Week 4

During this week we started working on the materials for the Science Fair. It would of course be excellent if we could show something physical that we made instead of just pictures on a computer screen or printed pictures.

So that is why we started working on a 3D-model that we could print using the 3D printer at the VU Innovation Lab. What we wanted to do for this model is to add the patterns that we found to different layers and somehow connect these. This appeared to be very difficult and needed to be done by hand, but that would take dozens of hours, if not hundreds, so we had to find another way. What we did manage to do is to extrude 2D images of three different patterns and put these on top of each other.

Presentation file

In the final days of the project, we finally managed to find a way to get the 2D patterns into one solid 3D model. The specific steps are explained in detail in “Our Ultimate Scaffold’ (link: http://bones2015.weblog.tudelft.nl/our-ultimate-scaffold/).

 

Now that we had a 3D model with a closed mesh, we could make a print of it. The model consists of 5 different layers that have been put on top of each other, as explained earlier.

image2

And although a 3D-printed model is the most exciting that we can show, it is also important to show our process and give some general information to understand what we did, so we also started working on posters and a video. For the video we started making a render of the original 3D model of the cartilage. But due to the complexity of this model, the render could not be done in the time that we were at the Innovation Lab and had to be done at home in the weekend.

 

Week 1 & 2 – Different tests

  • Making a solid in Rhino. Trying to simplify the model

One of our first ideas was to invert the 3D model so that we got geomeIMG_4688try were the lagunae are instead of the other way around. There a few complications in doing that however. The model we were using was very large, which slowed down our computers dramatically and some functions in the applications we used made our computers crash. Luckily, one of the staff-members at the 3D Innovation Lab could reduce the filesize from around 400 to 50mb without losing a lot of quality.

Another problem was that the model we were given wasn’t a closed mesh so Rhino and the other programs didn’t know what to do. Due to the complexity of the model this isn’t easy to solve.

  • Using the programs GOM & 3-Matic on computers of the 3D innovation Lab

At the 3D Innovation Lab at VUmC we got introIMG_4700duced to some new pieces of software. Some of those were free to download and others were licensed so we could only use them on the computers in the lab. Two of the main applications that are being used, are GOM and 3-Matic. Although these are professional pieces of software with a steep learning curve, they did give us some possibilities that we did not have with the software we were initially using. With some help of the staff at the lab we were able to most of the things we wanted with the software.

  • Trying out grasshopper

Our goal in this project is to find a pattern in the scaffold of cartilage and we assume this pattern is based on some mathematical law. Nature is very logical and everything works according to laws. A good example would be the golden ratio which can be found in pretty much everything nature creates. A shell doesn’t just accidentally get certain proportions, its growth works according to laws which give the shell its proportions. The same must apply to cartilage. It doesn’t randomly create lagunae (the holes), but they get created according to a law. And it’s this law that we have to find. When we find the pattern, Grasshopper would be an excellent application to create a 3D-model that can be easily modified to get the shape of the patients ear. Since grasshopper is a parametric program, the exact proportions of the ear do not really matter. Theoretically grasshopper could create a ear of infinite size. VUmC already has a parametric model in Grasshopper to create the shape of the ear, so this will have to be combined with a model that creates the scaffold to create the printable ear. We explored some of the features of grasshopper through a tutorial at Digital-Tutors.

Weblog Grashopper 1 Weblog Grasshopper 2 Weblog Grasshopper 3

 

  • Slicing the STL file 

Since we were given a pretty large file, we “sliced” the piece of cartilage in 6 layers to make the files smaller and simpler and to make it easier to further edit the file. Secondly we divided the piece of cartilage in 30 layers, to see if there could be found some sort of pattern or structure through making 2D images of the cross sections, see “creating 2D slices”. 

20151002_122051

  • Creating 2D slices

As mentioned before, one of the ideas was to put multiple cross sections through the 3D-model to get flat 2D pictures of the geometry in that cross section. There are multiple applications to do that, but we found that GOM gave us an excellent result without much work. The application allows you to easily create as many cross sections at any place you want and distribute them equally automatically. You can then control which cross sections you want to be visible, so you can look at one layer of cross sections at the time or several layers at once. We decided to create 30 cross sections to get a good chunk of data, but not drown in it. For every cross section we made a printscreen, resulting in 30 printscreens of cross sections. Now since every cross section has a unique structure, we came up with the idea to take the “average” of multiple cross section images with the help of the program Fiji. Fiji can take two images and take the “average” of these two images. So what we did was give every screenshot a number related to the location of the cross section within the piece of cartilage, and then opening screenshot 1 and 2 and taking the average of these, naming it “average first 2 layers”. Then, opening “average first 2 layers” and the 3rd layers, and taking the average of this layer naming it “average first 3 layers”, and so on. The idea was to make an average at every five layers, so an average of layer 1-5, one of layer 6-10 etcetera. This resulted in six different images of average layers. These six images could then be used to find a pattern, since all six images differ significantly.

Screenshot 1Fiji vbSchermafbeelding 2015-10-13 om 09.47.43

After the layers were processed in illustrator and photoshop  we were able to create a new bigger random cartilage pattern. We did this by using software called “Pixplant” that uses the algorithms to create a new pattern from different patterns combined. We could only use four of the six images, due to the fact that the upper cross section averages had less material and thus more gaps. We used averages of the bottom 20 cross sections, so images of layers 1-5, 6-10, 11-15 and 16-20.

These four layers of cartilage combined into one new seamless pattern looks like this:

Resultfourlayerscombined

 

 

 

  • Setting up a list of programs

The programs we use(d) are:

  • GOM
  • 3-matic
  • Rhino
  • Grasshopper
  • Catia
  • Matlab
  • Fiji
  • Maya
  • Pixplant