lines are grown in a single layer, and although this makes it easier to keep them happy, it is quite different to the way cells are arranged in our bodies, i.e. in multiple layers in a 3D space.
3D Bioprinting Cancer
With so many important functions of cancer due to the communication with other cells, it is beneficial for scientists to perform experiments on cancers that are as similar as possible to a living patient. Last year, researchers at the University of Connecticut and Harvard Medical School addressed this, published a review of 3D bioprinting focusing on its potential advantages for cancer research in the lab.
Cancers are a prime candidate for 3D bioprinting - many cancers exist as clumps of cells that lack specific structures, and thus do not require the typical scaffolding that bioprinting organs like ears or bones requires. By layering cells in 3D instead of 2D, a 3D printed tumor is better at replicating the structure of a tumor in a typical human body, and communication between cells in all directions can be achieved.
3D bioprinting also offers the possibility of mixing multiple cell types. This is important because cancer cells communicate not only with each other, but also healthy cells - for example, melanomas interact with surrounding skin cells. In fact, even within a tumor there may me multiple "versions" of cancer cells, all having different things to say each other. Since bioprinting multiple cell types is relatively simple, it is possible to recreate not only tumors themselves more effectively, but also their surroundings.
Current research already feeds into this, as there are already many different types of cancer cells available, and established techniques for getting them into a liquid form for 3D printing.
Customizable, reproducible experiments
It is incredibly important that the results of any research be reproducible, not only within a research group but also between research groups across the globe. Since bioprinting is done using 3D computer models, these can be easily distributed to other researchers. And with the ability to customize the construction of a tumor completely using bioprinting, scientists can validate their results and move faster to obtaining medical solutions.
One of the greatest challenges could be integrating 3D printing medical laboratory techniques that have been established for decades (the first cancer cell line was created in the 1950's). Luckily, companies like Biobots are capitalizing on this gap in the market, building accessible 3D bioprinters with standardized components. And repositories like Build With Life will hopefully hold not only bioprinting designs, but also important protocols that merge current medical research standards with 3D printing technology.
Medical applications
The utilization of bioprinted cancers could be important to the development of new medical treatments. By understanding the interactions between cancer cells and healthy cells in all dimensions, researchers can gain insights into the successful treatment of these cells. And all of the techniques mentioned above could be extended to a range of other diseases. Organovo has already capitalized on this idea, 3D printing liver cells for scientific testing.
One could even predict that, in the same way as 3D-printed organs of specific patients are being used to plan for surgery, 3D printed recreations of patient's tumors or diseases may be able to help tailor the most effective treatment for that patient. The future for integrating bioprinting into the workflows of laboratories around the world seems bright, and could offer faster and more accurate methods for carrying out early-stage research in cancer and many other diseases.
Image acknowledgements:
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The utility of modern three-dimensional printing techniques for bio-medical and clinical use has been demonstrated repeatedly in recent years, with applications ranging from surgical modelling to tissue engineering and beyond.
Despite the promise and potential of three-dimensional printing methods, impediments to their widespread clinical uptake still remain. Many of the printers used for medical applications are highly specialised pieces of equipment that require trained operators and controlled operational conditions as well as potentially costly and unique raw materials. These factors can result in high production costs, and the necessity of dedicated sites which can in turn lead to delays between fabrication and clinical application.
Recent work by engineers and researchers at Zhejiang University in China has shown that desktop 3D-printing techniques may represent a more practical alternative for certain clinical tasks.
Desktop 3D printers may cost as little as $500, much less than the $15,000–30,000 machines routinely used in academic institutions. As well as the lower costs, Desktop 3D printers are considered to be much easier to operate. An Liu and co-workers tested the potential of these machines to fabricate bio-absorbable interference screws, used to secure hamstring tendon grafts commonly utilised to repair damaged anterior cruciate ligaments (ACL).
A screw-like scaffold, made from the same polylactic acid filament commonly used for conventional bio-absorbable screws, was printed using fused deposition modelling techniques then coated with hydroxyapatite (HA) to improve its osteoconductivity. The construct was also coated with mesenchymal stem cells, as these cells are widely considered to be of therapeutic value for anterior cruciate ligament regeneration.
A 3D porous structure is considered to be valuable to bone ingrowth into the screw, as this supports the cellular migration and mineral deposition, as well as vascular development, all required as the screw is incorporated into a patient’s bone. Conventional methods have struggled to control to formation of these structures, but by using 3D-printing techniques they can be easily manipulated by surgeons and specialists alike.
Once fabricated the 3D-printed screws were tested upon anterior cruciate ligament repairs in rabbits for up to three months. Magnetic resonance imaging showed that all of the 3D-printed screws were correctly positioned in the bone tunnel without any breakage or major complications, and that over the course of twelve weeks they appeared to incorporate into the bone tissue.
The approximate cost of a 3D printed bio-absorbable screw was 50 cents using industrial grade polylactic acid, and it is estimated that this equates to less than 10 USD using medical grade materials
The successful manufacture of a functional surgical device using desktop 3D printing technology demonstrates the potential for in situ fabrication at the clinic and opens up a range of in-house manufacturing possibilities to clinical staff, circumventing the requirement for costly equipment and bespoke materials as well as trained specialist operators.
3D Printing Surgical Implants at the clinic: A Experimental Study on Anterior Cruciate Ligament Reconstruction. Sci Rep. 2016 Feb 15;6:21704. doi: 10.1038/srep21704
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3D Printing Is Now Mainstream In Surgery
Many doctors these days are now including 3D printing as part of their many surgical procedures. Dr. Jamie Levine from NYU Langone noted that there is a paradigm shift when it comes to doing surgical procedure in terms of using and relying on 3D printing.
A lot of hospitals all over the United States have already embraced 3D printing to create tools, models or craft tissues used for surgery. One of the hospitals that are leading the paradigm shift is the Institute for Reconstructive Plastic Surgery at NYU Langone. The surgeons from NYU Langone use special printers to create tools and 3D models that can save doctors from performing long and expensive surgeries. In fact, the hospital is able to save $20,000 to $30,000 for every reconstruction that the do.
The use of 3D printing in medical technology is very promising. In fact, the Food and Drug Administration has already approved the creation of 3D printed pills and vertebrae. There are also many researchers all over the world working with 3D printed organs to be used in organ transplantation.
Although medical-grade 3D printers still remain expensive, they can make infinite types of objects like surgical tools, anatomical models and other devices. Fortunately, there are now many companies that are developing cost-effective printers thus the cost is targeted to go down in the future.
There is a wide potential for innovation when it comes to using the 3D printing technology. With this technology, it is no wonder if many hospitals all over the world will rely on 3D printing technology to treat different diseases.
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3D Printing of Renal Mass from MRI Images
Every 3D printing case is different, and must be tailored for the individual patient’s specific clinical condition, anatomy, and imaging techniques.
A 47 year old woman with a renal mass was being evaluated for surgical treatment planning. A urologist familiar with my current 3D printing work requested a 3D printed model of the kidney. The purpose was to help demonstrate the anatomy of the mass with respect to the renal hilum, to help determine if a partial nephrectomy was possible, or if a total nephrectomy was required.
The patient had a documented reaction to radiographic iodinated contrast, and therefore an MRI was performed instead of a CT scan. The scan was performed on a 1.5 T GE Signa Excite system. The data set from a coronal 3D gradient echo pulse sequence acquisition was chosen because it best visualized the tumor encroachment into the renal sinus.
The 3D model was created from segmentation of the kidney from the 3D gradient echo acquisition. The renal parenchyma was then made into the digital 3D model, leaving the mass as negative space. This was then printed to demonstrate the entire kidney. An additional 3D model was created showing a bisected view of the kidney along the coronal plane. This was done to see which model would be of more utility.The patient’s DICOM image files from the MRI were processed using the Materialise Innovation Suite’s Mimics and 3-matic software.
Initially I used the Mimics software segmentation tool to segment the normal renal parenchymal tissue. This left a filling defect where the mass was. This negative space was useful for demonstrating the extent of the tumor.
Using the 3-matic application I then took the 3D digital representation and created a model cut in the coronal plane. This helped better define the extent of the tumor invasion into the renal hilum.
Both the full kidney and the coronal bisected models were printed for the surgeon and the patient to review. The STL (stereolithography or standard tesselation language) files generated for the 3D models were then imported into both the Cura and MakerBot slicing software applications to generate the gcode for the Ultimaker 2 and .x3g file for the MakerBot printers.Fused filament printing of the full kidney using Acrylonitrile Butadiene Styrene (ABS) on the MakerBot Replicator 2X Experimental Printer and sectioned kidney in Polylactic Acid (PLA) on the Ultimaker 2 printer.
In general I prefer PLA to ABS. With PLA there is less shrinkage and warping of the material during the printing process. PLA is of plant based origin (here in the US it is derived from corn starch) and can print lower layer height and sharper printed corners. PLA, a biodegradable plastic is used in medical devices and surgical implants, as it possesses the ability to degrade into inoffensive lactic acid in the body.
ABS is a petroleum-based recyclable non-biodegradable plastic. Unfortunately emits a potentially hazardous vapor during printing. The Replicator 2X however is optimized for ABS. http://pubs.acs.org/doi/pdf/10.1021/acs.est.5b04983
For more information about PLA/ABS see http://3dprintingforbeginners.com/filamentprimer/#sthash.p07fHBmh.dpuf
The urologist showed the models to the patient, and it help to convince her of the necessity of a total nephrectomy, rather than a partial nephrectomy.
Although the printed models showed the extent of the tumor invasion adequately for both the urologist and the patient to visualize, the models did not differentiate the mass from the renal sinus.
To better demonstrate the tumor invasion, a new model with two different color filaments was created. Hand segmentation of the 3D model of the mass was performed due to the limited tissue contrast between the mass and the surrounding soft tissue structures. Creation of two separate segmentation files and 3D models was made in Mimics.
This was then exported into 3-matic for local smoothing. Two separate STL files of both the mass and kidney were generated. The combined model was then bisected in the coronal plane and the additional two STL files were again generated.
Once the combined STL files were imported into the MakerBot software, they were repositioned on the build plate in an orientation to optimize the printing process. The STL models were positioned on the bed, above a ring spacer file. This is necessary for the proper printing contact. The model was oriented to minimize the amount of printing support structures.
When using the two filament colors, “purge walls” are generated by the software to help eliminate the small threads of filament from one color being deposited when the next color is laid down.
The two filament model enables the surgeon and the patient to better visualize the extent of the tumor invasion, clearly demonstrating normal from abnormal tissues.
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Getting from DICOM to 3D printable STL file in 3D Slicer is totally doable...but it is important to learn some fundamental skills in Slicer first if you are not familiar with the program.
This tutorial introduces the user to some basic concepts in 3D Slicer and demonstrates how to crop DICOM data in anticipation of segmentation and 3D model creation.
(Segmentation and STL file creation are explored in a companion tutorial )This tutorial is downloadable as a PDF file,
or can be looked through in image/slide format here in the blog
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Nice review paper on Medical Applications for 3D Printing: Current and Projected Uses:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189697
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Video: Dicom to STL
This a video demonstrating the use of Mimics software to convert patient dicom images into 3D printable files. Mimics software has many great features to improve and ease workflow. Like other software programs most segmentation and exporting can be accomplished in 15 minutes.
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3D Printing goes to Capitol Hill
The Coalition for Imaging and Bioengineering Research (CIBR) is a dedicated partnership of academic radiology departments, patient advocacy groups, and industry with the mission of enhancing patient care through advances in Biomedical Imaging. My good friend and colleague Dr. Beth Ripley and I recently participated in the sixth annual Medical Technology Showcase at Capitol Hill organized by CIBR, representing the Department of Radiology at the Brigham and Women’s Hospital (BWH) where we emphasized the importance of 3D printing in healthcare.
The annual Medical Technology showcase aims to bring examples of medical breakthroughs in imaging and bioengineering to members of congress and demonstrate how these advances are impacting patient care. In addition to educating policy makers and the public about innovative imaging technology, the event demonstrates the value of NIH funded academic research and the importance of collaborations between academia, industry and patient advocacy groups.
Our display booth comprised of the Department of Radiology at BWH, the Lung Cancer Alliance, and Fujifilm was a hit among attendees and we were pleased to see the level of interest in medical 3D printing. We displayed 3D printed models that have been used for different clinical applications and our booth partners from Fujifilm demonstrated Synapse 3D, a software that allows conversion of 2D image data from CT/MRI into 3D printable files.
Our goal was to demonstrate the importance of 3D printing in pre-surgical planning and how it can benefit patients by allowing surgeons to devise a patient specific treatment strategy and minimize post-surgical complications. Sheila Ross, a lung cancer survivor and patient advocate from the Lung Cancer Alliance emphasized how 3D printed models can give patients and their families a better understanding of the planned procedure.
A lung model from Fujifilm demonstrating a nodule (green) and surrounding bronchioles
The Lung & Brain cookies might have been slightly more popular than our 3D models
It is our hope that more funding and resources will be allocated to investigate innovative medical technologies such as 3D printing, which can then be translated to impact patient care. In order to transform 3D printing from being a fad, to a mainstream tool that fosters precision medicine, evidence based benefits of its different applications will need to be demonstrated in clinical trials which will require funding.
Tatiana Kelil, MD
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News and Thoughts about Medical 3D Printing
3D printing has been integrated into the surgical procedures of many physicians, as it has proved very useful in the planning stages of a surgery. It allows doctors to operate with more accuracy and precision by providing a means for surgeons to become acquainted with three-dimensional models of their subjects beforehand.
These models provide a holistic view of the part of the body under examination, which affords the surgeon time to assess the model and make changes in their surgical procedures or recommendations as required. Furthermore, viewing a 3D representation is far superior to that of a CT scan or MRI, as those technologies use flat images that are often difficult to read. A 3D model provides a more realistic view of the subject that is easier to understand. This ultimately gives the surgeon a greater understanding of the anatomy and allows practice before attempting surgery.
Dr. John Meara, plastic surgeon-in-chief at Boston Children's Hospital explained to the Boston Globe that, “In the past, sometimes you had to make many incisions in the operating room. Now I’m making those decisions on a model ahead of time.” By doing this, the doctor is able to reduce operating time and improve recovery time as the patient’s body experiences less trauma during surgery.
Before surgery, the 3D model can also help communication with patients, as the doctor can use the model to explain exactly how the procedure will take place. This increases the patient's trust and further improves the medical care and attention received by the patient.
Affordability Contributes To Increasing Medical Use Of 3D Printing
Surprisingly, 3D printing systems are not as expensive as one would think, and in fact are quite affordable, starting as low as a few thousand dollars for a basic 3D printer. Naturally, more sophisticated models fetch a higher price, but overall the cost of this technology is not insurmountable. This presents the opportunity for 3D printing systems to be used on a wider scale, and ultimately become as common a tool in the medical field as a stethoscope.
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It seems that there is no end to the animals that will benefit from 3D printing and now the process has become so common place it is child’s play. Stumpy came to the Oatland Island Wildlife Center in Savannah, Georgia with a bad infection to his right front leg. In order to save the 12 year old box turtle veterinarian Lesley Mailer amputated the leg. Stumpy lived, but had a very hard time getting around without his front leg. Luckily for Stumpy, Lesley Mailer remembered her daughter mentioning a 3D printer that her 5th grade class at May Howard Elementary was working with. So Mailer contacted the school about creating a new leg for Stumpy.
www.gizmag.com
The school took up the call and choose a few students who were interested in 3D printing and/or animals to work on the project. Six students and a teacher went to work right away to learn about box turtles to understand what Stumpy needed in a new leg. The students were eager to learn and help Stumpy, they spent time after school and during their lunches to design the new leg. Using 3DTin to create 15 prototypes over a month of development the students created a leg that they thought would work for Stumpy. Mailer was just as excited as the students and invited all of them to watch as Stumpy was fitted with his new leg. With just a few minor alterations, Stumpy’s new leg fit perfectly. Now this little box turtle can live out the next 20 to 30 years moving around just as easily as any other turtle. But that doesn’t mean these dedicated students are taking a break, they intend to improve upon their design this year.
Main Image Credit: www.3dprint.com
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Hello everybody it's Dr. Mike here again with another medical 3D printing tutorial. In this tutorial we are going to be going over freeware and open-source software options for medical 3D printing. This tutorial is based on a workshop I am giving at the 
Very few infectious diseases in recent years have commanded the kind of attention and concern that Zika Virus has. Although Zika outbreaks have been reported in Africa, Southeast Asia and other parts of the world since the 
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