3D Printing Hearts from MRI/CT images


Why is printing a 3D Heart from a patient’s MRI or CT scans useful?

There have been several cases in which a surgery was designed based on a 3D printed model. In some cases, the surgery was thought to be inoperable, until the 3D model helped surgeons to plan an alternative access point. http://www.cnn.com/2015/10/06/health/3d-printed-heart-simulated-organs/

3D Printing can allow surgeons to design patient-specific surgeries which could lead to smaller incision sites, better access, reduced surgery time and if a graft or device is being inserted, it could lead to a better fitting model/device. Patient-specific surgeries are very useful in the congenital heart disease community. Patients with congenital heart disease have unique anatomies and complex physiological systems. Surgical planning is often critical to a successful surgery in this patient population. Surgeons can even practice surgeries on the 3D printed models. 3d heart practice


Models can also be used for patient, provider, and medical student education. It is much easier to understand the physiology of an organ when you can hold it in your hand, versus scanning through images on a computer. http://www.jumpsimulation.org/innovation/3d-heart-library.html

A hub for 3D printing from medical images is the NIH 3D print exchange: http://3dprint.nih.gov/

The NIH has created a library of different medical models. These models will be able to make large morphological comparisons possible.

For my semester project, I was able to successfully print a heart from MRI images using Osirix and Meshmixer. Here is a picture of the final project.

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In the future, I hope to write a full tutorial of how to print the internal structures of the heart and how to optimize the printing supports in an extruder print setting.




Mending a Broken Heart

My first attempt at printing the heart is pictured below.










Unfortunately, my print was unable to finish, so the superior vasculature is not visible. However, the print did successfully print the smaller collateral vessels of the pulmonary arteries. I also need to experiment with printing the heart without the base and instead printing with supports. The base really takes away from the final product in my opinion. I have printed the heart this past week on the taller Ultimaker Extended so I will see next week if the print turned out. It took about 6.5 hours to print the final product.

I will be collaborating with a group in Peoria this summer to figure out how to make models of the inside of the heart as well. I will hopefully be able to figure out a way to do this using free or open source software. https://twitter.com/GwendolynDerk/status/724360255656751104


International Maker Labs: A makerspace directory

This week we learned about the new maker space starting up at Indiana University. Their space reminded me of the CU fab lab. There is an online directory of makerspaces around the world: http://spaces.makerspace.com/makerspace-directory


AND I didn’t see our maker space listed on the map! So I added it. The CU fab lab also needs to be added to the directory. This directory can allow local maker communities to unite into a larger international community. Now you can look up a maker space and 3D print where ever you go!

3D Sense Scanner and Meshmixer

We learned how we can scan objects (and even ourselves) to create 3D models which we can print. We scanned and printed busts of ourselves. In order to get the scan, the model needed to keep absolutely still as the scanner moved around the person. The model must be kept in the center of the visual field at all times or the scanner would lose track of what it was scanning. Every surface angle needs to be captured. If there are any holes that were not captured in the scanning process, these can be filled in and smoothed out in Meshmixer. Meshmixer is useful for modifying your 3D model and preparing it to be “printer ready.” The object must be on a completely flat surface, otherwise extensive supports will be required to print.


While printing a bust of yourself is not exactly that useful, this technology could be very useful if you wanted to print an object or part that you already had. Instead of redesigning the object from scratch, you could simply scan the object. I may try that this summer with one of the medical school’s skeletons.





The final week at the CU Fab Lab we learned how to use arduinos. We also learned how to read, write, and edit basic computer programs. Arduinos are ideal for prototyping devices. They utilize affordable open source hardware and software. They also sell kits which include all the parts you need to achieve your goal. Arduino was first introduced in 2005 and it has blown up into a multimillion dollar company.


In the lab we experimented with tuning a LED light, directing a motor, and making conductive fabric touch sensitive. The most interesting experiment was exploring the conductive fabric capabilities. This essentially created a resistance biosensor. When the resistance greatly increased once the fabric was touched which could be registered by a computer as “being touched.” It was fun to combine my knowledge from biosensors into an actual sensor. Arduinos are ideal for future device development.


Printing a 3D heart from a MRI or CT images: Semester Activity & Final Project Proposal

I researched tutorials for how to print a 3D heart model from a CT or MRI scan. There are currently no tutorials for printing 3D hearts that takes you all the way from the DICOM files to the printer. This was quite a challenge and I still have a lot more work to do. This tutorial is only for an external 3D model of the heart. I have not found an easy way to create an accurate 3D model of the internal chambers/structures of the heart. I will continue to research this throughout the semester and repost when I discover a succinct way to accomplish this (any advice is greatly appreciated).

I delved into three different techniques which each utilized a different software. First, I investigated 3D slicer, which is an open sourced NIH sponsored 3D imaging software. Slicer is the equivalent of R in the statistics world, which means there is infinite potential, but it is also not very user friendly. Slicer has plugins that you can download which sound like they outline and make automatic traces of certain body parts. This would be the perfect platform for what I would like to accomplish. Osirix also has plugins you can download, but development would be much slower since it is not open source. Osirix is also only for Mac, this is a huge limitation of the tutorial. I will eventually discover a nice way to create a model with a PC as well.

The second way in which I know people are creating 3D models of the heart is by using Mimics, which is a privately owned software by Materialise ($$$). In this software, you make things similar to the ROIs that we will make in Osirix called masks. I do not have access to this software so I was not able to play around with it.

The most widely used software and arguably the most well known to practicing Radiologists is OsiriX. OsiriX has a free version available to the public which you can download here: http://www.osirix-viewer.com/Downloads.html   This is the software we will use for my tutorial, again Macs only.

Now without further ado, here is a tutorial of how to convert  a CT or MRI scan into a .stl file which can be printed. In my final project, I will look into how to clean up the .stl file in Meshworks to make it amenable to the printing process. I also hope to find a succinct way to accurately print the internal structures of the heart.

Software you will need before you get started ( free versions):

1. OsiriX imaging software 3D slice


First, you need to download some free anonymous medical DICOM images here:


  • Open OsiriX. A box will pop up if you are using the free version, click agree that you understand this version is not intended for clinical use.
  • Click the import button on the top left corner of the tool bar. Select the study you would like to import from your file. (CT/MRI scans consist of multiple images and you want to import all the images of the study (i.e. The entire folder). IMAGE 2

import open whole file2


  • Click on the study name that appears after you import it. A series of images may pop up down below. Double click on one of the series to open the series in the 2D viewer. IMAGE 3

select study to open 3

  • The image you see should open to the transverse view by default. You can change the orientation in the top tool bar, but for now stay in transverse view. (the far left brain slice button on the top tool bar)
  • With your mouse in the 2D viewer you can now scroll through the images to see how they progress throughout the body in the transverse view. Try scrolling through untill you can see the “four chamber” view of the heart. IMAGE 4

Image 4 four chamber view

  • Then click the 2D/3D wheel cog at the top and select 3D volume rendering. IMAGE 9

image 9

  • I found the image easier to visual under the “No Shading” 3D presets which can be found under the “calendar-like” icon at the top bar IMAGE 10

image 10 volume no shading

  • Now you can view and rotate your 3D image to get a sense for your region of interest. The cube function at the top is my favorite to navigate around the model; it is similar to the autodesk/fusion 360 navigation. Now we will crop the image to get just our ROI. As you do this, keep 3D printing in mind so you can minimize the amount of supports the printer will use. For example, you want to crop the descending aorta so that it is in line with the inferior aspect or base of the heart. You can see in the picture I cropped all bones, surrounding body wall, and unnecessary pulmonary vasculature/collaterals. IMAGE 11

Image 11 crop

  • Now exit out of 3D rendering and go back to your 2D image slices. From here select the different views at the top and notice how the cropping has taken out all the unwanted segments.
  • Go to ROI in the dropdown menu and select “Grow Region 2D/3D segmentation” IMAGE 5

Image 5 roi segmentation

  • Now you need to select the ROI (region of interest) and choose a threshold. In the pop up box, select the following: 3D growing region, set lower threshold to 0, set upper threshold to 2000, select preview result when clicking, create ROI(s) in the original series, Brush ROI, set outside pixels to 0, and choose a name for the ROI (in this example I named it “Heart”). Now click on the heart and it should become highlighted. Then click compute. IMAGE 6

Image 6 roi selection

  • Now close the segmentation parameters. Go back to the ROI dropdown menu and select “Set pixel values to…” Now select ROIs with the same name as the selected ROI and Inside ROIs. The values should read: if current value is larger than -1024, if current value is smaller than 3071, and to this new value 3024 (white color). Then click okay. IMAGE 7

IMAGE 7 white

  • Again go back to the ROI dropdown menu and select “set pixel values to…” This time select ROIs with the same name as the selected ROI and OUTSIDE ROIs. The values should read: if current value is larger than -1024, if current value is smaller than 3071, and to this new value -3024 (black color).

image 8 black

  • Now again click the 2D/3D wheel cog at the top and select 3D surface rendering. IMAGE 12

image 12 surface rendering

  • This was by far the most frustrating part of the project. I finally realized that you have to go up to the ROI Manager at the top and click on your ROI to get it to show up. IMAGE 13

Image 13 surface show

  • Now you will export your file as a .stl file. Go up to the wheel cog at the top which says Export 3D-SR, a
    nd select “Export as STL (.stl)” IMAGE 14

Image 14 export as stl






Once you have your .stl file you can clean it up in Meshworks. I will continue to work on this tutorial. I appreciate any and all feedback you have for me. I also welcome questions! Thank you!


Build your own 3D printer

This week we build our own 3D printer from a Ultimaker original plus kit. I grew up building legos so this was so much fun. The representative from Ultimaker said that is would be a bit like building Ikea furniture. By far the most frustrating part was getting all of the screws in. The screws were not tapered at the end and therefore had to be forced into the parts. The switches were particularly difficult to screw in because they are small delicate structures which required more strategic maneuvers. It took us about 3.5 hours to build the outer frame of the printer, which was projected by the instructions to take about 90 minutes. The instructions from Ultimaker could be greatly improved with more accurate diagrams and descriptive pictures. The frame of the printer is made out of a thin wood which was varnished before by Stephen to protect the wood. The other members of our team worked on building the extruder. One of the tiniest pieces was missing from the kit. We measured the piece and 3D printed it! Problem solved! This was the most frustrating thing when building legos as a kid (losing one of the pieces).


Being able to build your own 3D printer also gives you the confidence to upgrade your 3D printer on your own, rather than just buying a new one. This will not only be more cost effective for you, but it is also much better for the environment. Furthermore, once you have your own 3D printer you are able to print out new parts/upgrades for the printer and other household items. This maker/DIY business model will completely change the consumer society.20160328_14122220160328_160601

The courage to solder


I honestly never thought I would make something like this. I know very little about electronics. My knowledge of electronics has mostly been learned from studying the conduction system of the heart. I never dreamed that I would one day solder my own electronic circuit. With proper instructions the process is remarkably simple. Mitch Altman was a great teacher. A few important things to remember while soldering:

1) always solder with a clean tip (keep a damp sponge nearby)

2) feed the soldering material below the tip and closer to the circuit to make more accurate connections

3) if your soldering spots are touching others on your circuit, it’s possible that your device will not work (this happened to me at first. You can scrape away the excess flux to create a separation and this may fix your problem.)

Now that I know soldering is so easy, I feel much more confident to try to create other devices. I have long known about Adafruit, a awesome website that sells packages for different electronic projects, but I felt that all of it was way over my head. But not anymore!! I’m excited to combine some of their programmable lights to some wooden tribals masks that I collect. I will be sure to publish the results once it is complete.


Champaign Urbana Community Fab Lab – Major Laser

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This week we spent our time in the Fab Lab at CU learning how to laser cut materials. Lasers can be used to cut in two ways: 1) raster: which is more like etching 2) vector: fully cuts through your material. Using Inkscape software, we found an image from the internet and reformatted the image to be vector (bitmap) rather than a bunch of pixels. The vector images are mathematical equations that create a nice clean edge whereas the jpegs are often pixelated and have blurry lines when the view is zoomed in. You must convert your image to a vector before laser cutting if you want the image to turn out clear.

You can use a variety to different items in the lab, including moleskin notebooks, acrylic, and wood. You can even raster your own glass items which could be very practical for kitchen storage. I personally made a two designs for a moleskin notebook. My first design was very intricate, and due to the size of the notebook, the details did not turn out as well as I would have liked. If your design is very intricate I would be aware of the size of the material that you choose to cut on.


I simplified my next design and I think it came out much better.


I plan to come back on my own time to print my own business cards. I have tried using other platforms in the past like vistaprint, but it is infinitely better when you can hold the prototype in your own hand and see if you like it. Twice now I have printed over 500 business cards and been dissatisfied with the result. By using the Fab Lab, I can print several business cards and even have different cards for different purposes. And next week I will finally get to learn about Arduinos!

Embroidery at the Fab Lab


The embroidery workshop at the CU Fab Lab was a lot of fun. I have a few suggestions for picking your design. The embroidery machines handed thicker lines better than thin ones. I was advised to stay away from letters or writing in my design, however I already had my heart set on making my yoga studio’s logo. As you can see below, you can print letters and they can come out well, but I had to spend a lot of time rendering the image in the SewArt software. I hand to increase the thickness of every line by hand. There is both a free hand tool and also a line tool that I used. After you complete your patch, they will give you a sticker that you can iron on to the back of your patch so that you could iron your patch onto whatever fabric you like after. A word of caution: don’t hold the iron straight down on the patch for too long, it will burn your patch! You also don’t want to place the iron directly on your threads when you iron your patch onto something; it can burn your design. A few other side notes:

  • The machine is limited in length to ~4 inches.
  • The border of your patch will fray if it is not stitched, so you can either stitch a border (which is best done in your initial design) or you can hem the ends like I did with my patch.

Here is a picture of the patch that I made:


My studio loves the patches. I hope to make a few more to give out to other Iyengar yoga enthusiasts and friends.

I also stumbled upon this awesome bag that Jessica is making:


Those black panels are solar panels and it has a USB charger inside so you can charge your phone! This would be a GREAT travel bag!