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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.
3D printing technologies have opened up the capabilities for customization in a wide variety of applications in the medical field. Using bio-compatible and drug-contact materials, medical devices can be produced that are perfectly suited for a particular individual. Another trend enabled by 3D printing is mass customization, in that multiple individualized items can be produced simultaneously, saving time and energy while improving manufacturing efficiency.
3D printers are used to manufacture a variety of medical devices, including those with complex geometry or features that match a patient’s unique anatomy.
Some devices are printed from a standard design to make multiple identical copies of the same device. Other devices, called patient-matched or patient-specific devices, are created from a specific patient’s imaging data.
Commercially available 3D printed medical devices include:
- Instrumentation (e.g., guides to assist with proper surgical placement of a device)
- Implants (e.g., cranial plates or hip joints)
- External prostheses (e.g., hands)
- Prescription Glasses
- Hearing Aids
In summary, the 3D Printing medical device market looks exciting and promising, Various Reports and surveys suggest the unexpected growth and demand for 3D Printing in medical device industry and it is expected to blossom more but a number of existing application areas for 3D printing in healthcare sector require specialized materials that meet rigid and stringent bio-compatibility standards, Future 3D printing applications for the medical device field will certainly emerge with the development of suitable additional materials for diagnostic and therapeutic use that meet CE and FDA guidelines.
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.
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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Note: This tutorial accompanies a workshop I presented at the 2016 Radiological Society of North America (RSNA) meeting. The workflow and techniques presented in this tutorial and the conference workshop are identical.
In this tutorial we will be using two different ways to create a 3-D printable medical model of a head and neck which will be derived from a real contrast-enhanced CT scan. The model will show detailed anatomy of the bones, as well as the veins and arteries. We will independently create this model using two separate methods. First, we will automatically generate the model using the free online service embodi3D.com. Next, we will create the same file using free desktop software programs 3D Slicer and Meshmixer.
If you haven't already, please download the associated file pack which contains the files you'll need to follow along with this tutorial. Following along with the actual files used here will make learning these techniques much easier. The file pack is free. You need to be logged into your embodi3D account to download, but registration is also free and only takes a minute. Also, you'll need an embodi3D.com account in order to use the online service. Registration is worth it, so if you haven't already go ahead and register now.
Online Service: embodi3D.com
Step 1: Go to the embodi3D.com website and click on the democratiz3D menu item in the naw bar. Click on the "Launch democratizD" link, as shown in Figure 1.
Figure 1: Opening the free online 3D model making service service democratiz3D.
Step 2: Now you have to upload your imaging file. Drag and drop the file MANIX Angio CT.nrrd from the File Pack, as shown in Figure 2. This contains the CT scan of the head and neck in NRRD file format. If you are using a file other NRRD that provided by the file pack, please be aware the file must contain a CT scan (NOT MRI!) and the file must be in NRRD format. If you don't know how to create an NRRD file, here is a simple tutorial that explains how.
Figure 2: Dragging and dropping the NRRD file to start uploading.
Step 3: Type in basic information on the file being uploaded, including File name, file description, and whether you want to share the file or keep it private. Bear in mind that this information pertains to the uploaded file, not the file that will be generated by the service.
Step 4: Type in basic parameters for file processing. Turn on the processing slider. Here you will enter in basic information about how you would like the file to be processed. Under Operation, select CT NRRD to Bone STL Detailed, as shown in Figure 3. This will convert a CT scan in NRRD format to a bone STL with high detail. You also have the option to create muscle and skin STL files. The standard operation, CT NRRD to Bone STL sacrifices some detail for a smoother output model. Leave the default threshold at 150.
Figure 3: Selecting an operation for file conversion.
Next, choose the quality of your output file. Low-quality files process quickly and are appropriate for structures with simple geometry. High quality files take longer to process and are appropriate for very complex geometry. The geometry of our model will be quite complex, so choose high quality. This may take a long time to process however, sometimes up to 40 minutes. If you don't wish to wait so long, you can choose medium quality, as shown in Figure 4, and have a pretty decent output file in about 12 minutes or so.
Figure 4: Choosing a quality setting.
Finally, specify whether you want your processed file to be shared with the community (encouraged) or private and accessible only to you. If you do decide to share you will need to fill out a few items, such as which CreativeCommons license to share under. If you're not sure, the defaults are appropriate for most people. If you do decide to share thanks very much! The 3D printing community thanks you!
Click on the submit button and your file will be submitted for processing! Now all you have to do is wait. The service will do all the work for you!
Step 5: Download your file. In 5 to 40 minutes you should receive an email indicating that your file is done and is ready for download. Follow the link in the email message or, if you are already on the embodi3D.com website, click on your profile to view your latest activity, including files belonging to you. Open the download page for your file and click on the "Download this file" button to download your newly created STL file!
Figure 5: Downloading your newly completed STL file.
Step 1: Create an STL file with 3D Slicer. Open 3D Slicer. Drag and drop the file MANIX Angio CT.nrrd from the file pack onto the 3D Slicer window. This should load the file into 3D Slicer, as shown in Figure 6. When Slicer asks you to confirm whether you want to add the file, click OK.
Figure 6: Opening the NRRD file in 3D Slicer using drag-and-drop.
Step 2: Convert the CT scan into an STL file. From within Slicer, open the Modules menu item and choose All Modules, Grayscale Model Maker, as shown in Figure 7.
Figure 7: Opening the Grayscale Model Maker module.
Next, enter the conversion parameters for Grayscale Model Maker in the parameters window on the left. Under Input Volume select MANIX Angio CT. Under Output Geometry choose "Create new model." Slicer will create a new model with the default name such as "Output Geometry. If you wish to rename this to something more descriptive, choose Rename current model under the same menu. For this tutorial I am calling the model "RSNA model."
For Threshold, set the value to 150. Under Decimate, set the value to 0.75. Double check your settings to make sure everything is correct. When everything is filled in correctly click the Apply button, as shown in Figure 8. Slicer will process for about a minute.
Figure 8: Filling in the Grayscale Model Maker parameters.
Step 3: Save the new model to STL file format. Now it is time to create an STL file from our digital model. Click on the Save button on the upper left-hand corner of the Slicer window. The Save Scene pop-up window is now shown. Find the row that corresponds to the model name you have given the model. In my case it is called "RSNA model." Make sure that the checkbox next to this row is checked, and all other rows are unchecked. Next, under the File Format column make sure to specify STL. Finally, specify the directory that the new STL file is to be saved into. Double check everything. When you are ready, click Saved. This is all shown in Figure 9. Now that you've created an STL file, we need to postprocessing in Meshmixer.
Figure 9: Saving your file to STL format.
Step 4: Open Meshmixer, and drag-and-drop the newly created STL file onto the Meshmixer window to open it. Once the model opens, you will notice that there are many red dots scattered throughout the model. These represent errors in the mesh and need to be corrected, as shown in Figure 10.
Figure 10: Errors in the mesh as shown in Meshmixer. Each red dot corresponds to an error.
Step 5: Remove disconnected elements from the mesh. There are many disconnected elements in this model that we do not want in our final model. An example of unwanted mesh are the flat plates on either side of the head from the pillow that was used to secure the head during the CT scan. Let's get rid of this unwanted mesh.
First use the select tool and place the cursor over the four head of the model and left click. The area under the cursor should turn orange, indicating that those polygons have been selected, as shown in Figure 11.
Figure 11: Selecting a small zone on the forehead.
Next, we are going to expand the selection to encompass all geometry that is attached to the area that we currently have selected. Go to the Modify menu item and select Expand to Connected. Alternatively, you can use the keyboard shortcut and select the E key. This operation is shown in Figure 12.
Figure 12: Expanding the selection to all connected parts.
You will notice that the right clavicle and right scapula have not been selected. This is because these parts are not directly connected to the rest of the skeleton, as shown in Figure 13. We wish to include these in our model, so using the select tool left click on each of these parts to highlight a small area. Then expand the selection to connected again by hitting the E key.
Figure 13: The right clavicle and right scapula are not included in the selection because they are not connected to the rest of the skeleton. Individually select these parts and expand the selection again to include them.
At this point you should have all the geometry we want included in the model selected in orange, as shown in Figure 14.
Figure 14: All the desired geometry is selected in orange
Next we are going to delete all the unwanted geometry that is currently unselected. To start this we will first invert the selection. Under the modify menu, select Invert. Alternatively, you can use the keyboard shortcut I, as shown in Figure 15.
Figure 15: Inverting the selection.
At this point only the undesired geometry should be highlighted in orange, as shown in Figure 16. This unwanted geometry cannot be deleted by going to the Edit menu and selecting Discard. Alternatively you can use the keyboard shortcut X.
Figure 16: Only the unwanted geometry is highlighted in orange. This is ready to delete.
Step 6: Correcting mesh errors using the Inspector tool. Meshmixer has a nice tool that will automatically fix many mesh errors. Click on the Analysis button and choose Inspector. Meshmixer will now identify all of the errors currently in the mesh. These are indicated by red, blue, and pink balls with lines pointing to the location of the error. As you can see from Figure 17, there are hundreds of errors still within our mesh. We can attempt to auto repair them by clicking on the Auto Repair All button. At the end of the operation most of the errors have been fixed, but if you remain. This can be seen in Figure 18.
Figure 17: Errors in the mesh. Most of these can be corrected using the Inspector tool.
Figure 18: Only a few errors remain after auto correction with the Inspector tool.
Step 7: Correcting the remaining errors using the Remesh tool. Click on the select button to turn on the select tool. Expand the selection to connected parts by choosing Modify, Expand to Connected. The entire model should now be highlighted and origin color. Next under the edit menu choose Remesh, or use the R keyboard shortcut, as shown in Figure 19. This operation will take some time, six or eight minutes depending on the speed of your computer. What remesh does is it recalculates the surface topography of the model and replaces each of the surface triangles with new triangles that are more regular and uniform in appearance. Since our model has a considerable amount of surface area and polygons, the remesh operation takes some time. Remesh also has the ability to eliminate some geometric problems that can prevent all errors from being automatically fixed in Inspector.
Figure 19: Using the Remesh tool.
Step 8: Fixing the remaining errors using the Inspector tool. Once the remesh operation is completed we will go back and repeat Step 6 and run the Inspector tool again. Click on Analysis and choose Inspector. Inspector will highlight the errors. Currently there are only two, as shown in Figure 20. These two remaining errors can be easily auto repair using the Auto Repair All button. Go ahead and click on this.
Figure 20: running the Inspector tool again.
At this point the model is now completed and ready for 3D printing as shown in Figure 21. The mesh is error-free and ready to go! Congratulations!
Figure 21: The final, error-free model ready for 3D printing.
Complex bone and vascular models, such as the head and neck model we created in this tutorial, can be created using either the free online service at embodi3D.com or using free desktop software. Each approach has its benefits. The online service is easier to use, faster, and produces high quality models with minimal user input. Additionally, multiple models can be processed simultaneously so it is possible to batch process multiple files at once. The desktop approach using 3D Slicer and Meshmixer requires more user input and thus more time, however the user has greater control over individual design decisions about the model. Both methods are viable for creating high quality 3D printable medical models.
Thank you very much for reading this tutorial. Please share your medical 3D printing designs on the embodi3D.com website. Happy 3D printing!
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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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My recent anatomy projects forced me to start importing my 3d models into 3d pdf documents. So I'll share with you some of my findings.
The positive things about 3d pdf's are:
1. You can import a big sized 3d model and compress it into a small 3d pdf. 40 Mb stl model is converted into 750 Kb pdf.
2. You can run the 3d pdf on every computer with the recent versions of Adobe Acrobat Reader. Which means literally EVERY computer.
3. You can rotate, pan, zoom in and zoom out 3d models in the 3d pdf. You can add some simple animations like spinning, sequence animations and explosion of multi component models.
4. You can add colors to the models and to create a 3d scene.
5. You can upload it on a website and it can be viewed in the browser (if Adobe Acrobat Reader is installed).
The negative things are:
1. Adobe Reader is a buggy 3d viewer. If you import a big model (bigger than 50 Mb) and your computer is business class (core I3 or I5, 4 Gb ram, integrated video card), you'll experience some nasty lag and the animation will look terrible. On the same computer regular 3d viewer will do the trick much better.
2. You can experience some difficulties with multi component models. During the rotation, some of the components will disappear, others will change their color. Also the model navigation toolbar is somewhat hard to control.
3. The transparent and wireframe polygon are not as good as in the regular 3d viewers.
If you want to demonstrate your models to a large audience, to sent it via email and to observe them on every computer, 3d pdf is your format. For a presentation it's better to use a regular 3d viewer, even the portable ones will do the trick. But if the performance is not the goal, 3d pdf's are a good alternative.
Here is a model of atlas and axis as 3d pfg: https://www.dropbox.com/s/2gm7occq5ur50um/vertebra.pdf?dl=0
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.
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About Blogs on Embodi3D
Select members of the Embodi3D community may be given the ability to create a blog and publish blog articles on the Embodi3D website. Blogging for new member is turned off by default as a spam reduction measure. Longtime members who have reliably contributed to the Embodi3D community through discussions in the forums, comments, or file sharing can ask to have blogging enabled on their accounts. Blog articles are featured on the Embodi3D.com homepage and are promoted using the Embodi3D social media accounts (Twitter, Facebook, Google+, LinkedIn, etc) and may provide significant exposure for the blogger.
1) Share your biomedical 3D printing work
2) Share you insights on current biomedical 3D printing topics and news
3) Help others with tutorials and shared 3D printable files
1) Post spam
2) Use the blog to promote outside commercial interests
3) Post hateful or disrespectful content, or use bad language.
To request blogging on your account, send a message to embodi3d via the Messenger in the top navigation bar.
Step 1: Start Creating your Blog
Once blogging is enabled on your account, you can create a blog. From the Blogs tab, click on the Manage Blogs button.
Step 2: From the Manage Blogs page, click "Create a Blog" Button
Step 3: Agree to the terms for having a blog
Basically this just says you won't use your blog for evil purposes.
Step 4: Configure the basics of your blog
Enter your blog name and description. Under Blog type, select "Local Blog." Embodi3D does not support external blogs.
Step 5: Set up the detailed parameters of your blog.
The default settings are fine more most people. Click "Save" when you are done
Step 6: Create your first blog post
There are two ways you can create a blog entry.
Method 1: From the Manage Blogs page clicking on Options and select Post New Entry, as shown below.
Method 2: From the Blogs section, click on the Add Entry button.
Once you have started writing a post you will need to know how to create links, add images and add Youtube videos.
Instructions for Creating Links
To get a link, first, using your cursor highlight the text within the article, then in the editor tool bar click the chain icon with a + on it. This will then prompt you for the web page link. In the URL field enter the web site address. For example, http://yahoo.com. then click OK.
Working with images
Each article needs an entry image. Entry Image is located above the editor tool bar where it says "Entry Image". Click Browse... and then find the image on your local computer.
For other images you will need to do a 2 step process.
1) First you will need to click on "Create New Gallery Album" which is located just under "Entry Image" . In this album put the images you want to include in the article.
2) Then when you get to a place in the article where you need an image click on "My Media" in the editor. Then select Gallery Images and select the previously uploaded images you put in this gallery.
Inserting Youtube Videos
The blogging editor only supports Youtube videos. To get a video to show and play within the blog post it requires just a link. When you find a video you like on Youtube click on Share instead of Embed. The Youtube link will look something like this: 'https://youtu.be/c3LgY0W5QSo
Copy the Youtube link and then paste it into your blog post here on emobodi3d.com. It usually works best if there is one line space above and one line space below the Youtube link. If the link is pasted with text surrounding it the link may not be recognized as a video.
That's it! Congratulations and welcome as an Embodi3D blogger!
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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.
Slicer Functions used:
- Load Data/Load DICOM
- Volume Rendering
- Crop Volume
- Grayscale Model Maker
Load a DICOM directory or .nrrd file.
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!
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."
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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.
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.
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.
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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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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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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.
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
Nice review paper on Medical Applications for 3D Printing: Current and Projected Uses:
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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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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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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.
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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