A research project or thesis exploring a question related to the field of biomedical visualization is one aspect of completing a Masters in Biomedical Visualization here at UIC. This original investigation enables greater insight into scholarship, understanding of the research process, and emphasizes original and critical thinking. Graduate students complete a written proposal, final research or thesis paper, give a final oral presentation and defense which all enable a student to develop advanced communication skills. This year, we are sitting down with our graduate students after their final defense for a quick chat about them and their research.
Recently, Kate Zumach defended her project: “Documenting Visualization Methodology and Decision-Making in Digital Reconstruction of Norellius nyctisaurops”
Taking a page from lolmythesis.com, how would you describe your research in one sentence?
Kate: Reconstructing, animating, and 3d printing Dr. Paul Sereno’s tiny Squamate skull
Sounds adorable, but what is it?
A Squamate is a reptile in the order Squamata, the largest extant order of reptiles that includes all lizards and snakes. With over 10,000 species what makes them unique are their scaly skin and movable quadrate bones.
How did you get involved with this research?
I became involved by taking a trip to Dr. Sereno’s Paleontology lab at University of Chicago with a fellow classmate, Andy Schulte.
How did you plan out the animation to highlight the morphological structures of importance?
The morphological traits of N. ncytisaurops skull were the most important aspects of the animation. I knew from the start that they needed to be highlighted in a way that would be beneficial for both a lay and professional audience. I went about using simple 2d animations with differing opacities to illuminate traits and structures that Dr. Sereno talked about in his research. I wanted to really make each trait visible but keep the animation simple so that the viewer didn’t get disoriented. I also used call outs to focus on the smaller traits like the primitive pterygoid teeth.
What was the 3D printing process like?
3D Printing was a real challenge. The first print I had I remember staring at it for the hour just to make sure nothing went wrong. I printed in several different places as well to test out different printing materials. Before printing, every mesh had to be watertight and the topology of the models needed to be lower than 5 mb. I also have parts that interlocked with each other so I had to keep track of the printing dimensions to make sure they were uniform for all of the different prints. I used an Afinia printer and two different Makerbot printers.
ZBrush seems to be one of your 3D sculpting programs of choice. What are some of your favorite ZBrush features? How do you use them?
ZBrush was my hero for this project along with Materialize Mimics. I used ZBrush for all of the detailed sculpting and retopology. My favorite feature that I used was “skinning” my models so that I could fill the holes of the fragmented fossil bones while keeping the integrity (shape and size) of the original fossil.
You implemented a database system to keep track of your reconstruction work. Can you talk to us more about the impetus for this portion of the project and what it is?
The database really came about through the realization during the project that there were no checks and balances systems in this sort of work. Reconstructions are often presented as a fait accompli with little to no documentation regarding the many decisions made along the way and with limited access to these stages of the digital reconstruction itself. With the database, all of the decisions, sources, and results could be found in one organized and easily accessible place. Before the database I was trying to stay organized but I was only sending screen shots of pictures with questions in a word document and hoping that it was legible. That’s when the frustration was too much and I thought there had to be a better way to collaborate with my content expert and stay more organized.
In academia, there’s an emphasis on citing references when writing a paper but not the same requirement when creating images, even though the visual references we use do impact the final image’s scientific accuracy. Do you think that such a database could be used for housing the visual references used in creating other kinds of scientific images?
Absolutely! I feel that these sorts of checks and balances are extremely helpful for creatives who are creating images that involve scientific and medical concepts. When working with a client, it would be more streamlined and efficient to use a database form to house all of the information you need for example, all of your sketches, process work, references used, descriptions, separate files, date project was started, how much time is spent, etc. Not only do you stay organized but you have a way to show all of the work and defend decisions that were made. The database format can be customized for whatever project that is needed and is not limited to certain fields.
What are your plans for the future?
My plans for the future are exciting and fast approaching! I am touring in Ireland for now and right when I get back to the states I am heading to work as a medical illustrator and animator at Swarm Interactive in Chapel Hill, NC. I am thrilled to be joining the team at Swarm!